1m15 Citations

Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights.

Acta Crystallogr. D Biol. Crystallogr. 58 2009-17 (2002)
Cited: 38 times
EuropePMC logo PMID: 12454458

Abstract

The three-dimensional crystal structure of an arginine kinase transition-state analogue complex has been refined at 1.2 A resolution, with an overall R factor of 12.3%. The current model provides a unique opportunity to analyze the structure of a bimolecular (phosphagen kinase) enzyme in its transition state. This atomic resolution structure confirms in-line transfer of the phosphoryl group and the catalytic importance of the precise alignment of the substrates. The structure is consistent with a concerted proton transfer that has been proposed for an unrelated kinase. Refinement of anisotropic temperature factors and translation-libration-screw (TLS) analyses led to the identification of four rigid groups and their prevalent modes of motion in the transition state. The relative magnitudes of the mobility of rigid groups are consistent with their proposed roles in catalysis.

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  1. Evolutionarily conserved amino acids that control TCR-MHC interaction. Marrack P, Scott-Browne JP, Dai S, Gapin L, Kappler JW. Annu. Rev. Immunol. 26 171-203 (2008)

Articles - 1m15 mentioned but not cited (13)

  1. The RCSB Protein Data Bank: new resources for research and education. Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne PE. Nucleic Acids Res. 41 D475-82 (2013)
  2. A tyrosine kinase and its activator control the activity of the CtsR heat shock repressor in B. subtilis. Kirstein J, Zühlke D, Gerth U, Turgay K, Hecker M. EMBO J 24 3435-3445 (2005)
  3. 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)
  4. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Wang S, Peng J, Xu J. Bioinformatics 27 2537-2545 (2011)
  5. Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility. Niu X, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Brüschweiler R, Chapman MS. J Mol Biol 405 479-496 (2011)
  6. Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains. Fan S, Wu Y, Wang S, Wang Z, Jiang B, Liu Y, Liang R, Zhou W, Zhang N, Xia C. J. Virol. 90 6625-6641 (2016)
  7. Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus. Laino A, Lopez-Zavala AA, Garcia-Orozco KD, Carrasco-Miranda JS, Santana M, Stojanoff V, Sotelo-Mundo RR, Garcia CF. PeerJ 5 e3787 (2017)
  8. Common hydrogen bond interactions in diverse phosphoryl transfer active sites. Summerton JC, Martin GM, Evanseck JD, Chapman MS. PLoS One 9 e108310 (2014)
  9. Kinetics for Zinc Ion Induced Sepia Pharaonis Arginine Kinase Inactivation and Aggregation. Si YX, Lee J, Cheng JG, Yin SJ, Park YD, Qian GY, Jiang XM. Protein Pept. Lett. 23 508-517 (2016)
  10. Pi-Pi contacts are an overlooked protein feature relevant to phase separation. Vernon RM, Chong PA, Tsang B, Kim TH, Bah A, Farber P, Lin H, Forman-Kay JD. Elife 7 (2018)
  11. The Michaelis Complex of Arginine Kinase Samples the Transition State at a Frequency That Matches the Catalytic Rate. Peng Y, Hansen AL, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Chapman MS, Brüschweiler R. J. Am. Chem. Soc. 139 4846-4853 (2017)
  12. The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase. Godsey MH, Davulcu O, Nix JC, Skalicky JJ, Brüschweiler RP, Chapman MS. Structure 24 1658-1667 (2016)
  13. The substrate-free and -bound crystal structures of the duplicated taurocyamine kinase from the human parasite Schistosoma mansoni. Merceron R, Awama AM, Montserret R, Marcillat O, Gouet P. J. Biol. Chem. 290 12951-12963 (2015)


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Articles citing this publication (21)

  1. Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis. Mao L, Wang Y, Liu Y, Hu X. J Mol Biol 336 787-807 (2004)
  2. Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome. Korostelev A, Trakhanov S, Asahara H, Laurberg M, Lancaster L, Noller HF. Proc Natl Acad Sci U S A 104 16840-16843 (2007)
  3. The atomic resolution crystal structure of the YajL (ThiJ) protein from Escherichia coli: a close prokaryotic homologue of the Parkinsonism-associated protein DJ-1. Wilson MA, Ringe D, Petsko GA. J Mol Biol 353 678-691 (2005)
  4. The role of phosphagen specificity loops in arginine kinase. Azzi A, Clark SA, Ellington WR, Chapman MS. Protein Sci 13 575-585 (2004)
  5. The crystal structure of Trypanosoma cruzi arginine kinase. Fernandez P, Haouz A, Pereira CA, Aguilar C, Alzari PM. Proteins 69 209-212 (2007)
  6. Unassisted refolding of urea-denatured arginine kinase from shrimp Feneropenaeus chinensis: evidence for two equilibrium intermediates in the refolding pathway. Pan JC, Yu Z, Su XY, Sun YQ, Rao XM, Zhou HM. Protein Sci 13 1892-1901 (2004)
  7. YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays. Lehmann C, Doseeva V, Pullalarevu S, Krajewski W, Howard A, Herzberg O. Proteins 56 376-383 (2004)
  8. PPIase independent chaperone-like function of recombinant human Cyclophilin A during arginine kinase refolding. Zhang XC, Wang WD, Wang JS, Pan JC. FEBS Lett 587 666-672 (2013)
  9. The structure of lombricine kinase: implications for phosphagen kinase conformational changes. Bush DJ, Kirillova O, Clark SA, Davulcu O, Fabiola F, Xie Q, Somasundaram T, Ellington WR, Chapman MS. J Biol Chem 286 9338-9350 (2011)
  10. Crystal structure of shrimp arginine kinase in binary complex with arginine-a molecular view of the phosphagen precursor binding to the enzyme. López-Zavala AA, García-Orozco KD, Carrasco-Miranda JS, Sugich-Miranda R, Velázquez-Contreras EF, Criscitiello MF, Brieba LG, Rudiño-Piñera E, Sotelo-Mundo RR. J Bioenerg Biomembr 45 511-518 (2013)
  11. Conformational change and inactivation of arginine kinase from shrimp Feneropenaeus chinensis in oxidized dithiothreitol solutions. Pan JC, Yu ZH, Hui EF, Zhou HM. Biochem Cell Biol 82 361-367 (2004)
  12. Domain motions of glucosamine-6P synthase: comparison of the anisotropic displacements in the crystals and the catalytic hinge-bending rotation. Mouilleron S, Golinelli-Pimpaneau B. Protein Sci 16 485-493 (2007)
  13. The role of Cys271 in conformational changes of arginine kinase. Liu N, Wang JS, Wang WD, Pan JC. Int J Biol Macromol 49 98-102 (2011)
  14. Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. Clark SA, Davulcu O, Chapman MS. Biochem Biophys Res Commun 427 212-217 (2012)
  15. Crystallization and X-ray analysis of the Schistosoma mansoni guanidino kinase. Awama AM, Paracuellos P, Laurent S, Dissous C, Marcillat O, Gouet P. Acta Crystallogr Sect F Struct Biol Cryst Commun 64 854-857 (2008)
  16. Identification, characterization and activation mechanism of a tyrosine kinase of Bacillus anthracis. Mattoo AR, Arora A, Maiti S, Singh Y. FEBS J 275 6237-6247 (2008)
  17. Crystal structures of carbamate kinase from Giardia lamblia bound with citric acid and AMP-PNP. Lim K, Kulakova L, Galkin A, Herzberg O. PLoS One 8 e64004 (2013)
  18. Dynamical properties of the loop 320s of substrate-free and substrate-bound muscle creatine kinase by NMR: evidence for independent subunits. Rivière G, Hologne M, Marcillat O, Lancelin JM. FEBS J 279 2863-2875 (2012)
  19. Deceleration of arginine kinase refolding by induced helical structures. Li HL, Zhou SM, Park D, Jeong HO, Chung HY, Yang JM, Meng FG, Hu WJ. Protein J 31 267-274 (2012)
  20. Hyperconjugation-mediated solvent effects in phosphoanhydride bonds. Summerton JC, Evanseck JD, Chapman MS. J Phys Chem A 116 10209-10217 (2012)
  21. Comment Normalizing normal mode analysis. Chapman MS. Structure 15 135-136 (2007)


Related citations provided by authors (3)

  1. Critical Initial Real-Space Refinement in the Structure Determination of Arginine Kinase. Zhou G, Somasundaram T, Blanc E, Chen Z, Chapman MS Acta Crystallogr. D Biol. Crystallogr. 55 835-845 (1999)
  2. Expression, Purification from Inclusion Bodies, and Crystal Characterization of a Transition State Analog Complex of Arginine Kinase: A Model for Studying Phosphagen Kinases. Zhou G, Parthasarathy G, Somasundaram T, Ables A, Roy L, Strong SJ, Ellington WR, Chapman MS Protein Sci. 6 444-449 (1997)
  3. Transition State Structure of Arginine Kinase: Implications for Catalysis of Bimolecular Reactions. Zhou G, Somasundaram T, Blanc E, Parthasarathy G, Ellington WR, Chapman MS Proc. Natl. Acad. Sci. U.S.A. 95 8449-8454 (1998)