1atp › Citations

2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor.

Zheng J, Trafny EA, Knighton DR, Xuong NH, Taylor SS, Ten Eyck LF, Sowadski JM
Acta Crystallogr D Biol Crystallogr 49 362-5 (1993)
Cited: 410 times
EuropePMC logo PMID: 15299527

Abstract

. The crystal structure of a ternary complex containing the catalytic subunit of cAMP-dependent protein kinase, ATP and a 20-residue inhibitor peptide was refined at a resolution of 2.2 A to an R value of 0.177. In order to identify the metal binding sites, the crystals, originally grown in the presence of low concentrations of Mg(2+), were soaked in Mn(2+). Two Mn(2+) ions were identified using an anomalous Fourier map. One Mn(2+) ion bridges the gamma- and beta-phosphates and interacts with Asp184 and two water molecules. The second Mn(2+) ion interacts with the side chains of Asn171 and Asp l84 as well as with a water molecule. Modeling a serine into the P site of the inhibitor peptide suggests a mechanism for phosphotransfer.

Reviews - 1atp mentioned but not cited (36)

  1. Protein kinases: evolution of dynamic regulatory proteins. Taylor SS, Kornev AP. Trends Biochem. Sci. 36 65-77 (2011)
  2. Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms. Jura N, Zhang X, Endres NF, Seeliger MA, Schindler T, Kuriyan J. Mol. Cell 42 9-22 (2011)
  3. Eukaryote-like serine/threonine kinases and phosphatases in bacteria. Pereira SF, Goss L, Dworkin J. Microbiol. Mol. Biol. Rev. 75 192-212 (2011)
  4. Signaling through cAMP and cAMP-dependent protein kinase: diverse strategies for drug design. Taylor SS, Kim C, Cheng CY, Brown SH, Wu J, Kannan N. Biochim. Biophys. Acta 1784 16-26 (2008)
  5. Defining the conserved internal architecture of a protein kinase. Kornev AP, Taylor SS. Biochim. Biophys. Acta 1804 440-444 (2010)
  6. Pseudokinases-remnants of evolution or key allosteric regulators? Zeqiraj E, van Aalten DM. Curr. Opin. Struct. Biol. 20 772-781 (2010)
  7. Substrate and docking interactions in serine/threonine protein kinases. Goldsmith EJ, Akella R, Min X, Zhou T, Humphreys JM. Chem. Rev. 107 5065-5081 (2007)
  8. Dynamics-Driven Allostery in Protein Kinases. Kornev AP, Taylor SS. Trends Biochem. Sci. 40 628-647 (2015)
  9. Histone acetyltransferases: Rising ancient counterparts to protein kinases. Yuan H, Marmorstein R. Biopolymers 99 98-111 (2013)
  10. Structural Basis for the Non-catalytic Functions of Protein Kinases. Kung JE, Jura N. Structure 24 7-24 (2016)
  11. Solution NMR Spectroscopy for the Study of Enzyme Allostery. Lisi GP, Loria JP. Chem. Rev. 116 6323-6369 (2016)
  12. Allostery and binding cooperativity of the catalytic subunit of protein kinase A by NMR spectroscopy and molecular dynamics simulations. Masterson LR, Cembran A, Shi L, Veglia G. Adv Protein Chem Struct Biol 87 363-389 (2012)
  13. Design principles underpinning the regulatory diversity of protein kinases. Oruganty K, Kannan N. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 367 2529-2539 (2012)
  14. Exploring the Plasmodium falciparum cyclic-adenosine monophosphate (cAMP)-dependent protein kinase (PfPKA) as a therapeutic target. Haste NM, Talabani H, Doo A, Merckx A, Langsley G, Taylor SS. Microbes Infect. 14 838-850 (2012)
  15. Discoidin domain receptor 1 (DDR1) kinase as target for structure-based drug discovery. Kothiwale S, Borza CM, Lowe EW, Pozzi A, Meiler J. Drug Discov. Today 20 255-261 (2015)
  16. Disordered Protein Kinase Regions in Regulation of Kinase Domain Cores. Gógl G, Kornev AP, Reményi A, Taylor SS. Trends Biochem Sci 44 300-311 (2019)
  17. There's more to death than life: Noncatalytic functions in kinase and pseudokinase signaling. Mace PD, Murphy JM. J Biol Chem 296 100705 (2021)
  18. Analogous regulatory sites within the alphaC-beta4 loop regions of ZAP-70 tyrosine kinase and AGC kinases. Kannan N, Neuwald AF, Taylor SS. Biochim. Biophys. Acta 1784 27-32 (2008)
  19. Cataloguing the dead: breathing new life into pseudokinase research. Shrestha S, Byrne DP, Harris JA, Kannan N, Eyers PA. FEBS J 287 4150-4169 (2020)
  20. Role of conformational entropy in the activity and regulation of the catalytic subunit of protein kinase A. Veglia G, Cembran A. FEBS J. 280 5608-5615 (2013)
  21. Implementation of linked data in the life sciences at BioHackathon 2011. Aoki-Kinoshita KF, Kinjo AR, Morita M, Igarashi Y, Chen YA, Shigemoto Y, Fujisawa T, Akune Y, Katoda T, Kokubu A, Mori T, Nakao M, Kawashima S, Okamoto S, Katayama T, Ogishima S. J Biomed Semantics 6 3 (2015)
  22. Structural insight into effector proteins of Gram-negative bacterial pathogens that modulate the phosphoproteome of their host. Grishin AM, Beyrakhova KA, Cygler M. Protein Sci. 24 604-620 (2015)
  23. MAP kinase modules: the excursion model and the steps that count. Piala AT, Humphreys JM, Goldsmith EJ. Biophys. J. 107 2006-2015 (2014)
  24. Cdc-Like Kinases (CLKs): Biology, Chemical Probes, and Therapeutic Potential. Martín Moyano P, Němec V, Paruch K. Int J Mol Sci 21 E7549 (2020)
  25. Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease. Yeung W, Ruan Z, Kannan N. IUBMB Life 72 1189-1202 (2020)
  26. The unusual mechanism of inhibition of the p90 ribosomal S6 kinase (RSK) by flavonol rhamnosides. Utepbergenov D, Derewenda ZS. Biochim. Biophys. Acta 1834 1285-1291 (2013)
  27. Overview of protein structural and functional folds. Sun PD, Foster CE, Boyington JC. Curr Protoc Protein Sci Chapter 17 Unit 17.1 (2004)
  28. Structure and Physiological Regulation of AMPK. Yan Y, Zhou XE, Xu HE, Melcher K. Int J Mol Sci 19 (2018)
  29. The structural and functional workings of KEOPS. Beenstock J, Sicheri F. Nucleic Acids Res 49 10818-10834 (2021)
  30. Computational tools and resources for pseudokinase research. O'Boyle B, Shrestha S, Kochut K, Eyers PA, Kannan N. Methods Enzymol 667 403-426 (2022)
  31. Dynamic equilibria in protein kinases. Pegram LM, Anderson JW, Ahn NG. Curr Opin Struct Biol 71 215-222 (2021)
  32. Emerging functions of pseudoenzymes. Goldberg T, Sreelatha A. Biochem J 480 715-728 (2023)
  33. Looking lively: emerging principles of pseudokinase signaling. Sheetz JB, Lemmon MA. Trends Biochem Sci 47 875-891 (2022)
  34. Metabolic protein kinase signalling in neuroblastoma. Smiles WJ, Catalano L, Stefan VE, Weber DD, Kofler B. Mol Metab 75 101771 (2023)
  35. Post-translational modifications at the ATP-positioning G-loop that regulate protein kinase activity. Steinberg SF. Pharmacol. Res. 135 181-187 (2018)
  36. Rotary mechanism of V/A-ATPases-how is ATP hydrolysis converted into a mechanical step rotation in rotary ATPases? Yokoyama K. Front Mol Biosci 10 1176114 (2023)

Articles - 1atp mentioned but not cited (236)

  1. The importance of intrinsic disorder for protein phosphorylation. Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK. Nucleic Acids Res. 32 1037-1049 (2004)
  2. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE. Sci Signal 3 ra12 (2010)
  3. Recognition of functional sites in protein structures. Shulman-Peleg A, Nussinov R, Wolfson HJ. J Mol Biol 339 607-633 (2004)
  4. Identification of a pocket in the PDK1 kinase domain that interacts with PIF and the C-terminal residues of PKA. Biondi RM, Cheung PC, Casamayor A, Deak M, Currie RA, Alessi DR. EMBO J. 19 979-988 (2000)
  5. Structural and functional diversity of the microbial kinome. Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G. PLoS Biol. 5 e17 (2007)
  6. Structure of the LKB1-STRAD-MO25 complex reveals an allosteric mechanism of kinase activation. Zeqiraj E, Filippi BM, Deak M, Alessi DR, van Aalten DM. Science 326 1707-1711 (2009)
  7. The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne PE. BMC Bioinformatics 6 21 (2005)
  8. Dynamics connect substrate recognition to catalysis in protein kinase A. Masterson LR, Cheng C, Yu T, Tonelli M, Kornev A, Taylor SS, Veglia G. Nat. Chem. Biol. 6 821-828 (2010)
  9. Identification of protein-protein interfaces by decreased amide proton solvent accessibility. Mandell JG, Falick AM, Komives EA. Proc. Natl. Acad. Sci. U.S.A. 95 14705-14710 (1998)
  10. The dictyostelium kinome--analysis of the protein kinases from a simple model organism. Goldberg JM, Manning G, Liu A, Fey P, Pilcher KE, Xu Y, Smith JL. PLoS Genet. 2 e38 (2006)
  11. Chloride sensing by WNK1 involves inhibition of autophosphorylation. Piala AT, Moon TM, Akella R, He H, Cobb MH, Goldsmith EJ. Sci Signal 7 ra41 (2014)
  12. Allosteric cooperativity in protein kinase A. Masterson LR, Mascioni A, Traaseth NJ, Taylor SS, Veglia G. Proc. Natl. Acad. Sci. U.S.A. 105 506-511 (2008)
  13. Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors. Goh G, Scholl UI, Healy JM, Choi M, Prasad ML, Nelson-Williams C, Kunstman JW, Korah R, Suttorp AC, Dietrich D, Haase M, Willenberg HS, Stålberg P, Hellman P, Akerström G, Björklund P, Carling T, Lifton RP. Nat. Genet. 46 613-617 (2014)
  14. The pseudoactive site of ILK is essential for its binding to alpha-Parvin and localization to focal adhesions. Fukuda K, Gupta S, Chen K, Wu C, Qin J. Mol. Cell 36 819-830 (2009)
  15. Crystal structure of inhibitor of κB kinase β. Xu G, Lo YC, Li Q, Napolitano G, Wu X, Jiang X, Dreano M, Karin M, Wu H. Nature 472 325-330 (2011)
  16. Trans-activation of the DNA-damage signalling protein kinase Chk2 by T-loop exchange. Oliver AW, Paul A, Boxall KJ, Barrie SE, Aherne GW, Garrett MD, Mittnacht S, Pearl LH. EMBO J. 25 3179-3190 (2006)
  17. Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy. Masterson LR, Shi L, Metcalfe E, Gao J, Taylor SS, Veglia G. Proc. Natl. Acad. Sci. U.S.A. 108 6969-6974 (2011)
  18. Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates. Nesić D, Miller MC, Quinkert ZT, Stein M, Chait BT, Stebbins CE. Nat. Struct. Mol. Biol. 17 130-132 (2010)
  19. Structural basis for the specific inhibition of protein kinase G, a virulence factor of Mycobacterium tuberculosis. Scherr N, Honnappa S, Kunz G, Mueller P, Jayachandran R, Winkler F, Pieters J, Steinmetz MO. Proc. Natl. Acad. Sci. U.S.A. 104 12151-12156 (2007)
  20. Deciphering the structural basis of eukaryotic protein kinase regulation. Meharena HS, Chang P, Keshwani MM, Oruganty K, Nene AK, Kannan N, Taylor SS, Kornev AP. PLoS Biol. 11 e1001680 (2013)
  21. A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by SRPK1. Ngo JC, Giang K, Chakrabarti S, Ma CT, Huynh N, Hagopian JC, Dorrestein PC, Fu XD, Adams JA, Ghosh G. Mol. Cell 29 563-576 (2008)
  22. Ligand-induced global transitions in the catalytic domain of protein kinase A. Hyeon C, Jennings PA, Adams JA, Onuchic JN. Proc. Natl. Acad. Sci. U.S.A. 106 3023-3028 (2009)
  23. Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation. Hauge C, Antal TL, Hirschberg D, Doehn U, Thorup K, Idrissova L, Hansen K, Jensen ON, Jørgensen TJ, Biondi RM, Frödin M. EMBO J. 26 2251-2261 (2007)
  24. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Yang S, Banavali NK, Roux B. Proc. Natl. Acad. Sci. U.S.A. 106 3776-3781 (2009)
  25. Allosteric activation of the protein kinase PDK1 with low molecular weight compounds. Engel M, Hindie V, Lopez-Garcia LA, Stroba A, Schaeffer F, Adrian I, Imig J, Idrissova L, Nastainczyk W, Zeuzem S, Alzari PM, Hartmann RW, Piiper A, Biondi RM. EMBO J. 25 5469-5480 (2006)
  26. Identification of the protein kinase A regulatory RIalpha-catalytic subunit interface by amide H/2H exchange and protein docking. Anand GS, Law D, Mandell JG, Snead AN, Tsigelny I, Taylor SS, Ten Eyck LF, Komives EA. Proc. Natl. Acad. Sci. U.S.A. 100 13264-13269 (2003)
  27. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. Kuhn D, Weskamp N, Schmitt S, Hüllermeier E, Klebe G. J Mol Biol 359 1023-1044 (2006)
  28. Structural basis for the regulation of protein kinase A by activation loop phosphorylation. Steichen JM, Kuchinskas M, Keshwani MM, Yang J, Adams JA, Taylor SS. J. Biol. Chem. 287 14672-14680 (2012)
  29. A conserved non-canonical motif in the pseudoactive site of the ROP5 pseudokinase domain mediates its effect on Toxoplasma virulence. Reese ML, Boothroyd JC. J. Biol. Chem. 286 29366-29375 (2011)
  30. Congenital disease SNPs target lineage specific structural elements in protein kinases. Torkamani A, Kannan N, Taylor SS, Schork NJ. Proc. Natl. Acad. Sci. U.S.A. 105 9011-9016 (2008)
  31. Elucidation of human choline kinase crystal structures in complex with the products ADP or phosphocholine. Malito E, Sekulic N, Too WC, Konrad M, Lavie A. J. Mol. Biol. 364 136-151 (2006)
  32. On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine. Tanramluk D, Schreyer A, Pitt WR, Blundell TL. Chem Biol Drug Des 74 16-24 (2009)
  33. PKR and GCN2 kinases and guanine nucleotide exchange factor eukaryotic translation initiation factor 2B (eIF2B) recognize overlapping surfaces on eIF2alpha. Dey M, Trieselmann B, Locke EG, Lu J, Cao C, Dar AC, Krishnamoorthy T, Dong J, Sicheri F, Dever TE. Mol. Cell. Biol. 25 3063-3075 (2005)
  34. Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii. Qiu W, Wernimont A, Tang K, Taylor S, Lunin V, Schapira M, Fentress S, Hui R, Sibley LD. EMBO J. 28 969-979 (2009)
  35. The crystal structure of BRAF in complex with an organoruthenium inhibitor reveals a mechanism for inhibition of an active form of BRAF kinase. Xie P, Streu C, Qin J, Bregman H, Pagano N, Meggers E, Marmorstein R. Biochemistry 48 5187-5198 (2009)
  36. Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication. Guarnera E, Berezovsky IN. PLoS Comput Biol 12 e1004678 (2016)
  37. E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis. Pruneda JN, Smith FD, Daurie A, Swaney DL, Villén J, Scott JD, Stadnyk AW, Le Trong I, Stenkamp RE, Klevit RE, Rohde JR, Brzovic PS. EMBO J. 33 437-449 (2014)
  38. Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop. Meng Y, Roux B. J. Mol. Biol. 426 423-435 (2014)
  39. cAMP-dependent protein kinase A selects the excited state of the membrane substrate phospholamban. Masterson LR, Yu T, Shi L, Wang Y, Gustavsson M, Mueller MM, Veglia G. J. Mol. Biol. 412 155-164 (2011)
  40. eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Kinoshita K, Murakami Y, Nakamura H. Nucleic Acids Res. 35 W398-402 (2007)
  41. Binding leverage as a molecular basis for allosteric regulation. Mitternacht S, Berezovsky IN. PLoS Comput. Biol. 7 e1002148 (2011)
  42. Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis. Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA, Pagliarini DJ. Mol. Cell 57 83-94 (2015)
  43. Contribution of non-catalytic core residues to activity and regulation in protein kinase A. Yang J, Kennedy EJ, Wu J, Deal MS, Pennypacker J, Ghosh G, Taylor SS. J. Biol. Chem. 284 6241-6248 (2009)
  44. Sequence determinants of a specific inactive protein kinase conformation. Hari SB, Merritt EA, Maly DJ. Chem. Biol. 20 806-815 (2013)
  45. Structural basis of the regulatory mechanism of the plant CIPK family of protein kinases controlling ion homeostasis and abiotic stress. Chaves-Sanjuan A, Sanchez-Barrena MJ, Gonzalez-Rubio JM, Moreno M, Ragel P, Jimenez M, Pardo JM, Martinez-Ripoll M, Quintero FJ, Albert A. Proc. Natl. Acad. Sci. U.S.A. 111 E4532-41 (2014)
  46. Comparative surface geometry of the protein kinase family. Thompson EE, Kornev AP, Kannan N, Kim C, Ten Eyck LF, Taylor SS. Protein Sci. 18 2016-2026 (2009)
  47. Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites. Binkowski TA, Joachimiak A. BMC Struct. Biol. 8 45 (2008)
  48. Synchronous opening and closing motions are essential for cAMP-dependent protein kinase A signaling. Srivastava AK, McDonald LR, Cembran A, Kim J, Masterson LR, McClendon CL, Taylor SS, Veglia G. Structure 22 1735-1743 (2014)
  49. Crystal structure of a human IκB kinase β asymmetric dimer. Liu S, Misquitta YR, Olland A, Johnson MA, Kelleher KS, Kriz R, Lin LL, Stahl M, Mosyak L. J. Biol. Chem. 288 22758-22767 (2013)
  50. Identifying protein kinase target preferences using mass spectrometry. Douglass J, Gunaratne R, Bradford D, Saeed F, Hoffert JD, Steinbach PJ, Knepper MA, Pisitkun T. Am. J. Physiol., Cell Physiol. 303 C715-27 (2012)
  51. Crystal structure of the E230Q mutant of cAMP-dependent protein kinase reveals an unexpected apoenzyme conformation and an extended N-terminal A helix. Wu J, Yang J, Kannan N, Madhusudan, Xuong NH, Ten Eyck LF, Taylor SS. Protein Sci. 14 2871-2879 (2005)
  52. Structural insights into the functions of TBK1 in innate antimicrobial immunity. Shu C, Sankaran B, Chaton CT, Herr AB, Mishra A, Peng J, Li P. Structure 21 1137-1148 (2013)
  53. DYRK1A haploinsufficiency causes a new recognizable syndrome with microcephaly, intellectual disability, speech impairment, and distinct facies. Ji J, Lee H, Argiropoulos B, Dorrani N, Mann J, Martinez-Agosto JA, Gomez-Ospina N, Gallant N, Bernstein JA, Hudgins L, Slattery L, Isidor B, Le Caignec C, David A, Obersztyn E, Wiśniowiecka-Kowalnik B, Fox M, Deignan JL, Vilain E, Hendricks E, Horton Harr M, Noon SE, Jackson JR, Wilkens A, Mirzaa G, Salamon N, Abramson J, Zackai EH, Krantz I, Innes AM, Nelson SF, Grody WW, Quintero-Rivera F. Eur. J. Hum. Genet. 23 1473-1481 (2015)
  54. Kinetic, mechanistic, and structural modeling studies of truncated wild-type leucine-rich repeat kinase 2 and the G2019S mutant. Liu M, Kang S, Ray S, Jackson J, Zaitsev AD, Gerber SA, Cuny GD, Glicksman MA. Biochemistry 50 9399-9408 (2011)
  55. PDBe: Protein Data Bank in Europe. Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ. Nucleic Acids Res. 39 D402-10 (2011)
  56. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, Wilkerson EM, Ruan Z, Aydin D, Hebert AS, Guo X, Freiberger EC, Reutenauer L, Jochem A, Chergova M, Johnson IE, Lohman DC, Rush MJP, Kwiecien NW, Singh PK, Schlagowski AI, Floyd BJ, Forsman U, Sindelar PJ, Westphall MS, Pierrel F, Zoll J, Dal Peraro M, Kannan N, Bingman CA, Coon JJ, Isope P, Puccio H, Pagliarini DJ. Mol. Cell 63 608-620 (2016)
  57. Crystal structures of the N-terminal kinase domain of human RSK1 bound to three different ligands: Implications for the design of RSK1 specific inhibitors. Ikuta M, Kornienko M, Byrne N, Reid JC, Mizuarai S, Kotani H, Munshi SK. Protein Sci. 16 2626-2635 (2007)
  58. Molecular basis of actin nucleation factor cooperativity: crystal structure of the Spir-1 kinase non-catalytic C-lobe domain (KIND)•formin-2 formin SPIR interaction motif (FSI) complex. Zeth K, Pechlivanis M, Samol A, Pleiser S, Vonrhein C, Kerkhoff E. J. Biol. Chem. 286 30732-30739 (2011)
  59. article-commentary Pseudokinases: functional insights gleaned from structure. Kornev AP, Taylor SS. Structure 17 5-7 (2009)
  60. A chimeric mechanism for polyvalent trans-phosphorylation of PKA by PDK1. Romano RA, Kannan N, Kornev AP, Allison CJ, Taylor SS. Protein Sci. 18 1486-1497 (2009)
  61. A novel and efficient tool for locating and characterizing protein cavities and binding sites. Tripathi A, Kellogg GE. Proteins 78 825-842 (2010)
  62. Conservation, variability and the modeling of active protein kinases. Knight JD, Qian B, Baker D, Kothary R. PLoS ONE 2 e982 (2007)
  63. Electronic measurements of single-molecule catalysis by cAMP-dependent protein kinase A. Sims PC, Moody IS, Choi Y, Dong C, Iftikhar M, Corso BL, Gul OT, Collins PG, Weiss GA. J. Am. Chem. Soc. 135 7861-7868 (2013)
  64. EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Beaver JE, Bourne PE, Ponomarenko JV. Immunome Res 3 3 (2007)
  65. NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Cembran A, Kim J, Gao J, Veglia G. Phys Chem Chem Phys 16 6508-6518 (2014)
  66. StoneHinge: hinge prediction by network analysis of individual protein structures. Keating KS, Flores SC, Gerstein MB, Kuhn LA. Protein Sci. 18 359-371 (2009)
  67. A conserved Glu-Arg salt bridge connects coevolved motifs that define the eukaryotic protein kinase fold. Yang J, Wu J, Steichen JM, Kornev AP, Deal MS, Li S, Sankaran B, Woods VL, Taylor SS. J. Mol. Biol. 415 666-679 (2012)
  68. Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. Röttig M, Rausch C, Kohlbacher O. PLoS Comput. Biol. 6 e1000636 (2010)
  69. Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study. Lu B, Wong CF, McCammon JA. Protein Sci. 14 159-168 (2005)
  70. The role of conserved water molecules in the catalytic domain of protein kinases. Knight JD, Hamelberg D, McCammon JA, Kothary R. Proteins 76 527-535 (2009)
  71. Activating mutations in TOR are in similar structures as oncogenic mutations in PI3KCalpha. Sturgill TW, Hall MN. ACS Chem. Biol. 4 999-1015 (2009)
  72. Cotranslational cis-phosphorylation of the COOH-terminal tail is a key priming step in the maturation of cAMP-dependent protein kinase. Keshwani MM, Klammt C, von Daake S, Ma Y, Kornev AP, Choe S, Insel PA, Taylor SS. Proc. Natl. Acad. Sci. U.S.A. 109 E1221-9 (2012)
  73. Dysfunctional conformational dynamics of protein kinase A induced by a lethal mutant of phospholamban hinder phosphorylation. Kim J, Masterson LR, Cembran A, Verardi R, Shi L, Gao J, Taylor SS, Veglia G. Proc. Natl. Acad. Sci. U.S.A. 112 3716-3721 (2015)
  74. How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study. Turjanski AG, Hummer G, Gutkind JS. J. Am. Chem. Soc. 131 6141-6148 (2009)
  75. A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity. Lopez VA, Park BC, Nowak D, Sreelatha A, Zembek P, Fernandez J, Servage KA, Gradowski M, Hennig J, Tomchick DR, Pawłowski K, Krzymowska M, Tagliabracci VS. Cell 179 205-218.e21 (2019)
  76. Blocking UV-induced eIF2alpha phosphorylation with small molecule inhibitors of GCN2. Robert F, Williams C, Yan Y, Donohue E, Cencic R, Burley SK, Pelletier J. Chem Biol Drug Des 74 57-67 (2009)
  77. Novel isoform-specific interfaces revealed by PKA RIIbeta holoenzyme structures. Brown SH, Wu J, Kim C, Alberto K, Taylor SS. J. Mol. Biol. 393 1070-1082 (2009)
  78. An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery. Brooijmans N, Chang YW, Mobilio D, Denny RA, Humblet C. Protein Sci. 19 763-774 (2010)
  79. Design of substrate-based BCR-ABL kinase inhibitors using the cyclotide scaffold. Huang YH, Henriques ST, Wang CK, Thorstholm L, Daly NL, Kaas Q, Craik DJ. Sci Rep 5 12974 (2015)
  80. Transition path theory analysis of c-Src kinase activation. Meng Y, Shukla D, Pande VS, Roux B. Proc. Natl. Acad. Sci. U.S.A. 113 9193-9198 (2016)
  81. ProKinO: a unified resource for mining the cancer kinome. McSkimming DI, Dastgheib S, Talevich E, Narayanan A, Katiyar S, Taylor SS, Kochut K, Kannan N. Hum. Mutat. 36 175-186 (2015)
  82. Structure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies. Chaikuad A, Keates T, Vincke C, Kaufholz M, Zenn M, Zimmermann B, Gutiérrez C, Zhang RG, Hatzos-Skintges C, Joachimiak A, Muyldermans S, Herberg FW, Knapp S, Müller S. Biochem. J. 459 59-69 (2014)
  83. Structure of the nuclear factor κB-inducing kinase (NIK) kinase domain reveals a constitutively active conformation. Liu J, Sudom A, Min X, Cao Z, Gao X, Ayres M, Lee F, Cao P, Johnstone S, Plotnikova O, Walker N, Chen G, Wang Z. J. Biol. Chem. 287 27326-27334 (2012)
  84. TNIK inhibition abrogates colorectal cancer stemness. Masuda M, Uno Y, Ohbayashi N, Ohata H, Mimata A, Kukimoto-Niino M, Moriyama H, Kashimoto S, Inoue T, Goto N, Okamoto K, Shirouzu M, Sawa M, Yamada T. Nat Commun 7 12586 (2016)
  85. The Mechanism of ATP-Dependent Allosteric Protection of Akt Kinase Phosphorylation. Lu S, Deng R, Jiang H, Song H, Li S, Shen Q, Huang W, Nussinov R, Yu J, Zhang J. Structure 23 1725-1734 (2015)
  86. Active site coupling in PDE:PKA complexes promotes resetting of mammalian cAMP signaling. Krishnamurthy S, Moorthy BS, Xin Xiang L, Xin Shan L, Bharatham K, Tulsian NK, Mihalek I, Anand GS. Biophys. J. 107 1426-1440 (2014)
  87. KinView: a visual comparative sequence analysis tool for integrated kinome research. McSkimming DI, Dastgheib S, Baffi TR, Byrne DP, Ferries S, Scott ST, Newton AC, Eyers CE, Kochut KJ, Eyers PA, Kannan N. Mol Biosyst 12 3651-3665 (2016)
  88. Molecular features of product release for the PKA catalytic cycle. Bastidas AC, Wu J, Taylor SS. Biochemistry 54 2-10 (2015)
  89. Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1. Callaway K, Waas WF, Rainey MA, Ren P, Dalby KN. Biochemistry 49 3619-3630 (2010)
  90. The Tribbles 2 (TRB2) pseudokinase binds to ATP and autophosphorylates in a metal-independent manner. Bailey FP, Byrne DP, Oruganty K, Eyers CE, Novotny CJ, Shokat KM, Kannan N, Eyers PA. Biochem. J. 467 47-62 (2015)
  91. Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling. Pickin KA, Chaudhury S, Dancy BC, Gray JJ, Cole PA. J. Am. Chem. Soc. 130 5667-5669 (2008)
  92. Characterization of Staphylococcus aureus EssB, an integral membrane component of the Type VII secretion system: atomic resolution crystal structure of the cytoplasmic segment. Zoltner M, Fyfe PK, Palmer T, Hunter WN. Biochem. J. 449 469-477 (2013)
  93. Conformational equilibrium of N-myristoylated cAMP-dependent protein kinase A by molecular dynamics simulations. Cembran A, Masterson LR, McClendon CL, Taylor SS, Gao J, Veglia G. Biochemistry 51 10186-10196 (2012)
  94. Structural analysis of Staphylococcus aureus serine/threonine kinase PknB. Rakette S, Donat S, Ohlsen K, Stehle T. PLoS ONE 7 e39136 (2012)
  95. Structural diversity of the active N-terminal kinase domain of p90 ribosomal S6 kinase 2. Malakhova M, Kurinov I, Liu K, Zheng D, D'Angelo I, Shim JH, Steinman V, Bode AM, Dong Z. PLoS ONE 4 e8044 (2009)
  96. Dentate gyrus-specific manipulation of beta-Ca2+/calmodulin-dependent kinase II disrupts memory consolidation. Cho MH, Cao X, Wang D, Tsien JZ. Proc. Natl. Acad. Sci. U.S.A. 104 16317-16322 (2007)
  97. FLAMEnGO 2.0: an enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances. Chao FA, Kim J, Xia Y, Milligan M, Rowe N, Veglia G. J. Magn. Reson. 245 17-23 (2014)
  98. R-subunit isoform specificity in protein kinase A: distinct features of protein interfaces in PKA types I and II by amide H/2H exchange mass spectrometry. Anand GS, Hotchko M, Brown SH, Ten Eyck LF, Komives EA, Taylor SS. J. Mol. Biol. 374 487-499 (2007)
  99. Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled. Hu J, Yuan Q, Kang X, Qin Y, Li L, Ha Y, Wu D. Nat Commun 6 8205 (2015)
  100. A model of a MAPK•substrate complex in an active conformation: a computational and experimental approach. Lee S, Warthaka M, Yan C, Kaoud TS, Piserchio A, Ghose R, Ren P, Dalby KN. PLoS ONE 6 e18594 (2011)
  101. DFGmodel: predicting protein kinase structures in inactive states for structure-based discovery of type-II inhibitors. Ung PM, Schlessinger A. ACS Chem. Biol. 10 269-278 (2015)
  102. Extracellular-regulated kinase 2 is activated by the enhancement of hinge flexibility. Sours KM, Xiao Y, Ahn NG. J. Mol. Biol. 426 1925-1935 (2014)
  103. Identification of a hidden strain switch provides clues to an ancient structural mechanism in protein kinases. Oruganty K, Talathi NS, Wood ZA, Kannan N. Proc. Natl. Acad. Sci. U.S.A. 110 924-929 (2013)
  104. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S. Nucleic Acids Res. 46 D486-D492 (2018)
  105. Regulation of a third conserved phosphorylation site in SGK1. Chen W, Chen Y, Xu BE, Juang YC, Stippec S, Zhao Y, Cobb MH. J. Biol. Chem. 284 3453-3460 (2009)
  106. A novel benzodioxole-containing inhibitor of Toxoplasma gondii growth alters the parasite cell cycle. Kamau E, Meehan T, Lavine MD, Arrizabalaga G, Mustata Wilson G, Boyle J. Antimicrob. Agents Chemother. 55 5438-5451 (2011)
  107. Conformational dependence of a protein kinase phosphate transfer reaction. Henkelman G, LaBute MX, Tung CS, Fenimore PW, McMahon BH. Proc. Natl. Acad. Sci. U.S.A. 102 15347-15351 (2005)
  108. Low- and room-temperature X-ray structures of protein kinase A ternary complexes shed new light on its activity. Kovalevsky AY, Johnson H, Hanson BL, Waltman MJ, Fisher SZ, Taylor S, Langan P. Acta Crystallogr. D Biol. Crystallogr. 68 854-860 (2012)
  109. Structure of PINK1 and mechanisms of Parkinson's disease-associated mutations. Kumar A, Tamjar J, Waddell AD, Woodroof HI, Raimi OG, Shaw AM, Peggie M, Muqit MM, van Aalten DM. Elife 6 (2017)
  110. Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps. Yip KY, Utz L, Sitwell S, Hu X, Sidhu SS, Turk BE, Gerstein M, Kim PM. BMC Biol. 9 53 (2011)
  111. Integration of signaling in the kinome: Architecture and regulation of the αC Helix. Taylor SS, Shaw AS, Kannan N, Kornev AP. Biochim. Biophys. Acta 1854 1567-1574 (2015)
  112. MolLoc: a web tool for the local structural alignment of molecular surfaces. Angaran S, Bock ME, Garutti C, Guerra C. Nucleic Acids Res. 37 W565-70 (2009)
  113. Phosphoryl Transfer Reaction Snapshots in Crystals: INSIGHTS INTO THE MECHANISM OF PROTEIN KINASE A CATALYTIC SUBUNIT. Gerlits O, Tian J, Das A, Langan P, Heller WT, Kovalevsky A. J. Biol. Chem. 290 15538-15548 (2015)
  114. Ternary structure reveals mechanism of a membrane diacylglycerol kinase. Li D, Stansfeld PJ, Sansom MSP, Keogh A, Vogeley L, Howe N, Lyons JA, Aragao D, Fromme P, Fromme R, Basu S, Grotjohann I, Kupitz C, Rendek K, Weierstall U, Zatsepin NA, Cherezov V, Liu W, Bandaru S, English NJ, Gati C, Barty A, Yefanov O, Chapman HN, Diederichs K, Messerschmidt M, Boutet S, Williams GJ, Marvin Seibert M, Caffrey M. Nat Commun 6 10140 (2015)
  115. A Phosphorylated Intermediate in the Activation of WNK Kinases. Akella R, Drozdz MA, Humphreys JM, Jiou J, Durbacz MZ, Mohammed ZJ, He H, Liwocha J, Sekulski K, Goldsmith EJ. Biochemistry 59 1747-1755 (2020)
  116. A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily. Shrestha S, Katiyar S, Sanz-Rodriguez CE, Kemppinen NR, Kim HW, Kadirvelraj R, Panagos C, Keyhaninejad N, Colonna M, Chopra P, Byrne DP, Boons GJ, van der Knaap E, Eyers PA, Edison AS, Wood ZA, Kannan N. Sci Signal 13 eaax6313 (2020)
  117. Effect of mutating the regulatory phosphoserine and conserved threonine on the activity of the expressed catalytic domain of Acanthamoeba myosin I heavy chain kinase. Szczepanowska J, Ramachandran U, Herring CJ, Gruschus JM, Qin J, Korn ED, Brzeska H. Proc. Natl. Acad. Sci. U.S.A. 95 4146-4151 (1998)
  118. Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A. Olivieri C, Wang Y, Li GC, V S M, Kim J, Stultz BR, Neibergall M, Porcelli F, Muretta JM, Thomas DD, Gao J, Blumenthal DK, Taylor SS, Veglia G. Elife 9 e55607 (2020)
  119. Co-conserved features associated with cis regulation of ErbB tyrosine kinases. Mirza A, Mustafa M, Talevich E, Kannan N. PLoS ONE 5 e14310 (2010)
  120. Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping. Ben-Shimon A, Niv MY. PLoS Comput. Biol. 7 e1002288 (2011)
  121. Dynamics of protein kinases: insights from nuclear magnetic resonance. Xiao Y, Liddle JC, Pardi A, Ahn NG. Acc. Chem. Res. 48 1106-1114 (2015)
  122. IL-6 regulates autophagy and chemotherapy resistance by promoting BECN1 phosphorylation. Hu F, Song D, Yan Y, Huang C, Shen C, Lan J, Chen Y, Liu A, Wu Q, Sun L, Xu F, Hu F, Chen L, Luo X, Feng Y, Huang S, Hu J, Wang G. Nat Commun 12 3651 (2021)
  123. Identifying critical non-catalytic residues that modulate protein kinase A activity. Kennedy EJ, Yang J, Pillus L, Taylor SS, Ghosh G. PLoS ONE 4 e4746 (2009)
  124. IκB kinase β (IKBKB) mutations in lymphomas that constitutively activate canonical nuclear factor κB (NFκB) signaling. Kai X, Chellappa V, Donado C, Reyon D, Sekigami Y, Ataca D, Louissaint A, Mattoo H, Joung JK, Pillai S. J. Biol. Chem. 289 26960-26972 (2014)
  125. Phosphorylation of spore coat proteins by a family of atypical protein kinases. Nguyen KB, Sreelatha A, Durrant ES, Lopez-Garrido J, Muszewska A, Dudkiewicz M, Grynberg M, Yee S, Pogliano K, Tomchick DR, Pawłowski K, Dixon JE, Tagliabracci VS. Proc. Natl. Acad. Sci. U.S.A. 113 E3482-91 (2016)
  126. Structure of Aurora B-INCENP in complex with barasertib reveals a potential transinhibitory mechanism. Sessa F, Villa F. Acta Crystallogr F Struct Biol Commun 70 294-298 (2014)
  127. Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA. Mena-Ulecia K, Vergara-Jaque A, Poblete H, Tiznado W, Caballero J. PLoS ONE 9 e109639 (2014)
  128. The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape. Fajer M, Meng Y, Roux B. J Phys Chem B 121 3352-3363 (2017)
  129. Correlated mutation analysis on the catalytic domains of serine/threonine protein kinases. Xu F, Du P, Shen H, Hu H, Wu Q, Xie J, Yu L. PLoS ONE 4 e5913 (2009)
  130. Crystal structure of the Ca²⁺/calmodulin-dependent protein kinase kinase in complex with the inhibitor STO-609. Kukimoto-Niino M, Yoshikawa S, Takagi T, Ohsawa N, Tomabechi Y, Terada T, Shirouzu M, Suzuki A, Lee S, Yamauchi T, Okada-Iwabu M, Iwabu M, Kadowaki T, Minokoshi Y, Yokoyama S. J. Biol. Chem. 286 22570-22579 (2011)
  131. Generation and characterization of ATP analog-specific protein kinase Cδ. Kumar V, Weng YC, Geldenhuys WJ, Wang D, Han X, Messing RO, Chou WH. J. Biol. Chem. 290 1936-1951 (2015)
  132. Mapping the Hydrogen Bond Networks in the Catalytic Subunit of Protein Kinase A Using H/D Fractionation Factors. Li GC, Srivastava AK, Kim J, Taylor SS, Veglia G. Biochemistry 54 4042-4049 (2015)
  133. RET Functions as a Dual-Specificity Kinase that Requires Allosteric Inputs from Juxtamembrane Elements. Plaza-Menacho I, Barnouin K, Barry R, Borg A, Orme M, Chauhan R, Mouilleron S, Martínez-Torres RJ, Meier P, McDonald NQ. Cell Rep 17 3319-3332 (2016)
  134. Similarity search for local protein structures at atomic resolution by exploiting a database management system. Kinjo AR, Nakamura H. Biophysics (Nagoya-shi) 3 75-84 (2007)
  135. Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR. Sudha G, Yamunadevi S, Tyagi N, Das S, Srinivasan N. BMC Struct. Biol. 12 28 (2012)
  136. The pseudokinase domains of guanylyl cyclase-A and -B allosterically increase the affinity of their catalytic domains for substrate. Edmund AB, Walseth TF, Levinson NM, Potter LR. Sci Signal 12 eaau5378 (2019)
  137. The yin-yang of kinase activation and unfolding explains the peculiarity of Val600 in the activation segment of BRAF. Kiel C, Benisty H, Lloréns-Rico V, Serrano L. Elife 5 e12814 (2016)
  138. Uncoupling Catalytic and Binding Functions in the Cyclic AMP-Dependent Protein Kinase A. Kim J, Li G, Walters MA, Taylor SS, Veglia G. Structure 24 353-363 (2016)
  139. A computational study of the phosphorylation mechanism of the insulin receptor tyrosine kinase. Zhou B, Wong CF. J Phys Chem A 113 5144-5150 (2009)
  140. Decoding the Interactions Regulating the Active State Mechanics of Eukaryotic Protein Kinases. Meharena HS, Fan X, Ahuja LG, Keshwani MM, McClendon CL, Chen AM, Adams JA, Taylor SS. PLoS Biol. 14 e2000127 (2016)
  141. Identification of a Non-Gatekeeper Hot Spot for Drug-Resistant Mutations in mTOR Kinase. Wu TJ, Wang X, Zhang Y, Meng L, Kerrigan JE, Burley SK, Zheng XF. Cell Rep 11 446-459 (2015)
  142. Structural analysis of ATP analogues compatible with kinase-catalyzed labeling. Suwal S, Senevirathne C, Garre S, Pflum MK. Bioconjug. Chem. 23 2386-2391 (2012)
  143. Structural insight into the mechanism of synergistic autoinhibition of SAD kinases. Wu JX, Cheng YS, Wang J, Chen L, Ding M, Wu JW. Nat Commun 6 8953 (2015)
  144. The Crystal Structure of Cancer Osaka Thyroid Kinase Reveals an Unexpected Kinase Domain Fold. Gutmann S, Hinniger A, Fendrich G, Drückes P, Antz S, Mattes H, Möbitz H, Ofner S, Schmiedeberg N, Stojanovic A, Rieffel S, Strauss A, Troxler T, Glatthar R, Sparrer H. J. Biol. Chem. 290 15210-15218 (2015)
  145. The mechanism of RNA capping by SARS-CoV-2. Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. Nature 609 793-800 (2022)
  146. Truncation- and motif-based pan-cancer analysis reveals tumor-suppressing kinases. Hudson AM, Stephenson NL, Li C, Trotter E, Fletcher AJ, Katona G, Bieniasz-Krzywiec P, Howell M, Wirth C, Furney S, Miller CJ, Brognard J. Sci Signal 11 eaan6776 (2018)
  147. Two PKA RIα holoenzyme states define ATP as an isoform-specific orthosteric inhibitor that competes with the allosteric activator, cAMP. Lu TW, Wu J, Aoto PC, Weng JH, Ahuja LG, Sun N, Cheng CY, Zhang P, Taylor SS. Proc Natl Acad Sci U S A 116 16347-16356 (2019)
  148. A comparative study of ATP analogs for phosphorylation-dependent kinase-substrate crosslinking. Garre S, Senevirathne C, Pflum MK. Bioorg. Med. Chem. 22 1620-1625 (2014)
  149. A global optimization algorithm for protein surface alignment. Bertolazzi P, Guerra C, Liuzzi G. BMC Bioinformatics 11 488 (2010)
  150. Calculating pKa values in the cAMP-dependent protein kinase: the effect of conformational change and ligand binding. Bjarnadottir U, Nielsen JE. Protein Sci. 19 2485-2497 (2010)
  151. Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα. Borsari C, Keles E, McPhail JA, Schaefer A, Sriramaratnam R, Goch W, Schaefer T, De Pascale M, Bal W, Gstaiger M, Burke JE, Wymann MP. J Am Chem Soc 144 6326-6342 (2022)
  152. Discovery of Allostery in PKA Signaling. Zhang P, Kornev AP, Wu J, Taylor SS. Biophys Rev 7 227-238 (2015)
  153. Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach. Rashid S, Saraswathi S, Kloczkowski A, Sundaram S, Kolinski A. BMC Bioinformatics 17 362 (2016)
  154. Redefining the Protein Kinase Conformational Space with Machine Learning. Ung PM, Rahman R, Schlessinger A. Cell Chem Biol 25 916-924.e2 (2018)
  155. STK40 Is a Pseudokinase that Binds the E3 Ubiquitin Ligase COP1. Durzynska I, Xu X, Adelmant G, Ficarro SB, Marto JA, Sliz P, Uljon S, Blacklow SC. Structure 25 287-294 (2017)
  156. Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization. Agnew C, Ayaz P, Kashima R, Loving HS, Ghatpande P, Kung JE, Underbakke ES, Shan Y, Shaw DE, Hata A, Jura N. Nat Commun 12 4950 (2021)
  157. Structural insights into an atypical secretory pathway kinase crucial for Toxoplasma gondii invasion. Lentini G, Ben Chaabene R, Vadas O, Ramakrishnan C, Mukherjee B, Mehta V, Lunghi M, Grossmann J, Maco B, Visentin R, Hehl AB, Korkhov VM, Soldati-Favre D. Nat Commun 12 3788 (2021)
  158. The MASTL/PP2A cell cycle kinase-phosphatase module restrains PI3K-Akt activity in an mTORC1-dependent manner. Sanz-Castillo B, Hurtado B, Vara-Ciruelos D, El Bakkali A, Hermida D, Salvador-Barbero B, Martínez-Alonso D, González-Martínez J, Santiveri C, Campos-Olivas R, Ximénez-Embún P, Muñoz J, Álvarez-Fernández M, Malumbres M. EMBO J 42 e110833 (2023)
  159. Unique kinase catalytic mechanism of AceK with a single magnesium ion. Li Q, Zheng J, Tan H, Li X, Chen G, Jia Z. PLoS ONE 8 e72048 (2013)
  160. An atlas of substrate specificities for the human serine/threonine kinome. Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC. Nature 613 759-766 (2023)
  161. Characterization of the Catalytic and Nucleotide Binding Properties of the α-Kinase Domain of Dictyostelium Myosin-II Heavy Chain Kinase A. Yang Y, Ye Q, Jia Z, Côté GP. J. Biol. Chem. 290 23935-23946 (2015)
  162. Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A. Olivieri C, Walker C, Karamafrooz A, Wang Y, Manu VS, Porcelli F, Blumenthal DK, Thomas DD, Bernlohr DA, Simon SM, Taylor SS, Veglia G. Commun Biol 4 321 (2021)
  163. Impact of altered phosphorylation on loss of function of juvenile Parkinsonism-associated genetic variants of the E3 ligase parkin. Aguirre JD, Dunkerley KM, Lam R, Rusal M, Shaw GS. J. Biol. Chem. 293 6337-6348 (2018)
  164. LRRK2 dynamics analysis identifies allosteric control of the crosstalk between its catalytic domains. Weng JH, Aoto PC, Lorenz R, Wu J, Schmidt SH, Manschwetus JT, Kaila-Sharma P, Silletti S, Mathea S, Chatterjee D, Knapp S, Herberg FW, Taylor SS. PLoS Biol 20 e3001427 (2022)
  165. Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics. Joshi MK, Burton RA, Wu H, Lipchik AM, Craddock BP, Mo H, Parker LL, Miller WT, Post CB. Protein Sci 29 350-359 (2020)
  166. Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. Simon B, Lou HJ, Huet-Calderwood C, Shi G, Boggon TJ, Turk BE, Calderwood DA. Nat Commun 13 749 (2022)
  167. Acylated-acyl carrier protein stabilizes the Pseudomonas aeruginosa WaaP lipopolysaccharide heptose kinase. Kreamer NNK, Chopra R, Caughlan RE, Fabbro D, Fang E, Gee P, Hunt I, Li M, Leon BC, Muller L, Vash B, Woods AL, Stams T, Dean CR, Uehara T. Sci Rep 8 14124 (2018)
  168. Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways. Chu WT, Chu X, Wang J. Proc. Natl. Acad. Sci. U.S.A. 114 E7959-E7968 (2017)
  169. Conformational stability of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) dictates its substrate selectivity. Gosein V, Miller GJ. J. Biol. Chem. 288 36788-36795 (2013)
  170. Exploring Obscurin and SPEG Kinase Biology. Fleming JR, Rani A, Kraft J, Zenker S, Börgeson E, Lange S. J Clin Med 10 984 (2021)
  171. Feedforward Control of Plant Nitrate Transporter NRT1.1 Biphasic Adaptive Activity. Rashid M, Bera S, Banerjee M, Medvinsky AB, Sun GQ, Li BL, Sljoka A, Chakraborty A. Biophys J 118 898-908 (2020)
  172. GRP78: A possible relationship of COVID-19 and the mucormycosis; in silico perspective. Elgohary AM, Elfiky AA, Barakat K. Comput Biol Med 139 104956 (2021)
  173. Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2). Li J, Flick F, Verheugd P, Carloni P, Lüscher B, Rossetti G. PLoS ONE 10 e0139095 (2015)
  174. Is Disrupted Nucleotide-Substrate Cooperativity a Common Trait for Cushing's Syndrome Driving Mutations of Protein Kinase A? Walker C, Wang Y, Olivieri C, V S M, Gao J, Bernlohr DA, Calebiro D, Taylor SS, Veglia G. J Mol Biol 433 167123 (2021)
  175. KSR induces RAS-independent MAPK pathway activation and modulates the efficacy of KRAS inhibitors. Paniagua G, Jacob HKC, Brehey O, García-Alonso S, Lechuga CG, Pons T, Musteanu M, Guerra C, Drosten M, Barbacid M. Mol Oncol 16 3066-3081 (2022)
  176. Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. Barber KW, Miller CJ, Jun JW, Lou HJ, Turk BE, Rinehart J. Biochemistry 57 4717-4725 (2018)
  177. Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms. Kalaivani R, Narwani TJ, de Brevern AG, Srinivasan N. Protein Sci 28 543-560 (2019)
  178. Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy. Yu Q, Gong X, Tong Y, Wang M, Duan K, Zhang X, Ge F, Yu X, Li S, Li S. Nat Commun 13 5675 (2022)
  179. Structure of a PKA RIα Recurrent Acrodysostosis Mutant Explains Defective cAMP-Dependent Activation. Bruystens JG, Wu J, Fortezzo A, Del Rio J, Nielsen C, Blumenthal DK, Rock R, Stefan E, Taylor SS. J. Mol. Biol. 428 4890-4904 (2016)
  180. Cleavage Alters the Molecular Determinants of Protein Kinase C-δ Catalytic Activity. Gong J, Park M, Steinberg SF. Mol. Cell. Biol. 37 (2017)
  181. Computational prediction of hinge axes in proteins. Shamsuddin R, Doktorova M, Jaswal S, Lee-St John A, McMenimen K. BMC Bioinformatics 15 Suppl 8 S2 (2014)
  182. Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma. Tomasini MD, Wang Y, Karamafrooz A, Li G, Beuming T, Gao J, Taylor SS, Veglia G, Simon SM. Sci Rep 8 720 (2018)
  183. Conformational preference of ChaK1 binding peptides: a molecular dynamics study. Zhang J, King CA, Dalby K, Ren P. PMC Biophys 3 2 (2010)
  184. Germinal-center kinase-like kinase co-crystal structure reveals a swapped activation loop and C-terminal extension. Marcotte D, Rushe M, M Arduini R, Lukacs C, Atkins K, Sun X, Little K, Cullivan M, Paramasivam M, Patterson TA, Hesson T, D McKee T, May-Dracka TL, Xin Z, Bertolotti-Ciarlet A, Bhisetti GR, Lyssikatos JP, Silvian LF. Protein Sci. 26 152-162 (2017)
  185. High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM. Herzik MA, Wu M, Lander GC. Nat Commun 10 1032 (2019)
  186. How activating mutations affect MEK1 regulation and function. Jindal GA, Goyal Y, Humphreys JM, Yeung E, Tian K, Patterson VL, He H, Burdine RD, Goldsmith EJ, Shvartsman SY. J. Biol. Chem. 292 18814-18820 (2017)
  187. Kinase Activation by Small Conformational Changes. Lopez ED, Burastero O, Arcon JP, Defelipe LA, Ahn NG, Marti MA, Turjanski AG. J Chem Inf Model 60 821-832 (2020)
  188. Mechanism of substrate specificity of phosphatidylinositol phosphate kinases. Muftuoglu Y, Xue Y, Gao X, Wu D, Ha Y. Proc. Natl. Acad. Sci. U.S.A. 113 8711-8716 (2016)
  189. Phosphorylation at Ser²⁶ in the ATP-binding site of Ca²⁺/calmodulin-dependent kinase II as a mechanism for switching off the kinase activity. Yilmaz M, Gangopadhyay SS, Leavis P, Grabarek Z, Morgan KG. Biosci. Rep. 33 (2013)
  190. Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction. Huang LC, Yeung W, Wang Y, Cheng H, Venkat A, Li S, Ma P, Rasheed K, Kannan N. BMC Bioinformatics 21 520 (2020)
  191. Reciprocally coupled residues crucial for protein kinase Pak2 activity calculated by statistical coupling analysis. Hsu YH, Traugh JA. PLoS ONE 5 e9455 (2010)
  192. SCEDS: protein fragments for molecular replacement in Phaser. McCoy AJ, Nicholls RA, Schneider TR. Acta Crystallogr. D Biol. Crystallogr. 69 2216-2225 (2013)
  193. Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment. Aquino B, Couñago RM, Verza N, Ferreira LM, Massirer KB, Gileadi O, Arruda P. Front Plant Sci 8 852 (2017)
  194. Substrate binding allosterically relieves autoinhibition of the pseudokinase TRIB1. Jamieson SA, Ruan Z, Burgess AE, Curry JR, McMillan HD, Brewster JL, Dunbier AK, Axtman AD, Kannan N, Mace PD. Sci Signal 11 (2018)
  195. A Stapled Peptide Mimic of the Pseudosubstrate Inhibitor PKI Inhibits Protein Kinase A. Manschwetus JT, Bendzunas GN, Limaye AJ, Knape MJ, Herberg FW, Kennedy EJ. Molecules 24 (2019)
  196. A Tetratricopeptide Repeat Scaffold Couples Signal Detection to OdhI Phosphorylation in Metabolic Control by the Protein Kinase PknG. Lisa MN, Sogues A, Barilone N, Baumgart M, Gil M, Graña M, Durán R, Biondi RM, Bellinzoni M, Bott M, Alzari PM. mBio 12 e0171721 (2021)
  197. ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy. Olivieri C, Li GC, Wang Y, V S M, Walker C, Kim J, Camilloni C, De Simone A, Vendruscolo M, Bernlohr DA, Taylor SS, Veglia G. Sci Adv 8 eabo0696 (2022)
  198. Activation State-Dependent Substrate Gating in Ca2+/Calmodulin-Dependent Protein Kinase II. Johnson DE, Hudmon A. Neural Plast. 2017 9601046 (2017)
  199. An allosteric switch between the activation loop and a c-terminal palindromic phospho-motif controls c-Src function. Cuesta-Hernández HN, Contreras J, Soriano-Maldonado P, Sánchez-Wandelmer J, Yeung W, Martín-Hurtado A, Muñoz IG, Kannan N, Llimargas M, Muñoz J, Plaza-Menacho I. Nat Commun 14 6548 (2023)
  200. Anomalous dispersion analysis of inhibitor flexibility: a case study of the kinase inhibitor H-89. Pflug A, Johnson KA, Engh RA. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 873-877 (2012)
  201. Computational Analysis of Crystallization Additives for the Identification of New Allosteric Sites. Fogha J, Diharce J, Obled A, Aci-Sèche S, Bonnet P. ACS Omega 5 2114-2122 (2020)
  202. Computational delineation of tyrosyl-substrate recognition and catalytic landscapes by the epidermal growth factor receptor tyrosine kinase domain. Liu Y, Radhakrishnan R. Mol Biosyst 10 1890-1904 (2014)
  203. correction Correction for Scherr et al., Structural basis for the specific inhibition of protein kinase G, a virulence factor of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. 104 16388-16388 (2007)
  204. Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding. Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K. J Biol Chem 299 102884 (2023)
  205. Crystal Structures Reveal Hidden Domain Mechanics in Protein Kinase A (PKA). Welsh CL, Conklin AE, Madan LK. Biology (Basel) 12 1370 (2023)
  206. Cushing's syndrome driver mutation disrupts protein kinase A allosteric network, altering both regulation and substrate specificity. Walker C, Wang Y, Olivieri C, Karamafrooz A, Casby J, Bathon K, Calebiro D, Gao J, Bernlohr DA, Taylor SS, Veglia G. Sci Adv 5 eaaw9298 (2019)
  207. Divergent kinase WNG1 is regulated by phosphorylation of an atypical activation sub-domain. Dewangan PS, Beraki TG, Paiz EA, Appiah Mensah D, Chen Z, Reese ML. Biochem J 479 1877-1889 (2022)
  208. Divergent kinase regulates membrane ultrastructure of the Toxoplasma parasitophorous vacuole. Beraki T, Hu X, Broncel M, Young JC, O'Shaughnessy WJ, Borek D, Treeck M, Reese ML. Proc. Natl. Acad. Sci. U.S.A. 116 6361-6370 (2019)
  209. Evolution of protein kinase substrate recognition at the active site. Bradley D, Beltrao P. PLoS Biol. 17 e3000341 (2019)
  210. Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases. Hardianto A, Yusuf M, Liu F, Ranganathan S. BMC Bioinformatics 18 572 (2017)
  211. Feedback inhibition of cAMP effector signaling by a chaperone-assisted ubiquitin system. Rinaldi L, Delle Donne R, Catalanotti B, Torres-Quesada O, Enzler F, Moraca F, Nisticò R, Chiuso F, Piccinin S, Bachmann V, Lindner HH, Garbi C, Scorziello A, Russo NA, Synofzik M, Stelzl U, Annunziato L, Stefan E, Feliciello A. Nat Commun 10 2572 (2019)
  212. Glc7/PP1 dephosphorylates histone H3T11 to regulate autophagy and telomere silencing in response to nutrient availability. Zhang X, Yu Q, Wu Y, Zhang Y, He Y, Wang R, Yu X, Li S. Cell Discov 9 71 (2023)
  213. Globally correlated conformational entropy underlies positive and negative cooperativity in a kinase's enzymatic cycle. Wang Y, V S M, Kim J, Li G, Ahuja LG, Aoto P, Taylor SS, Veglia G. Nat Commun 10 799 (2019)
  214. How Far Are We from the Rapid Prediction of Drug Resistance Arising Due to Kinase Mutations? Erguven M, Karakulak T, Diril MK, Karaca E. ACS Omega 6 1254-1265 (2021)
  215. Hyperactivation of Oncogenic JAK3 Mutants Depend on ATP Binding to the Pseudokinase Domain. Raivola J, Hammarén HM, Virtanen AT, Bulleeraz V, Ward AC, Silvennoinen O. Front Oncol 8 560 (2018)
  216. IRAK3 modulates downstream innate immune signalling through its guanylate cyclase activity. Freihat LA, Wheeler JI, Wong A, Turek I, Manallack DT, Irving HR. Sci Rep 9 15468 (2019)
  217. Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures. Al-Masri C, Trozzi F, Lin SH, Tran O, Sahni N, Patek M, Cichonska A, Ravikumar B, Rahman R. Bioinform Adv 3 vbad129 (2023)
  218. Mapping the 3D structures of small molecule binding sites. Meyers J, Brown N, Blagg J. J Cheminform 8 (2016)
  219. research-article Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases. Venkat A, Watterson G, Byrne DP, O'Boyle B, Shrestha S, Gravel N, Fairweather EE, Daly LA, Bunn C, Yeung W, Aggarwal I, Katiyar S, Eyers CE, Eyers PA, Kannan N. bioRxiv 2023.03.29.534689 (2023)
  220. Modeling conformational flexibility of kinases in inactive states. Schwarz D, Merget B, Deane C, Fulle S. Proteins 87 943-951 (2019)
  221. research-article Protein Kinase Structure and Dynamics: Role of the αC-β4 Loop. Wu J, Jonniya NA, Hirakis SP, Olivieri C, Veglia G, Kornev AP, Taylor SS. bioRxiv 2023.08.31.555822 (2023)
  222. Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer. Kubota Y, Fujioka Y, Patil A, Takagi Y, Matsubara D, Iijima M, Momose I, Naka R, Nakai K, Noda NN, Takekawa M. Nat Commun 13 4063 (2022)
  223. Redox Modification of PKA-Cα Differentially Affects Its Substrate Selection. Delva-Wiley J, Ekhator ES, Adams LL, Patwardhan S, Dong M, Newman RH. Life (Basel) 13 1811 (2023)
  224. Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance. Ohira T, Minowa K, Sugiyama K, Yamashita S, Sakaguchi Y, Miyauchi K, Noguchi R, Kaneko A, Orita I, Fukui T, Tomita K, Suzuki T. Nature 605 372-379 (2022)
  225. Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases. Bradley D, Viéitez C, Rajeeve V, Selkrig J, Cutillas PR, Beltrao P. Cell Rep 34 108602 (2021)
  226. Structural insights into lethal contractural syndrome type 3 (LCCS3) caused by a missense mutation of PIP5Kγ. Zeng X, Uyar A, Sui D, Donyapour N, Wu D, Dickson A, Hu J. Biochem. J. 475 2257-2269 (2018)
  227. Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3. Torosyan H, Paul MD, Forget A, Lo M, Diwanji D, Pawłowski K, Krogan NJ, Jura N, Verba KA. Nat Commun 14 3543 (2023)
  228. Structure and function of H+/K+ pump mutants reveal Na+/K+ pump mechanisms. Young VC, Nakanishi H, Meyer DJ, Nishizawa T, Oshima A, Artigas P, Abe K. Nat Commun 13 5270 (2022)
  229. Structure-Based Target-Specific Screening Leads to Small-Molecule CaMKII Inhibitors. Xu D, Li L, Zhou D, Liu D, Hudmon A, Meroueh SO. ChemMedChem 12 660-677 (2017)
  230. Structures of the cGMP-dependent protein kinase in malaria parasites reveal a unique structural relay mechanism for activation. El Bakkouri M, Kouidmi I, Wernimont AK, Amani M, Hutchinson A, Loppnau P, Kim JJ, Flueck C, Walker JR, Seitova A, Senisterra G, Kakihara Y, Kim C, Blackman MJ, Calmettes C, Baker DA, Hui R. Proc. Natl. Acad. Sci. U.S.A. 116 14164-14173 (2019)
  231. The Interaction between the Drosophila EAG Potassium Channel and the Protein Kinase CaMKII Involves an Extensive Interface at the Active Site of the Kinase. Castro-Rodrigues AF, Zhao Y, Fonseca F, Gabant G, Cadene M, Robertson GA, Morais-Cabral JH. J. Mol. Biol. 430 5029-5049 (2018)
  232. research-article The mechanism of RNA capping by SARS-CoV-2. Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. Res Sq rs.3.rs-1336910 (2022)
  233. The protein kinase CK2 catalytic domain from Plasmodium falciparum: crystal structure, tyrosine kinase activity and inhibition. Ruiz-Carrillo D, Lin J, El Sahili A, Wei M, Sze SK, Cheung PCF, Doerig C, Lescar J. Sci Rep 8 7365 (2018)
  234. The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation. Khandelwal NK, Millan CR, Zangari SI, Avila S, Williams D, Thaker TM, Tomasiak TM. Nat Commun 13 1278 (2022)
  235. research-article The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase A. Olivieri C, Wang Y, Walker C, Subrahmanian MV, Ha KN, Bernlohr DA, Gao J, Camilloni C, Vendruscolo M, Taylor SS, Veglia G. bioRxiv 2023.09.12.557419 (2023)
  236. Understanding allosteric interactions in hMLKL protein that modulate necroptosis and its inhibition. Bansal N, Sciabola S, Bhisetti G. Sci Rep 9 16853 (2019)


Reviews citing this publication (24)

  1. Mechanisms of specificity in protein phosphorylation. Ubersax JA, Ferrell JE. Nat. Rev. Mol. Cell Biol. 8 530-541 (2007)
  2. Regulation of protein kinases; controlling activity through activation segment conformation. Nolen B, Taylor S, Ghosh G. Mol. Cell 15 661-675 (2004)
  3. Structures of Src-family tyrosine kinases. Sicheri F, Kuriyan J. Curr. Opin. Struct. Biol. 7 777-785 (1997)
  4. Three protein kinase structures define a common motif. Taylor SS, Radzio-Andzelm E. Structure 2 345-355 (1994)
  5. The versatility of Helicobacter pylori CagA effector protein functions: The master key hypothesis. Backert S, Tegtmeyer N, Selbach M. Helicobacter 15 163-176 (2010)
  6. The Eleventh Datta Lecture. The structural basis for substrate recognition and control by protein kinases. Johnson LN, Lowe ED, Noble ME, Owen DJ. FEBS Lett. 430 1-11 (1998)
  7. The glycine-rich sequence of protein kinases: a multifunctional element. Bossemeyer D. Trends Biochem. Sci. 19 201-205 (1994)
  8. Domain movements in protein kinases. Cox S, Radzio-Andzelm E, Taylor SS. Curr. Opin. Struct. Biol. 4 893-901 (1994)
  9. Water at biomolecular binding interfaces. Li Z, Lazaridis T. Phys Chem Chem Phys 9 573-581 (2007)
  10. Protein kinase regulation: insights from crystal structure analysis. Morgan DO, De Bondt HL. Curr. Opin. Cell Biol. 6 239-246 (1994)
  11. Atg1 family kinases in autophagy initiation. Noda NN, Fujioka Y. Cell. Mol. Life Sci. 72 3083-3096 (2015)
  12. Towards the discovery of drug-like RNA ligands? Foloppe N, Matassova N, Aboul-Ela F. Drug Discov. Today 11 1019-1027 (2006)
  13. Structures of staurosporine bound to CDK2 and cAPK--new tools for structure-based design of protein kinase inhibitors. Toledo LM, Lydon NB. Structure 5 1551-1556 (1997)
  14. Trends in kinase drug discovery: targets, indications and inhibitor design. Attwood MM, Fabbro D, Sokolov AV, Knapp S, Schiöth HB. Nat Rev Drug Discov 20 839-861 (2021)
  15. Non-competitive inhibition by active site binders. Blat Y. Chem Biol Drug Des 75 535-540 (2010)
  16. Large-scale shape changes in proteins and macromolecular complexes. Wall ME, Gallagher SC, Trewhella J. Annu Rev Phys Chem 51 355-380 (2000)
  17. A multi-angular mass spectrometric view at cyclic nucleotide dependent protein kinases: in vivo characterization and structure/function relationships. Scholten A, Aye TT, Heck AJ. Mass Spectrom Rev 27 331-353 (2008)
  18. Analysis of the regulatory and catalytic domains of PTEN-induced kinase-1 (PINK1). Sim CH, Gabriel K, Mills RD, Culvenor JG, Cheng HC. Hum. Mutat. 33 1408-1422 (2012)
  19. Structural and functional diversity in the activity and regulation of DAPK-related protein kinases. Temmerman K, Simon B, Wilmanns M. FEBS J. 280 5533-5550 (2013)
  20. Prospects for pharmacological targeting of pseudokinases. Kung JE, Jura N. Nat Rev Drug Discov 18 501-526 (2019)
  21. Structure, activity, regulation, and inhibitor discovery for a protein kinase associated with apoptosis and neuronal death. Velentza AV, Schumacher AM, Watterson DM. Pharmacol. Ther. 93 217-224 (2002)
  22. Conformational diversity of catalytic cores of protein kinases. Sowadski JM, Epstein LF, Lankiewicz L, Karlsson R. Pharmacol. Ther. 82 157-164 (1999)
  23. The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases. Shah NH, Amacher JF, Nocka LM, Kuriyan J. Crit. Rev. Biochem. Mol. Biol. 53 535-563 (2018)
  24. New insights into the structure of PINK1 and the mechanism of ubiquitin phosphorylation. Rasool S, Trempe JF. Crit. Rev. Biochem. Mol. Biol. 53 515-534 (2018)

Articles citing this publication (114)

  1. Crystal structure of the tyrosine kinase domain of the human insulin receptor. Hubbard SR, Wei L, Ellis L, Hendrickson WA. Nature 372 746-754 (1994)
  2. Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog. Hubbard SR. EMBO J. 16 5572-5581 (1997)
  3. The pseudokinase MLKL mediates necroptosis via a molecular switch mechanism. Murphy JM, Czabotar PE, Hildebrand JM, Lucet IS, Zhang JG, Alvarez-Diaz S, Lewis R, Lalaoui N, Metcalf D, Webb AI, Young SN, Varghese LN, Tannahill GM, Hatchell EC, Majewski IJ, Okamoto T, Dobson RC, Hilton DJ, Babon JJ, Nicola NA, Strasser A, Silke J, Alexander WS. Immunity 39 443-453 (2013)
  4. Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition. Ohren JF, Chen H, Pavlovsky A, Whitehead C, Zhang E, Kuffa P, Yan C, McConnell P, Spessard C, Banotai C, Mueller WT, Delaney A, Omer C, Sebolt-Leopold J, Dudley DT, Leung IK, Flamme C, Warmus J, Kaufman M, Barrett S, Tecle H, Hasemann CA. Nat. Struct. Mol. Biol. 11 1192-1197 (2004)
  5. Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor. Schindler T, Sicheri F, Pico A, Gazit A, Levitzki A, Kuriyan J. Mol. Cell 3 639-648 (1999)
  6. Lapatinib, a HER2 tyrosine kinase inhibitor, induces stabilization and accumulation of HER2 and potentiates trastuzumab-dependent cell cytotoxicity. Scaltriti M, Verma C, Guzman M, Jimenez J, Parra JL, Pedersen K, Smith DJ, Landolfi S, Ramon y Cajal S, Arribas J, Baselga J. Oncogene 28 803-814 (2009)
  7. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ. Proc. Natl. Acad. Sci. U.S.A. 107 11889-11894 (2010)
  8. Structural basis for the autoinhibition of calcium/calmodulin-dependent protein kinase I. Goldberg J, Nairn AC, Kuriyan J. Cell 84 875-887 (1996)
  9. cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer. Madhusudan, Trafny EA, Xuong NH, Adams JA, Ten Eyck LF, Taylor SS, Sowadski JM. Protein Sci. 3 176-187 (1994)
  10. Crystal structure of JNK3: a kinase implicated in neuronal apoptosis. Xie X, Gu Y, Fox T, Coll JT, Fleming MA, Markland W, Caron PR, Wilson KP, Su MS. Structure 6 983-991 (1998)
  11. Multiple modes of ligand recognition: crystal structures of cyclin-dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine. Schulze-Gahmen U, Brandsen J, Jones HD, Morgan DO, Meijer L, Vesely J, Kim SH. Proteins 22 378-391 (1995)
  12. Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits. Mol CD, Harris JM, McIntosh EM, Tainer JA. Structure 4 1077-1092 (1996)
  13. Two structures of the catalytic domain of phosphorylase kinase: an active protein kinase complexed with substrate analogue and product. Owen DJ, Noble ME, Garman EF, Papageorgiou AC, Johnson LN. Structure 3 467-482 (1995)
  14. A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility. Narayana N, Cox S, Nguyen-huu X, Ten Eyck LF, Taylor SS. Structure 5 921-935 (1997)
  15. The structure of phosphorylated p38gamma is monomeric and reveals a conserved activation-loop conformation. Bellon S, Fitzgibbon MJ, Fox T, Hsiao HM, Wilson KP. Structure 7 1057-1065 (1999)
  16. Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. Desjardins CA, Champion MD, Holder JW, Muszewska A, Goldberg J, Bailão AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M, Gujja S, Heiman DI, Henn MR, Kodira CD, León-Narváez H, Longo LV, Ma LJ, Malavazi I, Matsuo AL, Morais FV, Pereira M, Rodríguez-Brito S, Sakthikumar S, Salem-Izacc SM, Sykes SM, Teixeira MM, Vallejo MC, Walter ME, Yandava C, Young S, Zeng Q, Zucker J, Felipe MS, Goldman GH, Haas BJ, McEwen JG, Nino-Vega G, Puccia R, San-Blas G, Soares CM, Birren BW, Cuomo CA. PLoS Genet. 7 e1002345 (2011)
  17. Molecular basis of Tank-binding kinase 1 activation by transautophosphorylation. Ma X, Helgason E, Phung QT, Quan CL, Iyer RS, Lee MW, Bowman KK, Starovasnik MA, Dueber EC. Proc. Natl. Acad. Sci. U.S.A. 109 9378-9383 (2012)
  18. Structural principles governing domain motions in proteins. Hayward S. Proteins 36 425-435 (1999)
  19. PKA type IIalpha holoenzyme reveals a combinatorial strategy for isoform diversity. Wu J, Brown SH, von Daake S, Taylor SS. Science 318 274-279 (2007)
  20. Structures of rhodopsin kinase in different ligand states reveal key elements involved in G protein-coupled receptor kinase activation. Singh P, Wang B, Maeda T, Palczewski K, Tesmer JJ. J. Biol. Chem. 283 14053-14062 (2008)
  21. Induced fit in guanidino kinases--comparison of substrate-free and transition state analog structures of arginine kinase. Yousef MS, Clark SA, Pruett PK, Somasundaram T, Ellington WR, Chapman MS. Protein Sci. 12 103-111 (2003)
  22. Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. Hayward S. J. Mol. Biol. 339 1001-1021 (2004)
  23. A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases. Hegeman AD, Rodriguez M, Han BW, Uno Y, Phillips GN, Hrabak EM, Cushman JC, Harper JF, Harmon AC, Sussman MR. Proteomics 6 3649-3664 (2006)
  24. Structural basis for chromosome X-linked agammaglobulinemia: a tyrosine kinase disease. Vihinen M, Vetrie D, Maniar HS, Ochs HD, Zhu Q, Vorechovský I, Webster AD, Notarangelo LD, Nilsson L, Sowadski JM. Proc. Natl. Acad. Sci. U.S.A. 91 12803-12807 (1994)
  25. Conserved water molecules contribute to the extensive network of interactions at the active site of protein kinase A. Shaltiel S, Cox S, Taylor SS. Proc. Natl. Acad. Sci. U.S.A. 95 484-491 (1998)
  26. Precision substrate targeting of protein kinases. The cGMP- and cAMP-dependent protein kinases. Wood JS, Yan X, Mendelow M, Corbin JD, Francis SH, Lawrence DS. J. Biol. Chem. 271 174-179 (1996)
  27. Her4 and Her2/neu tyrosine kinase domains dimerize and activate in a reconstituted in vitro system. Monsey J, Shen W, Schlesinger P, Bose R. J. Biol. Chem. 285 7035-7044 (2010)
  28. Insights into the evolution of divergent nucleotide-binding mechanisms among pseudokinases revealed by crystal structures of human and mouse MLKL. Murphy JM, Lucet IS, Hildebrand JM, Tanzer MC, Young SN, Sharma P, Lessene G, Alexander WS, Babon JJ, Silke J, Czabotar PE. Biochem. J. 457 369-377 (2014)
  29. Phosphoryl transfer by protein kinase A is captured in a crystal lattice. Bastidas AC, Deal MS, Steichen JM, Guo Y, Wu J, Taylor SS. J. Am. Chem. Soc. 135 4788-4798 (2013)
  30. Mitogen-activated protein kinase (MAPK) phosphatase 3-mediated cross-talk between MAPKs ERK2 and p38alpha. Zhang YY, Wu JW, Wang ZX. J. Biol. Chem. 286 16150-16162 (2011)
  31. A conserved dimer and global conformational changes in the structure of apo-PknE Ser/Thr protein kinase from Mycobacterium tuberculosis. Gay LM, Ng HL, Alber T. J. Mol. Biol. 360 409-420 (2006)
  32. Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Banavali NK, Roux B. Proteins 67 1096-1112 (2007)
  33. A function-structure model for NGF-activated TRK. Cunningham ME, Greene LA. EMBO J. 17 7282-7293 (1998)
  34. Realizing the allosteric potential of the tetrameric protein kinase A RIα holoenzyme. Boettcher AJ, Wu J, Kim C, Yang J, Bruystens J, Cheung N, Pennypacker JK, Blumenthal DA, Kornev AP, Taylor SS. Structure 19 265-276 (2011)
  35. The structural basis of ATP as an allosteric modulator. Lu S, Huang W, Wang Q, Shen Q, Li S, Nussinov R, Zhang J. PLoS Comput. Biol. 10 e1003831 (2014)
  36. Localization and quaternary structure of the PKA RIβ holoenzyme. Ilouz R, Bubis J, Wu J, Yim YY, Deal MS, Kornev AP, Ma Y, Blumenthal DK, Taylor SS. Proc. Natl. Acad. Sci. U.S.A. 109 12443-12448 (2012)
  37. Mutants of protein kinase A that mimic the ATP-binding site of protein kinase B (AKT). Gassel M, Breitenlechner CB, Rüger P, Jucknischke U, Schneider T, Huber R, Bossemeyer D, Engh RA. J. Mol. Biol. 329 1021-1034 (2003)
  38. Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase. Jacobsen DM, Bao ZQ, O'Brien P, Brooks CL, Young MA. J. Am. Chem. Soc. 134 15357-15370 (2012)
  39. Identification of a buried pocket for potent and selective inhibition of Chk1: prediction and verification. Foloppe N, Fisher LM, Francis G, Howes R, Kierstan P, Potter A. Bioorg. Med. Chem. 14 1792-1804 (2006)
  40. Structural basis for reduced FGFR2 activity in LADD syndrome: Implications for FGFR autoinhibition and activation. Lew ED, Bae JH, Rohmann E, Wollnik B, Schlessinger J. Proc. Natl. Acad. Sci. U.S.A. 104 19802-19807 (2007)
  41. Substrate recognition mechanism of atypical protein kinase Cs revealed by the structure of PKCι in complex with a substrate peptide from Par-3. Wang C, Shang Y, Yu J, Zhang M. Structure 20 791-801 (2012)
  42. Crystal structure of the kinase domain of serum and glucocorticoid-regulated kinase 1 in complex with AMP PNP. Zhao B, Lehr R, Smallwood AM, Ho TF, Maley K, Randall T, Head MS, Koretke KK, Schnackenberg CG. Protein Sci. 16 2761-2769 (2007)
  43. Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases. Chen Y, Gallois-Montbrun S, Schneider B, Véron M, Moréra S, Deville-Bonne D, Janin J. J. Mol. Biol. 332 915-926 (2003)
  44. Molecular design and biological activity of potent and selective protein kinase inhibitors related to balanol. Koide K, Bunnage ME, Gomez Paloma L, Kanter JR, Taylor SS, Brunton LL, Nicolaou KC. Chem. Biol. 2 601-608 (1995)
  45. 2.0 A resolution structure of a ternary complex of pig muscle phosphoglycerate kinase containing 3-phospho-D-glycerate and the nucleotide Mn adenylylimidodiphosphate. May A, Vas M, Harlos K, Blake C. Proteins 24 292-303 (1996)
  46. A structural model of the complex formed by phospholamban and the calcium pump of sarcoplasmic reticulum obtained by molecular mechanics. Hutter MC, Krebs J, Meiler J, Griesinger C, Carafoli E, Helms V. Chembiochem 3 1200-1208 (2002)
  47. Induced-fit docking studies of the active and inactive states of protein tyrosine kinases. Zhong H, Tran LM, Stang JL. J. Mol. Graph. Model. 28 336-346 (2009)
  48. PINK1 rendered temperature sensitive by disease-associated and engineered mutations. Narendra DP, Wang C, Youle RJ, Walker JE. Hum. Mol. Genet. 22 2572-2589 (2013)
  49. Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding. Ku SY, Yip P, Cornell KA, Riscoe MK, Behr JB, Guillerm G, Howell PL. J Biol Chem 282 22195-22206 (2007)
  50. Enzymatic activity with an incomplete catalytic spine: insights from a comparative structural analysis of human CK2α and its paralogous isoform CK2α'. Bischoff N, Raaf J, Olsen B, Bretner M, Issinger OG, Niefind K. Mol. Cell. Biochem. 356 57-65 (2011)
  51. Purification and characterization of the CK2alpha'-based holoenzyme, an isozyme of CK2alpha: a comparative analysis. Olsen BB, Boldyreff B, Niefind K, Issinger OG. Protein Expr. Purif. 47 651-661 (2006)
  52. Synthesis and structure activity relationship studies of benzothieno[3,2-b]furan derivatives as a novel class of IKKbeta inhibitors. Sugiyama H, Yoshida M, Mori K, Kawamoto T, Sogabe S, Takagi T, Oki H, Tanaka T, Kimura H, Ikeura Y. Chem. Pharm. Bull. 55 613-624 (2007)
  53. Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases. Kondo Y, Ognjenović J, Banerjee S, Karandur D, Merk A, Kulhanek K, Wong K, Roose JP, Subramaniam S, Kuriyan J. Science 366 109-115 (2019)
  54. Structure and function of APH(4)-Ia, a hygromycin B resistance enzyme. Stogios PJ, Shakya T, Evdokimova E, Savchenko A, Wright GD. J. Biol. Chem. 286 1966-1975 (2011)
  55. Influence of key residues on the reaction mechanism of the cAMP-dependent protein kinase. Hutter MC, Helms V. Protein Sci 8 2728-2733 (1999)
  56. NleH defines a new family of bacterial effector kinases. Grishin AM, Cherney M, Anderson DH, Phanse S, Babu M, Cygler M. Structure 22 250-259 (2014)
  57. Structure of WbdD: a bifunctional kinase and methyltransferase that regulates the chain length of the O antigen in Escherichia coli O9a. Hagelueken G, Huang H, Clarke BR, Lebl T, Whitfield C, Naismith JH. Mol. Microbiol. 86 730-742 (2012)
  58. Molecular modeling of purinergic receptor P2Y12 and interaction with its antagonists. Zhan C, Yang J, Dong XC, Wang YL. J. Mol. Graph. Model. 26 20-31 (2007)
  59. Structure-based design and biological profile of (E)-N-(4-Nitrobenzylidene)-2-naphthohydrazide, a novel small molecule inhibitor of IκB kinase-β. Avila CM, Lopes AB, Gonçalves AS, da Silva LL, Romeiro NC, Miranda AL, Sant'Anna CM, Barreiro EJ, Fraga CA. Eur J Med Chem 46 1245-1253 (2011)
  60. Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Behnen J, Köster H, Neudert G, Craan T, Heine A, Klebe G. ChemMedChem 7 248-261 (2012)
  61. Flexible 3D pharmacophores as descriptors of dynamic biological space. Nettles JH, Jenkins JL, Williams C, Clark AM, Bender A, Deng Z, Davies JW, Glick M. J. Mol. Graph. Model. 26 622-633 (2007)
  62. A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant. Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. J Comput Aided Mol Des 28 1077-1091 (2014)
  63. All-atomic molecular dynamic studies of human CDK8: insight into the A-loop, point mutations and binding with its partner CycC. Xu W, Amire-Brahimi B, Xie XJ, Huang L, Ji JY. Comput Biol Chem 51 1-11 (2014)
  64. Identification of SRC as a potent drug target for asthma, using an integrative approach of protein interactome analysis and in silico drug discovery. Randhawa V, Bagler G. OMICS 16 513-526 (2012)
  65. A computational analysis of substrate binding strength by phosphorylase kinase and protein kinase A. Brinkworth RI, Horne J, Kobe B. J. Mol. Recognit. 15 104-111 (2002)
  66. Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains. Miyafusa T, Caaveiro JM, Tanaka Y, Tsumoto K. Biochem. J. 443 671-680 (2012)
  67. Evidence that phosphorylation of threonine in the GT motif triggers activation of PknA, a eukaryotic-type serine/threonine kinase from Mycobacterium tuberculosis. Ravala SK, Singh S, Yadav GS, Kumar S, Karthikeyan S, Chakraborti PK. FEBS J. 282 1419-1431 (2015)
  68. Møller-Plesset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method. Jung J, Sugita Y, Ten-no S. J Chem Phys 132 084106 (2010)
  69. A QM/MM study of Kemptide phosphorylation catalyzed by protein kinase A. The role of Asp166 as a general acid/base catalyst. Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. Phys Chem Chem Phys 17 3497-3511 (2015)
  70. Dimeric Structure of the Pseudokinase IRAK3 Suggests an Allosteric Mechanism for Negative Regulation. Lange SM, Nelen MI, Cohen P, Kulathu Y. Structure 29 238-251.e4 (2021)
  71. Insights from soft X-rays: the chlorine and sulfur sub-structures of a CK2alpha/DRB complex. Raaf J, Issinger OG, Niefind K. Mol. Cell. Biochem. 316 15-23 (2008)
  72. Structural insights into IKKbeta inhibition by natural products staurosporine and quercetin. Avila CM, Romeiro NC, Sant'Anna CM, Barreiro EJ, Fraga CA. Bioorg. Med. Chem. Lett. 19 6907-6910 (2009)
  73. Structures of the PKA RIα Holoenzyme with the FLHCC Driver J-PKAcα or Wild-Type PKAcα. Cao B, Lu TW, Martinez Fiesco JA, Tomasini M, Fan L, Simon SM, Taylor SS, Zhang P. Structure 27 816-828.e4 (2019)
  74. Identification and classification of small molecule kinases: insights into substrate recognition and specificity. Oruganty K, Talevich EE, Neuwald AF, Kannan N. BMC Evol. Biol. 16 7 (2016)
  75. Increased intracellular magnesium attenuates β-adrenergic stimulation of the cardiac Ca(V)1.2 channel. Brunet S, Scheuer T, Catterall WA. J. Gen. Physiol. 141 85-94 (2013)
  76. Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site. Pujadas G, Palau J. Protein Sci. 10 1645-1657 (2001)
  77. A Novel Phosphoregulatory Switch Controls the Activity and Function of the Major Catalytic Subunit of Protein Kinase A in Aspergillus fumigatus. Shwab EK, Juvvadi PR, Waitt G, Soderblom EJ, Moseley MA, Nicely NI, Asfaw YG, Steinbach WJ. MBio 8 (2017)
  78. AMP-activated protein kinase selectively inhibited by the type II inhibitor SBI-0206965. Dite TA, Langendorf CG, Hoque A, Galic S, Rebello RJ, Ovens AJ, Lindqvist LM, Ngoei KRW, Ling NXY, Furic L, Kemp BE, Scott JW, Oakhill JS. J. Biol. Chem. 293 8874-8885 (2018)
  79. Activation loop phosphorylation-independent kinase activity of human protein kinase C zeta. Ranganathan S, Wang Y, Kern FG, Qu Z, Li R. Proteins 67 709-719 (2007)
  80. Design, synthesis, and in vitro evaluation of a fluorescently labeled irreversible inhibitor of the catalytic subunit of cAMP-dependent protein kinase (PKACα). Coover RA, Luzi NM, Korwar S, Casile ME, Lyons CE, Peterson DL, Ellis KC. Org. Biomol. Chem. 14 4576-4581 (2016)
  81. E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor. Ung MU, Lu B, McCammon JA. Biopolymers 81 428-439 (2006)
  82. How oncogenic mutations activate human MAP kinase 1 (MEK1): a molecular dynamics simulation study. Liu Y, Zhu J, Guo X, Huang T, Han J, Gao J, Xu D, Han W. J Biomol Struct Dyn 38 3942-3958 (2020)
  83. Structure-Based Assignment of Ile, Leu, and Val Methyl Groups in the Active and Inactive Forms of the Mitogen-Activated Protein Kinase Extracellular Signal-Regulated Kinase 2. Xiao Y, Warner LR, Latham MP, Ahn NG, Pardi A. Biochemistry 54 4307-4319 (2015)
  84. Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study. Jin HX, Go ML, Yin P, Qiu XT, Zhu P, Yan XJ. PLoS ONE 10 e0124673 (2015)
  85. Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Creixell P, Pandey JP, Palmeri A, Bhattacharyya M, Creixell M, Ranganathan R, Pincus D, Yaffe MB. Cell Syst 7 371-383.e4 (2018)
  86. Stimulation of cGMP-dependent protein kinase I alpha by a peptide from its own sequence. An investigation by enzymology, circular dichroism and 1H NMR of the activity and structure of cGMP-dependent protein kinase I alpha-(546-576)-peptide amide. Huggins JP, Ganzhorn AJ, Saudek V, Pelton JT, Atkinson RA. Eur. J. Biochem. 221 581-593 (1994)
  87. Understanding how cAMP-dependent protein kinase can catalyze phosphoryl transfer in the presence of Ca2+ and Sr2+: a QM/MM study. Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. Phys Chem Chem Phys 19 10377-10394 (2017)
  88. An N-terminally truncated form of cyclic GMP-dependent protein kinase Iα (PKG Iα) is monomeric and autoinhibited and provides a model for activation. Moon TM, Sheehe JL, Nukareddy P, Nausch LW, Wohlfahrt J, Matthews DE, Blumenthal DK, Dostmann WR. J. Biol. Chem. 293 7916-7929 (2018)
  89. AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo-β-lactamases and indoleamine/tryptophan 2,3-dioxygenases. Dai Q, Yan Y, Ning X, Li G, Yu J, Deng J, Yang L, Li GB. Acta Pharm Sin B 11 1931-1946 (2021)
  90. Characterization of WY 14,643 and its Complex with Aldose Reductase. Sawaya MR, Verma M, Balendiran V, Rath NP, Cascio D, Balendiran GK. Sci Rep 6 34394 (2016)
  91. Computer modeling of the dynamic properties of the cAMP-dependent protein kinase catalytic subunit. Izvolski A, Järv J, Kuznetsov A. Comput Biol Chem 47 66-70 (2013)
  92. Conservation of structural fluctuations in homologous protein kinases and its implications on functional sites. Kalaivani R, de Brevern AG, Srinivasan N. Proteins 84 957-978 (2016)
  93. Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers. Li F, Fahie MA, Gilliam KM, Pham R, Chen M. Nat Commun 13 3541 (2022)
  94. Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases. Venkat A, Watterson G, Byrne DP, O'Boyle B, Shrestha S, Gravel N, Fairweather EE, Daly LA, Bunn C, Yeung W, Aggarwal I, Katiyar S, Eyers CE, Eyers PA, Kannan N. Elife 12 RP87958 (2023)
  95. MgATP-induced conformational change of the catalytic subunit of cAMP-dependent protein kinase. Yang S, Rogers KM, Johnson DA. Biophys. Chem. 113 193-199 (2005)
  96. Letter Phosphorylation of Aspergillus fumigatus PkaR impacts growth and cell wall integrity through novel mechanisms. Shwab EK, Juvvadi PR, Waitt G, Soderblom EJ, Moseley MA, Nicely NI, Steinbach WJ. FEBS Lett. 591 3730-3744 (2017)
  97. Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant. Li J, Vervoorts J, Carloni P, Rossetti G, Lüscher B. BMC Bioinformatics 18 15 (2017)
  98. Study of the affinity between the protein kinase PKA and homoarginine-containing peptides derived from kemptide: Free energy perturbation (FEP) calculations. Mena-Ulecia K, Gonzalez-Norambuena F, Vergara-Jaque A, Poblete H, Tiznado W, Caballero J. J Comput Chem 39 986-992 (2018)
  99. The crystal structure of PknI from Mycobacterium tuberculosis shows an inactive, pseudokinase-like conformation. Lisa MN, Wagner T, Alexandre M, Barilone N, Raynal B, Alzari PM, Bellinzoni M. FEBS J. 284 602-614 (2017)
  100. The negative charge of Glu-127 in protein kinase A and its biorecognition. Batkin M, Shaltiel S. FEBS Lett. 452 395-399 (1999)
  101. Acceleration of Binding Site Comparisons by Graph Partitioning. Krotzky T, Klebe G. Mol Inform 34 550-558 (2015)
  102. Analysis on sliding helices and strands in protein structural comparisons: a case study with protein kinases. Gowri VS, Anamika K, Gore S, Srinivasan N. J. Biosci. 32 921-928 (2007)
  103. Capturing Differences in the Regulation of LRRK2 Dynamics and Conformational States by Small Molecule Kinase Inhibitors. Weng JH, Ma W, Wu J, Sharma PK, Silletti S, McCammon JA, Taylor S. ACS Chem Biol 18 810-821 (2023)
  104. Characterization and prevalence of two novel CHEK2 large deletions in Greek breast cancer patients. Apostolou P, Fostira F, Mollaki V, Delimitsou A, Vlassi M, Pentheroudakis G, Faliakou E, Kollia P, Fountzilas G, Yannoukakos D, Konstantopoulou I. J. Hum. Genet. 63 877-886 (2018)
  105. Crystal structure of the phosphorylated Arabidopsis MKK5 reveals activation mechanism of MAPK kinases. Pei CJ, He QX, Luo Z, Yao H, Wang ZX, Wu JW. Acta Biochim Biophys Sin (Shanghai) 54 1159-1170 (2022)
  106. Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism. Li P, Xu D, Ma T, Wang D, Li W, He J, Ran T, Wang W. Biochem. J. 475 2209-2224 (2018)
  107. Edmond Fischer's kinase legacy: History of the protein kinase inhibitor and protein kinase A. Taylor SS, Herberg FW, Veglia G, Wu J. IUBMB Life 75 311-323 (2023)
  108. Letter Identification of NEK3 and MOK as novel targets for lithium. Bravo A, de Lucio H, Sánchez-Murcia PA, Jiménez-Ruiz A, Petrone PM, Gago F, Cortés Cabrera A. Chem Biol Drug Des 93 965-969 (2019)
  109. Intermolecular relaxation has little effect on intra-peptide exchange-transferred NOE intensities. Zabell AP, Post CB. J. Biomol. NMR 22 303-315 (2002)
  110. On the Origins of Enzymes: Phosphate-Binding Polypeptides Mediate Phosphoryl Transfer to Synthesize Adenosine Triphosphate. Vyas P, Malitsky S, Itkin M, Tawfik DS. J Am Chem Soc (2023)
  111. Perturbations of the ZED1 pseudokinase activate plant immunity. Bastedo DP, Khan M, Martel A, Seto D, Kireeva I, Zhang J, Masud W, Millar D, Lee JY, Lee AH, Gong Y, Santos-Severino A, Guttman DS, Desveaux D. PLoS Pathog. 15 e1007900 (2019)
  112. Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. Kalaivani R, Reema R, Srinivasan N. PLoS Comput. Biol. 14 e1005975 (2018)
  113. Remote laboratory training for high school students: grocery store based hands-on project in protein crystallography. Fox AL, Teteris AR, Mathews II. J Appl Crystallogr 56 1557-1568 (2023)
  114. Zooming in on protons: Neutron structure of protein kinase A trapped in a product complex. Gerlits O, Weiss KL, Blakeley MP, Veglia G, Taylor SS, Kovalevsky A. Sci Adv 5 eaav0482 (2019)


Related citations provided by authors (5)

  1. 2.0 Angstrom Refined Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with a Peptide Inhibitor and Detergent. Knighton DR, Bell SM, Zheng J, Teneyck LF, Xuong N-H, Taylor SS, Sowadski JM To be Published -
  2. Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase Complexed with Mg/ATP and Peptide Inhibitor. Zheng J, Knighton DR, Teneyck LF, Karlsson R, Xuong N-H, Taylor SS, Sowadski JM Biochemistry 32 2154- (1993)
  3. Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase.. Knighton DR, Zheng JH, Ten Eyck LF, Ashford VA, Xuong NH, Taylor SS, Sowadski JM Science 253 407-14 (1991)
  4. Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase.. Knighton DR, Zheng JH, Ten Eyck LF, Xuong NH, Taylor SS, Sowadski JM Science 253 414-20 (1991)
  5. Expression of the Catalytic Subunit of C/AMP-Dependent Protein Kinase in Escherichia Coli. Slice LW, Taylor SS J. Biol. Chem. 264 20940- (1989)

Quick links