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PDBsum entry 1cdk

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protein ligands metals Protein-protein interface(s) links
Transferase/transferase inhibitor PDB id
1cdk
Jmol
Contents
Protein chains
343 a.a. *
20 a.a. *
Ligands
ANP ×2
MYR ×2
Metals
_MN ×4
Waters ×312
* Residue conservation analysis
PDB id:
1cdk
Name: Transferase/transferase inhibitor
Title: Camp-dependent protein kinase catalytic subunit (E.C.2.7.1.3 (protein kinase a) complexed with protein kinase inhibitor fragment 5-24 (pki(5-24) isoelectric variant ca) and mn2+ a imidodiphosphate (mnamp-pnp) at ph 5.6 and 7c and 4c
Structure: Camp-dependent protein kinase. Chain: a, b. Synonym: protein kinase a. Protein kinase inhibitor. Chain: i, j. Synonym: pki(5-24). Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: heart. Tissue: heart isoform ca. Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.197    
Authors: D.Bossemeyer,R.A.Engh,V.Kinzel,H.Ponstingl,R.Huber
Key ref: D.Bossemeyer et al. (1993). Phosphotransferase and substrate binding mechanism of the cAMP-dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ adenylyl imidodiphosphate and inhibitor peptide PKI(5-24). EMBO J, 12, 849-859. PubMed id: 8384554
Date:
04-Jul-94     Release date:   15-Oct-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36887  (KAPCA_PIG) -  cAMP-dependent protein kinase catalytic subunit alpha
Seq:
Struc:
351 a.a.
343 a.a.*
Protein chains
Pfam   ArchSchema ?
P61926  (IPKA_RABIT) -  cAMP-dependent protein kinase inhibitor alpha
Seq:
Struc:
76 a.a.
20 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.2.7.11.11  - cAMP-dependent protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     phosphorylation   3 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
EMBO J 12:849-859 (1993)
PubMed id: 8384554  
 
 
Phosphotransferase and substrate binding mechanism of the cAMP-dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ adenylyl imidodiphosphate and inhibitor peptide PKI(5-24).
D.Bossemeyer, R.A.Engh, V.Kinzel, H.Ponstingl, R.Huber.
 
  ABSTRACT  
 
The crystal structure of the porcine heart catalytic subunit of cAMP-dependent protein kinase in a ternary complex with the MgATP analogue MnAMP-PNP and a pseudosubstrate inhibitor peptide, PKI(5-24), has been solved at 2.0 A resolution from monoclinic crystals of the catalytic subunit isoform CA. The refinement is presently at an R factor of 0.194 and the active site of the molecule is well defined. The glycine-rich phosphate anchor of the nucleotide binding fold motif of the protein kinase is a beta ribbon acting as a flap with conformational flexibility over the triphosphate group. The glycines seem to be conserved to avoid steric clash with ATP. The known synergistic effects of substrate binding can be explained by hydrogen bonds present only in the ternary complex. Implications for the kinetic scheme of binding order are discussed. The structure is assumed to represent a phosphotransfer competent conformation. The invariant conserved residue Asp166 is proposed to be the catalytic base and Lys168 to stabilize the transition state. In some tyrosine kinases Lys168 is functionally replaced by an Arg displaced by two residues in the primary sequence, suggesting invariance in three-dimensional space. The structure supports an in-line transfer with a pentacoordinate transition state at the phosphorus with very few nuclear movements.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21423167 G.Xu, Y.C.Lo, Q.Li, G.Napolitano, X.Wu, X.Jiang, M.Dreano, M.Karin, and H.Wu (2011).
Crystal structure of inhibitor of κB kinase β.
  Nature, 472, 325-330.
PDB codes: 3qa8 3qad 3rzf
21052604 M.Montenegro, M.Garcia-Viloca, J.M.Lluch, and A.González-Lafont (2011).
A QM/MM study of the phosphoryl transfer to the Kemptide substrate catalyzed by protein kinase A. The effect of the phosphorylation state of the protein on the mechanism.
  Phys Chem Chem Phys, 13, 530-539.  
21474065 N.Jura, X.Zhang, N.F.Endres, M.A.Seeliger, T.Schindler, and J.Kuriyan (2011).
Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms.
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20077512 E.D.Scheeff, H.L.Axelrod, M.D.Miller, H.J.Chiu, A.M.Deacon, I.A.Wilson, and G.Manning (2010).
Genomics, evolution, and crystal structure of a new family of bacterial spore kinases.
  Proteins, 78, 1470-1482.
PDB code: 2q83
20563625 P.Gruszczyński, M.Obuchowski, and R.Kaźmierkiewicz (2010).
Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis.
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20954248 U.Bjarnadottir, and J.E.Nielsen (2010).
Calculating pK(a) values in the cAMP-dependent protein kinase: The effect of conformational change and ligand binding.
  Protein Sci, 19, 2485-2497.  
20637424 Y.W.Ng, D.Raghunathan, P.M.Chan, Y.Baskaran, D.J.Smith, C.H.Lee, C.Verma, and E.Manser (2010).
Why an A-loop phospho-mimetic fails to activate PAK1: understanding an inaccessible kinase state by molecular dynamics simulations.
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19765263 A.Filatova, M.Leyerer, V.Gorboulev, C.Chintalapati, Y.Reinders, T.D.Müller, A.Srinivasan, S.Hübner, and H.Koepsell (2009).
Novel shuttling domain in a regulator (RSC1A1) of transporter SGLT1 steers cell cycle-dependent nuclear location.
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19334696 B.Zhou, and C.F.Wong (2009).
A computational study of the phosphorylation mechanism of the insulin receptor tyrosine kinase.
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19141289 E.D.Scheeff, J.Eswaran, G.Bunkoczi, S.Knapp, and G.Manning (2009).
Structure of the Pseudokinase VRK3 Reveals a Degraded Catalytic Site, a Highly Conserved Kinase Fold, and a Putative Regulatory Binding Site.
  Structure, 17, 128-138.
PDB codes: 2jii 2v62
19207465 F.A.Pasha, M.Muddassar, and S.Joo Cho (2009).
Molecular docking and 3D QSAR studies of Chk2 inhibitors.
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19122195 J.Yang, E.J.Kennedy, J.Wu, M.S.Deal, J.Pennypacker, G.Ghosh, and S.S.Taylor (2009).
Contribution of Non-catalytic Core Residues to Activity and Regulation in Protein Kinase A.
  J Biol Chem, 284, 6241-6248.
PDB code: 2qur
19159956 N.Wurtz, B.Pastorino, L.Almeras, S.Briolant, C.Villard, and D.Parzy (2009).
Expression and biochemical characterization of the Plasmodium falciparum protein kinase A catalytic subunit.
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19109437 Y.Shan, M.A.Seeliger, M.P.Eastwood, F.Frank, H.Xu, M...Jensen, R.O.Dror, J.Kuriyan, and D.E.Shaw (2009).
A conserved protonation-dependent switch controls drug binding in the Abl kinase.
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18765796 E.M.Puchner, A.Alexandrovich, A.L.Kho, U.Hensen, L.V.Schäfer, B.Brandmeier, F.Gräter, H.Grubmüller, H.E.Gaub, and M.Gautel (2008).
Mechanoenzymatics of titin kinase.
  Proc Natl Acad Sci U S A, 105, 13385-13390.  
17965184 B.Zhao, R.Lehr, A.M.Smallwood, T.F.Ho, K.Maley, T.Randall, M.S.Head, K.K.Koretke, and C.G.Schnackenberg (2007).
Crystal structure of the kinase domain of serum and glucocorticoid-regulated kinase 1 in complex with AMP PNP.
  Protein Sci, 16, 2761-2769.
PDB code: 2r5t
17397263 D.Desveaux, A.U.Singer, A.J.Wu, B.C.McNulty, L.Musselwhite, Z.Nimchuk, J.Sondek, and J.L.Dangl (2007).
Type III effector activation via nucleotide binding, phosphorylation, and host target interaction.
  PLoS Pathog, 3, e48.
PDB codes: 2nud 2nun
17240048 G.M.Cheetham, P.A.Charlton, J.M.Golec, and J.R.Pollard (2007).
Structural basis for potent inhibition of the Aurora kinases and a T315I multi-drug resistant mutant form of Abl kinase by VX-680.
  Cancer Lett, 251, 323-329.  
17585314 J.A.Ubersax, and J.E.Ferrell (2007).
Mechanisms of specificity in protein phosphorylation.
  Nat Rev Mol Cell Biol, 8, 530-541.  
17709340 J.L.Chung, J.E.Beaver, E.D.Scheeff, and P.E.Bourne (2007).
Con-Struct Map: a comparative contact map analysis tool.
  Bioinformatics, 23, 2491-2492.  
18008170 M.Montenegro, M.Garcia-Viloca, A.González-Lafont, and J.M.Lluch (2007).
Comparative study of the prereactive Protein Kinase A Michaelis complex with Kemptide substrate.
  J Comput Aided Mol Des, 21, 603-615.  
17694048 W.Xing, Y.Zou, Q.Liu, J.Liu, X.Luo, Q.Huang, S.Chen, L.Zhu, R.Bi, Q.Hao, J.W.Wu, J.M.Zhou, and J.Chai (2007).
The structural basis for activation of plant immunity by bacterial effector protein AvrPto.
  Nature, 449, 243-247.
PDB code: 2qkw
17214602 A.Lochner, and J.A.Moolman (2006).
The many faces of H89: a review.
  Cardiovasc Drug Rev, 24, 261-274.  
16794575 A.W.Oliver, A.Paul, K.J.Boxall, S.E.Barrie, G.W.Aherne, M.D.Garrett, S.Mittnacht, and L.H.Pearl (2006).
Trans-activation of the DNA-damage signalling protein kinase Chk2 by T-loop exchange.
  EMBO J, 25, 3179-3190.
PDB codes: 2cn5 2cn8
16467882 C.Z.Liu, Y.Chen, and S.F.Sui (2006).
The identification of a new actin-binding region in p57.
  Cell Res, 16, 106-112.  
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  J Biol Chem, 281, 16785-16793.
PDB code: 2acx
16699172 S.Bonn, S.Herrero, C.B.Breitenlechner, A.Erlbruch, W.Lehmann, R.A.Engh, M.Gassel, and D.Bossemeyer (2006).
Structural analysis of protein kinase A mutants with Rho-kinase inhibitor specificity.
  J Biol Chem, 281, 24818-24830.
PDB codes: 2gfc 2gnf 2gng 2gnh 2gni 2gnj 2gnl
16761096 T.J.Zhou, L.G.Sun, Y.Gao, and E.J.Goldsmith (2006).
Crystal structure of the MAP3K TAO2 kinase domain bound by an inhibitor staurosporine.
  Acta Biochim Biophys Sin (Shanghai), 38, 385-392.
PDB code: 2gcd
16723234 T.L.Nguyen, R.Gussio, J.A.Smith, D.A.Lannigan, S.M.Hecht, D.A.Scudiero, R.H.Shoemaker, and D.W.Zaharevitz (2006).
Homology model of RSK2 N-terminal kinase domain, structure-based identification of novel RSK2 inhibitors, and preliminary common pharmacophore.
  Bioorg Med Chem, 14, 6097-6105.  
16522793 Y.Cheng, Y.Zhang, and J.A.McCammon (2006).
How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study.
  Protein Sci, 15, 672-683.  
16207083 C.Hahnefeld, D.Moll, M.Goette, and F.W.Herberg (2005).
Rearrangements in a hydrophobic core region mediate cAMP action in the regulatory subunit of PKA.
  Biol Chem, 386, 623-631.  
16244704 E.D.Scheeff, and P.E.Bourne (2005).
Structural evolution of the protein kinase-like superfamily.
  PLoS Comput Biol, 1, e49.  
15531631 F.Gräter, J.Shen, H.Jiang, M.Gautel, and H.Grubmüller (2005).
Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations.
  Biophys J, 88, 790-804.  
15731862 J.López-Prados, F.Cuevas, N.C.Reichardt, J.L.de Paz, E.Q.Morales, and M.Martín-Lomas (2005).
Design and synthesis of inositolphosphoglycan putative insulin mediators.
  Org Biomol Chem, 3, 764-786.  
15759287 L.Pal, B.Dasgupta, and P.Chakrabarti (2005).
3(10)-Helix adjoining alpha-helix and beta-strand: sequence and structural features and their conservation.
  Biopolymers, 78, 147-162.  
15712318 M.Jenny, O.A.Wrulich, W.Schwaiger, and F.Ueberall (2005).
Relevance of atypical protein kinase C isotypes to the drug discovery process.
  Chembiochem, 6, 491-499.  
15326593 A.M.Aronov, and G.W.Bemis (2004).
A minimalist approach to fragment-based ligand design using common rings and linkers: application to kinase inhibitors.
  Proteins, 57, 36-50.  
14759363 J.Griffith, J.Black, C.Faerman, L.Swenson, M.Wynn, F.Lu, J.Lippke, and K.Saxena (2004).
The structural basis for autoinhibition of FLT3 by the juxtamembrane domain.
  Mol Cell, 13, 169-178.
PDB code: 1rjb
14960716 L.M.Iakoucheva, P.Radivojac, C.J.Brown, T.R.O'Connor, J.G.Sikes, Z.Obradovic, and A.K.Dunker (2004).
The importance of intrinsic disorder for protein phosphorylation.
  Nucleic Acids Res, 32, 1037-1049.  
14996846 M.Gassel, C.B.Breitenlechner, N.König, R.Huber, R.A.Engh, and D.Bossemeyer (2004).
The protein kinase C inhibitor bisindolyl maleimide 2 binds with reversed orientations to different conformations of protein kinase A.
  J Biol Chem, 279, 23679-23690.
PDB code: 1szm
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
14656443 C.Breitenlechner, M.Gassel, H.Hidaka, V.Kinzel, R.Huber, R.A.Engh, and D.Bossemeyer (2003).
Protein kinase A in complex with Rho-kinase inhibitors Y-27632, Fasudil, and H-1152P: structural basis of selectivity.
  Structure, 11, 1595-1607.
PDB codes: 1q8t 1q8u 1q8w
12551895 M.Ortiz-Lombardía, F.Pompeo, B.Boitel, and P.M.Alzari (2003).
Crystal structure of the catalytic domain of the PknB serine/threonine kinase from Mycobacterium tuberculosis.
  J Biol Chem, 278, 13094-13100.
PDB code: 1o6y
12502784 R.I.Brinkworth, R.A.Breinl, and B.Kobe (2003).
Structural basis and prediction of substrate specificity in protein serine/threonine kinases.
  Proc Natl Acad Sci U S A, 100, 74-79.  
14661952 S.Bhattacharya, E.Large, C.W.Heizmann, B.Hemmings, and W.J.Chazin (2003).
Structure of the Ca2+/S100B/NDR kinase peptide complex: insights into S100 target specificity and activation of the kinase.
  Biochemistry, 42, 14416-14426.
PDB code: 1psb
12517337 X.Huang, M.Begley, K.A.Morgenstern, Y.Gu, P.Rose, H.Zhao, and X.Zhu (2003).
Crystal structure of an inactive Akt2 kinase domain.
  Structure, 11, 21-30.
PDB codes: 1mrv 1mry
14500727 Z.Tu, and F.S.Lee (2003).
Subdomain VIII is a specificity-determining region in MEKK1.
  J Biol Chem, 278, 48498-48505.  
12044161 A.Cook, E.D.Lowe, E.D.Chrysina, V.T.Skamnaki, N.G.Oikonomakos, and L.N.Johnson (2002).
Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism.
  Biochemistry, 41, 7301-7311.
PDB code: 1gy3
12370306 A.M.Delaney, J.A.Printen, H.Chen, E.B.Fauman, and D.T.Dudley (2002).
Identification of a novel mitogen-activated protein kinase kinase activation domain recognized by the inhibitor PD 184352.
  Mol Cell Biol, 22, 7593-7602.  
11799117 C.S.Tung, D.A.Walsh, and J.Trewhella (2002).
A structural model of the catalytic subunit-regulatory subunit dimeric complex of the cAMP-dependent protein kinase.
  J Biol Chem, 277, 12423-12431.
PDB codes: 1kmu 1kmw
12237287 G.M.Cheetham, R.M.Knegtel, J.T.Coll, S.B.Renwick, L.Swenson, P.Weber, J.A.Lippke, and D.A.Austen (2002).
Crystal structure of aurora-2, an oncogenic serine/threonine kinase.
  J Biol Chem, 277, 42419-42422.
PDB code: 1muo
12434148 J.Yang, P.Cron, V.M.Good, V.Thompson, B.A.Hemmings, and D.Barford (2002).
Crystal structure of an activated Akt/protein kinase B ternary complex with GSK3-peptide and AMP-PNP.
  Nat Struct Biol, 9, 940-944.
PDB codes: 1o6k 1o6l
12015977 M.Huse, and J.Kuriyan (2002).
The conformational plasticity of protein kinases.
  Cell, 109, 275-282.  
11896404 Madhusudan, P.Akamine, N.H.Xuong, and S.S.Taylor (2002).
Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.
  Nat Struct Biol, 9, 273-277.
PDB code: 1l3r
12191603 R.A.Engh, and D.Bossemeyer (2002).
Structural aspects of protein kinase control-role of conformational flexibility.
  Pharmacol Ther, 93, 99.  
11954055 R.I.Brinkworth, J.Horne, and B.Kobe (2002).
A computational analysis of substrate binding strength by phosphorylase kinase and protein kinase A.
  J Mol Recognit, 15, 104-111.  
11141074 A.Tholey, R.Pipkorn, D.Bossemeyer, V.Kinzel, and J.Reed (2001).
Influence of myristoylation, phosphorylation, and deamidation on the structural behavior of the N-terminus of the catalytic subunit of cAMP-dependent protein kinase.
  Biochemistry, 40, 225-231.  
11389851 H.Yamaguchi, M.Matsushita, A.C.Nairn, and J.Kuriyan (2001).
Crystal structure of the atypical protein kinase domain of a TRP channel with phosphotransferase activity.
  Mol Cell, 7, 1047-1057.
PDB codes: 1ia9 1iah 1iaj
11455601 K.A.Denessiouk, V.V.Rantanen, and M.S.Johnson (2001).
Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins.
  Proteins, 44, 282-291.  
11296285 N.E.Robinson, and A.B.Robinson (2001).
Prediction of protein deamidation rates from primary and three-dimensional structure.
  Proc Natl Acad Sci U S A, 98, 4367-4372.  
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
  Proteins, 38, 310-326.  
10820007 M.Batkin, I.Schvartz, and S.Shaltiel (2000).
Snapping of the carboxyl terminal tail of the catalytic subunit of PKA onto its core: characterization of the sites by mutagenesis.
  Biochemistry, 39, 5366-5373.  
11031286 M.E.Wall, S.C.Gallagher, and J.Trewhella (2000).
Large-scale shape changes in proteins and macromolecular complexes.
  Annu Rev Phys Chem, 51, 355-380.  
10889042 R.T.Aimes, W.Hemmer, and S.S.Taylor (2000).
Serine-53 at the tip of the glycine-rich loop of cAMP-dependent protein kinase: role in catalysis, P-site specificity, and interaction with inhibitors.
  Biochemistry, 39, 8325-8332.  
10644696 S.Himpel, W.Tegge, R.Frank, S.Leder, H.G.Joost, and W.Becker (2000).
Specificity determinants of substrate recognition by the protein kinase DYRK1A.
  J Biol Chem, 275, 2431-2438.  
10966463 S.R.Hubbard, and J.H.Till (2000).
Protein tyrosine kinase structure and function.
  Annu Rev Biochem, 69, 373-398.  
10835366 T.Izard, and J.Ellis (2000).
The crystal structures of chloramphenicol phosphotransferase reveal a novel inactivation mechanism.
  EMBO J, 19, 2690-2700.
PDB codes: 1qhn 1qhs 1qhx 1qhy
11052681 T.J.Hirai, I.Tsigelny, and J.A.Adams (2000).
Catalytic assessment of the glycine-rich loop of the v-Fps oncoprotein using site-directed mutagenesis.
  Biochemistry, 39, 13276-13284.  
  10207111 A.Kurimasa, S.Kumano, N.V.Boubnov, M.D.Story, C.S.Tung, S.R.Peterson, and D.J.Chen (1999).
Requirement for the kinase activity of human DNA-dependent protein kinase catalytic subunit in DNA strand break rejoining.
  Mol Cell Biol, 19, 3877-3884.  
10197447 B.Guerra, and O.G.Issinger (1999).
Protein kinase CK2 and its role in cellular proliferation, development and pathology.
  Electrophoresis, 20, 391-408.  
10320366 F.W.Herberg, M.L.Doyle, S.Cox, and S.S.Taylor (1999).
Dissection of the nucleotide and metal-phosphate binding sites in cAMP-dependent protein kinase.
  Biochemistry, 38, 6352-6360.  
10479734 I.Tsigelny, J.P.Greenberg, S.Cox, W.L.Nichols, S.S.Taylor, and L.F.Ten Eyck (1999).
600 ps molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase.
  Biopolymers, 50, 513-524.  
10454194 J.M.Sowadski, L.F.Epstein, L.Lankiewicz, and R.Karlsson (1999).
Conformational diversity of catalytic cores of protein kinases.
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10024021 J.V.Lehtonen, K.Denessiouk, A.C.May, and M.S.Johnson (1999).
Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.
  Proteins, 34, 341-355.  
  10396139 M.Gautel, A.Mues, and P.Young (1999).
Control of sarcomeric assembly: the flow of information on titin.
  Rev Physiol Biochem Pharmacol, 138, 97.  
10029530 N.Narayana, T.C.Diller, K.Koide, M.E.Bunnage, K.C.Nicolaou, L.L.Brunton, N.H.Xuong, L.F.Ten Eyck, and S.S.Taylor (1999).
Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase.
  Biochemistry, 38, 2367-2376.
PDB code: 1bx6
10454191 N.Ono-Saito, I.Niki, and H.Hidaka (1999).
H-series protein kinase inhibitors and potential clinical applications.
  Pharmacol Ther, 82, 123-131.  
10085115 N.R.Brown, M.E.Noble, A.M.Lawrie, M.C.Morris, P.Tunnah, G.Divita, L.N.Johnson, and J.A.Endicott (1999).
Effects of phosphorylation of threonine 160 on cyclin-dependent kinase 2 structure and activity.
  J Biol Chem, 274, 8746-8756.
PDB codes: 1b38 1b39
10454199 P.A.Cole, D.Sondhi, and K.Kim (1999).
Chemical approaches to the study of protein tyrosine kinases and their implications for mechanism and inhibitor design.
  Pharmacol Ther, 82, 219-229.  
10029529 P.H.Hünenberger, V.Helms, N.Narayana, S.S.Taylor, and J.A.McCammon (1999).
Determinants of ligand binding to cAMP-dependent protein kinase.
  Biochemistry, 38, 2358-2366.  
10508788 S.Bellon, M.J.Fitzgibbon, T.Fox, H.M.Hsiao, and K.P.Wilson (1999).
The structure of phosphorylated p38gamma is monomeric and reveals a conserved activation-loop conformation.
  Structure, 7, 1057-1065.
PDB code: 1cm8
10454192 S.S.Taylor, E.Radzio-Andzelm, Madhusudan, X.Cheng, L.Ten Eyck, and N.Narayana (1999).
Catalytic subunit of cyclic AMP-dependent protein kinase: structure and dynamics of the active site cleft.
  Pharmacol Ther, 82, 133-141.  
10357805 S.Steinbacher, P.Hof, L.Eichinger, M.Schleicher, J.Gettemans, J.Vandekerckhove, R.Huber, and J.Benz (1999).
The crystal structure of the Physarum polycephalum actin-fragmin kinase: an atypical protein kinase with a specialized substrate-binding domain.
  EMBO J, 18, 2923-2929.
PDB code: 1cja
10545198 V.T.Skamnaki, D.J.Owen, M.E.Noble, E.D.Lowe, G.Lowe, N.G.Oikonomakos, and L.N.Johnson (1999).
Catalytic mechanism of phosphorylase kinase probed by mutational studies.
  Biochemistry, 38, 14718-14730.
PDB code: 1ql6
9562560 A.Matte, L.W.Tari, and L.T.Delbaere (1998).
How do kinases transfer phosphoryl groups?
  Structure, 6, 413-419.  
9601030 B.D.Grant, W.Hemmer, I.Tsigelny, J.A.Adams, and S.S.Taylor (1998).
Kinetic analyses of mutations in the glycine-rich loop of cAMP-dependent protein kinase.
  Biochemistry, 37, 7708-7715.  
9843450 C.V.Parast, B.Mroczkowski, C.Pinko, S.Misialek, G.Khambatta, and K.Appelt (1998).
Characterization and kinetic mechanism of catalytic domain of human vascular endothelial growth factor receptor-2 tyrosine kinase (VEGFR2 TK), a key enzyme in angiogenesis.
  Biochemistry, 37, 16788-16801.  
9422720 C.Zeng, A.E.Aleshin, G.Chen, R.B.Honzatko, and H.J.Fromm (1998).
The roles of glycine residues in the ATP binding site of human brain hexokinase.
  J Biol Chem, 273, 700-704.  
9662067 H.C.Chen, H.J.Kung, and D.Robinson (1998).
Digital cloning: identification of human cDNAs homologous to novel kinases through expressed sequence tag database searching.
  J Biomed Sci, 5, 86-92.  
9763421 J.D.Gary, A.E.Wurmser, C.J.Bonangelino, L.S.Weisman, and S.D.Emr (1998).
Fab1p is essential for PtdIns(3)P 5-kinase activity and the maintenance of vacuolar size and membrane homeostasis.
  J Cell Biol, 143, 65-79.  
9804812 J.Zhao, E.Hoye, S.Boylan, D.A.Walsh, and J.Trewhella (1998).
Quaternary structures of a catalytic subunit-regulatory subunit dimeric complex and the holoenzyme of the cAMP-dependent protein kinase by neutron contrast variation.
  J Biol Chem, 273, 30448-30459.  
  10082373 K.A.Denessiouk, J.V.Lehtonen, and M.S.Johnson (1998).
Enzyme-mononucleotide interactions: three different folds share common structural elements for ATP recognition.
  Protein Sci, 7, 1768-1771.  
  9605318 K.A.Denessiouk, J.V.Lehtonen, T.Korpela, and M.S.Johnson (1998).
Two "unrelated" families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites.
  Protein Sci, 7, 1136-1146.  
9564028 K.Niefind, B.Guerra, L.A.Pinna, O.G.Issinger, and D.Schomburg (1998).
Crystal structure of the catalytic subunit of protein kinase CK2 from Zea mays at 2.1 A resolution.
  EMBO J, 17, 2451-2462.
PDB code: 1a6o
10089519 N.Narayana, P.Akamine, N.H.Xuong, and S.S.Taylor (1998).
Crystallization and preliminary X-ray analysis of the unliganded recombinant catalytic subunit of cAMP-dependent protein kinase.
  Acta Crystallogr D Biol Crystallogr, 54, 1401-1404.  
  9521123 P.T.Jedrzejewski, A.Girod, A.Tholey, N.König, S.Thullner, V.Kinzel, and D.Bossemeyer (1998).
A conserved deamidation site at Asn 2 in the catalytic subunit of mammalian cAMP-dependent protein kinase detected by capillary LC-MS and tandem mass spectrometry.
  Protein Sci, 7, 457-469.  
9435218 S.Shaltiel, S.Cox, and S.S.Taylor (1998).
Conserved water molecules contribute to the extensive network of interactions at the active site of protein kinase A.
  Proc Natl Acad Sci U S A, 95, 484-491.  
9760235 X.Cheng, S.Shaltiel, and S.S.Taylor (1998).
Mapping substrate-induced conformational changes in cAMP-dependent protein kinase by protein footprinting.
  Biochemistry, 37, 14005-14013.  
9739089 X.Xie, Y.Gu, T.Fox, J.T.Coll, M.A.Fleming, W.Markland, P.R.Caron, K.P.Wilson, and M.S.Su (1998).
Crystal structure of JNK3: a kinase implicated in neuronal apoptosis.
  Structure, 6, 983-991.
PDB code: 1jnk
9362479 E.D.Lowe, M.E.Noble, V.T.Skamnaki, N.G.Oikonomakos, D.J.Owen, and L.N.Johnson (1997).
The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition.
  EMBO J, 16, 6646-6658.
PDB code: 2phk
9434895 F.Sicheri, and J.Kuriyan (1997).
Structures of Src-family tyrosine kinases.
  Curr Opin Struct Biol, 7, 777-785.  
9384563 G.Auerbach, R.Huber, M.Grättinger, K.Zaiss, H.Schurig, R.Jaenicke, and U.Jacob (1997).
Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
  Structure, 5, 1475-1483.
PDB code: 1vpe
8999821 J.Lew, N.Coruh, I.Tsigelny, S.Garrod, and S.S.Taylor (1997).
Synergistic binding of nucleotides and inhibitors to cAMP-dependent protein kinase examined by acrylodan fluorescence spectroscopy.
  J Biol Chem, 272, 1507-1513.  
9062128 J.Zhou, and J.A.Adams (1997).
Is there a catalytic base in the active site of cAMP-dependent protein kinase?
  Biochemistry, 36, 2977-2984.  
8995387 K.Nishikawa, A.Toker, F.J.Johannes, Z.Songyang, and L.C.Cantley (1997).
Determination of the specific substrate sequence motifs of protein kinase C isozymes.
  J Biol Chem, 272, 952-960.  
9342234 L.C.Etchebehere, M.X.Van Bemmelen, C.Anjard, F.Traincard, K.Assemat, C.Reymond, and M.Véron (1997).
The catalytic subunit of Dictyostelium cAMP-dependent protein kinase -- role of the N-terminal domain and of the C-terminal residues in catalytic activity and stability.
  Eur J Biochem, 248, 820-826.  
9045715 L.Stempka, A.Girod, H.J.Müller, G.Rincke, F.Marks, M.Gschwendt, and D.Bossemeyer (1997).
Phosphorylation of protein kinase Cdelta (PKCdelta) at threonine 505 is not a prerequisite for enzymatic activity. Expression of rat PKCdelta and an alanine 505 mutant in bacteria in a functional form.
  J Biol Chem, 272, 6805-6811.  
9095200 L.Tong, S.Pav, D.M.White, S.Rogers, K.M.Crane, C.L.Cywin, M.L.Brown, and C.A.Pargellis (1997).
A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket.
  Nat Struct Biol, 4, 311-316.
PDB code: 1ian
8989312 N.Kobayashi, and N.Go (1997).
ATP binding proteins with different folds share a common ATP-binding structural motif.
  Nat Struct Biol, 4, 6-7.  
9261084 N.Narayana, S.Cox, X.Nguyen-huu, L.F.Ten Eyck, and S.S.Taylor (1997).
A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility.
  Structure, 5, 921-935.
PDB code: 1bkx
9377173 P.Lessard, M.Kreis, and M.Thomas (1997).
[Protein phosphatases and protein kinases in higher plants].
  C R Acad Sci III, 320, 675-688.  
9312016 S.R.Hubbard (1997).
Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog.
  EMBO J, 16, 5572-5581.
PDB code: 1ir3
9667861 S.S.Taylor, and E.Radzio-Andzelm (1997).
Protein kinase inhibition: natural and synthetic variations on a theme.
  Curr Opin Chem Biol, 1, 219-226.  
9305961 S.Sarno, P.Vaglio, O.Marin, O.G.Issinger, K.Ruffato, and L.A.Pinna (1997).
Mutational analysis of residues implicated in the interaction between protein kinase CK2 and peptide substrates.
  Biochemistry, 36, 11717-11724.  
  9385635 V.Helms, and J.A.McCammon (1997).
Kinase conformations: a computational study of the effect of ligand binding.
  Protein Sci, 6, 2336-2343.  
9202006 W.Hemmer, M.McGlone, I.Tsigelny, and S.S.Taylor (1997).
Role of the glycine triad in the ATP-binding site of cAMP-dependent protein kinase.
  J Biol Chem, 272, 16946-16954.  
8664289 A.Krehan, P.Lorenz, M.Plana-Coll, and W.Pyerin (1996).
Interaction sites between catalytic and regulatory subunits in human protein kinase CK2 holoenzymes as indicated by chemical cross-linking and immunological investigations.
  Biochemistry, 35, 4966-4975.  
8555168 A.Y.Woody, S.S.Eaton, P.A.Osumi-Davis, and R.W.Woody (1996).
Asp537 and Asp812 in bacteriophage T7 RNA polymerase as metal ion-binding sites studied by EPR, flow-dialysis, and transcription.
  Biochemistry, 35, 144-152.  
  9003756 B.Kobe, J.Heierhorst, S.C.Feil, M.W.Parker, G.M.Benian, K.R.Weiss, and B.E.Kemp (1996).
Giant protein kinases: domain interactions and structural basis of autoregulation.
  EMBO J, 15, 6810-6821.
PDB codes: 1koa 1kob
8798432 C.Chan, and G.N.Gill (1996).
Mutational analysis of the nucleotide binding site of the epidermal growth factor receptor and v-Src protein-tyrosine kinases.
  J Biol Chem, 271, 22619-22623.  
8805593 C.D.Mol, J.M.Harris, E.M.McIntosh, and J.A.Tainer (1996).
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
  Structure, 4, 1077-1092.
PDB codes: 1q5h 1q5u
8900199 J.G.Aparicio, and M.L.Applebury (1996).
The photoreceptor guanylate cyclase is an autophosphorylating protein kinase.
  J Biol Chem, 271, 27083-27089.  
8601311 J.Goldberg, A.C.Nairn, and J.Kuriyan (1996).
Structural basis for the autoinhibition of calcium/calmodulin-dependent protein kinase I.
  Cell, 84, 875-887.
PDB code: 1a06
  8947030 J.L.Smith, L.A.Silveira, and J.A.Spudich (1996).
Activation of Dictyostelium myosin light chain kinase A by phosphorylation of Thr166.
  EMBO J, 15, 6075-6083.  
  8786241 J.M.Sowadski, C.A.Ellis, and Madhusudan (1996).
Detergent binding to unmyristylated protein kinase A--structural implications for the role of myristate.
  J Bioenerg Biomembr, 28, 7.  
8550555 J.S.Wood, X.Yan, M.Mendelow, J.D.Corbin, S.H.Francis, and D.S.Lawrence (1996).
Precision substrate targeting of protein kinases. The cGMP- and cAMP-dependent protein kinases.
  J Biol Chem, 271, 174-179.  
8662877 J.Y.Su, E.Erikson, and J.L.Maller (1996).
Cloning and characterization of a novel serine/threonine protein kinase expressed in early Xenopus embryos.
  J Biol Chem, 271, 14430-14437.  
8612268 L.N.Johnson, M.E.Noble, and D.J.Owen (1996).
Active and inactive protein kinases: structural basis for regulation.
  Cell, 85, 149-158.  
8994876 L.N.Johnson, and M.O'Reilly (1996).
Control by phosphorylation.
  Curr Opin Struct Biol, 6, 762-769.  
8885720 P.T.Mattsson, M.Vihinen, and C.I.Smith (1996).
X-linked agammaglobulinemia (XLA): a genetic tyrosine kinase (Btk) disease.
  Bioessays, 18, 825-834.  
8824261 R.A.Engh, A.Girod, V.Kinzel, R.Huber, and D.Bossemeyer (1996).
Crystal structures of catalytic subunit of cAMP-dependent protein kinase in complex with isoquinolinesulfonyl protein kinase inhibitors H7, H8, and H89. Structural implications for selectivity.
  J Biol Chem, 271, 26157-26164.
PDB codes: 1ydr 1yds 1ydt
8610110 W.F.De Azevedo, H.J.Mueller-Dieckmann, U.Schulze-Gahmen, P.J.Worland, E.Sausville, and S.H.Kim (1996).
Structural basis for specificity and potency of a flavonoid inhibitor of human CDK2, a cell cycle kinase.
  Proc Natl Acad Sci U S A, 93, 2735-2740.  
7759549 A.M.Fry, S.J.Schultz, J.Bartek, and E.A.Nigg (1995).
Substrate specificity and cell cycle regulation of the Nek2 protein kinase, a potential human homolog of the mitotic regulator NIMA of Aspergillus nidulans.
  J Biol Chem, 270, 12899-12905.  
7706257 C.Y.Huang, C.J.Yuan, D.K.Blumenthal, and D.J.Graves (1995).
Identification of the substrate and pseudosubstrate binding sites of phosphorylase kinase gamma-subunit.
  J Biol Chem, 270, 7183-7188.  
8846213 D.Barford, Z.Jia, and N.K.Tonks (1995).
Protein tyrosine phosphatases take off.
  Nat Struct Biol, 2, 1043-1053.  
8591024 E.Radzio-Andzelm, J.Lew, and S.Taylor (1995).
Bound to activate: conformational consequences of cyclin binding to CDK2.
  Structure, 3, 1135-1141.  
9383464 K.Koide, M.E.Bunnage, L.Gomez Paloma, J.R.Kanter, S.S.Taylor, L.L.Brunton, and K.C.Nicolaou (1995).
Molecular design and biological activity of potent and selective protein kinase inhibitors related to balanol.
  Chem Biol, 2, 601-608.  
  7529876 M.B.Calalb, T.R.Polte, and S.K.Hanks (1995).
Tyrosine phosphorylation of focal adhesion kinase at sites in the catalytic domain regulates kinase activity: a role for Src family kinases.
  Mol Cell Biol, 15, 954-963.  
7673185 P.A.Cole, M.R.Grace, R.S.Phillips, P.Burn, and C.T.Walsh (1995).
The role of the catalytic base in the protein tyrosine kinase Csk.
  J Biol Chem, 270, 22105-22108.  
8789188 P.Furet, G.Caravatti, N.Lydon, J.P.Priestle, J.M.Sowadski, U.Trinks, and P.Traxler (1995).
Modelling study of protein kinase inhibitors: binding mode of staurosporine and origin of the selectivity of CGP 52411.
  J Comput Aided Mol Des, 9, 465-472.  
7601142 R.Jakobi, and J.A.Traugh (1995).
Site-directed mutagenesis and structure/function studies of casein kinase II correlate stimulation of activity by the beta subunit with changes in conformation and ATP/GTP utilization.
  Eur J Biochem, 230, 1111-1117.  
  7889932 R.M.Xu, G.Carmel, R.M.Sweet, J.Kuret, and X.Cheng (1995).
Crystal structure of casein kinase-1, a phosphate-directed protein kinase.
  EMBO J, 14, 1015-1023.
PDB code: 1csn
7479711 U.Schulze-Gahmen, J.Brandsen, H.D.Jones, D.O.Morgan, L.Meijer, J.Vesely, and S.H.Kim (1995).
Multiple modes of ligand recognition: crystal structures of cyclin-dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine.
  Proteins, 22, 378-391.
PDB codes: 1w0x 2exm
8048162 D.Bossemeyer (1994).
The glycine-rich sequence of protein kinases: a multifunctional element.
  Trends Biochem Sci, 19, 201-205.  
7517688 D.O.Morgan, and H.L.De Bondt (1994).
Protein kinase regulation: insights from crystal structure analysis.
  Curr Opin Cell Biol, 6, 239-246.  
7712287 E.J.Goldsmith, and M.H.Cobb (1994).
Protein kinases.
  Curr Opin Struct Biol, 4, 833-840.  
  7935404 H.K.Shu, C.M.Chang, L.Ravi, L.Ling, C.M.Castellano, E.Walter, R.J.Pelley, and H.J.Kung (1994).
Modulation of erbB kinase activity and oncogenic potential by single point mutations in the glycine loop of the catalytic domain.
  Mol Cell Biol, 14, 6868-6878.  
  8313877 J.Cavarelli, G.Eriani, B.Rees, M.Ruff, M.Boeglin, A.Mitschler, F.Martin, J.Gangloff, J.C.Thierry, and D.Moras (1994).
The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction.
  EMBO J, 13, 327-337.
PDB code: 1asz
8168546 J.P.Huggins, A.J.Ganzhorn, V.Saudek, J.T.Pelton, and R.A.Atkinson (1994).
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.
  Eur J Biochem, 221, 581-593.  
  7849589 L.N.Johnson, and D.Barford (1994).
Electrostatic effects in the control of glycogen phosphorylase by phosphorylation.
  Protein Sci, 3, 1726-1730.  
7809124 M.Vihinen, D.Vetrie, H.S.Maniar, H.D.Ochs, Q.Zhu, I.Vorechovský, A.D.Webster, L.D.Notarangelo, L.Nilsson, and J.M.Sowadski (1994).
Structural basis for chromosome X-linked agammaglobulinemia: a tyrosine kinase disease.
  Proc Natl Acad Sci U S A, 91, 12803-12807.  
  8003955 Madhusudan, E.A.Trafny, N.H.Xuong, J.A.Adams, L.F.Ten Eyck, S.S.Taylor, and J.M.Sowadski (1994).
cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer.
  Protein Sci, 3, 176-187.
PDB codes: 1jbp 1jlu
7712293 S.Cox, E.Radzio-Andzelm, and S.S.Taylor (1994).
Domain movements in protein kinases.
  Curr Opin Struct Biol, 4, 893-901.  
8081750 S.S.Taylor, and E.Radzio-Andzelm (1994).
Three protein kinase structures define a common motif.
  Structure, 2, 345-355.  
7874496 Z.Songyang, S.Blechner, N.Hoagland, M.F.Hoekstra, H.Piwnica-Worms, and L.C.Cantley (1994).
Use of an oriented peptide library to determine the optimal substrates of protein kinases.
  Curr Biol, 4, 973-982.  
  8251932 J.Zheng, D.R.Knighton, N.H.Xuong, S.S.Taylor, J.M.Sowadski, and L.F.Ten Eyck (1993).
Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations.
  Protein Sci, 2, 1559-1573.
PDB code: 1cmk
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