PDBsum entry 1atp

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transferase(phosphotransferase) PDB id
Protein chains
336 a.a. *
20 a.a. *
_MN ×2
Waters ×103
* Residue conservation analysis
PDB id:
Name: Transferase(phosphotransferase)
Title: 2.2 angstrom refined crystal structure of the catalytic subunit of camp-dependent protein kinase complexed with mnatp and a peptide inhibitor
Structure: Camp-dependent protein kinase. Chain: e. Engineered: yes. Peptide inhibitor pki(5-24). Chain: i. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090
Biol. unit: Dimer (from PQS)
2.20Å     R-factor:   0.177    
Authors: J.Zheng,E.A.Trafny,D.R.Knighton,N.-H.Xuong,S.S.Taylor, L.F.Teneyck,J.M.Sowadski
Key ref:
J.Zheng et al. (1993). 2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor. Acta Crystallogr D Biol Crystallogr, 49, 362-365. PubMed id: 15299527 DOI: 10.1107/S0907444993000423
08-Jan-93     Release date:   15-Apr-93    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P05132  (KAPCA_MOUSE) -  cAMP-dependent protein kinase catalytic subunit alpha
351 a.a.
336 a.a.*
Protein chain
Pfam   ArchSchema ?
P63248  (IPKA_MOUSE) -  cAMP-dependent protein kinase inhibitor alpha
76 a.a.
20 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain E: E.C.  - cAMP-dependent protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
Bound ligand (Het Group name = ATP)
corresponds exactly
+ protein
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     sperm midpiece   16 terms 
  Biological process     regulation of proteasomal protein catabolic process   19 terms 
  Biochemical function     nucleotide binding     14 terms  


DOI no: 10.1107/S0907444993000423 Acta Crystallogr D Biol Crystallogr 49:362-365 (1993)
PubMed id: 15299527  
2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor.
J.Zheng, E.A.Trafny, D.R.Knighton, N.H.Xuong, S.S.Taylor, L.F.Ten Eyck, J.M.Sowadski.
. 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.
  Selected figure(s)  
Figure 2.
Fig. 2. Environment of conserved amino acis surrounding the site of phosphotransfer. For this diagram a serine (shown in red) was modeled into the P site so that distances between the "y-phosphate and a protein substrate could be estimated. The primary metal site, OM382, is coordinated by the invariant Asp184, as well as two water molecules as indicated above. The secondary inhibitory metal site, OM383, is coordiated by the invariant Asnl7, by invariant Asp184, as well as by one water molecule. Asp14, therefore, is shared by both metal sites in this inhibited complex.
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 362-365) copyright 1993.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22820988 R.M.Bandaranayake, D.Ungureanu, Y.Shan, D.E.Shaw, O.Silvennoinen, and S.R.Hubbard (2012).
Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F.
  Nat Struct Mol Biol, 19, 754-759.
PDB codes: 4fvp 4fvq 4fvr
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
19966800 D.Nesić, M.C.Miller, Z.T.Quinkert, M.Stein, B.T.Chait, and C.E.Stebbins (2010).
Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates.
  Nat Struct Mol Biol, 17, 130-132.
PDB code: 3iec
20547848 J.E.Stajich, S.K.Wilke, D.Ahrén, C.H.Au, B.W.Birren, M.Borodovsky, C.Burns, B.Canbäck, L.A.Casselton, C.K.Cheng, J.Deng, F.S.Dietrich, D.C.Fargo, M.L.Farman, A.C.Gathman, J.Goldberg, R.Guigó, P.J.Hoegger, J.B.Hooker, A.Huggins, T.Y.James, T.Kamada, S.Kilaru, C.Kodira, U.Kües, D.Kupfer, H.S.Kwan, A.Lomsadze, W.Li, W.W.Lilly, L.J.Ma, A.J.Mackey, G.Manning, F.Martin, H.Muraguchi, D.O.Natvig, H.Palmerini, M.A.Ramesh, C.J.Rehmeyer, B.A.Roe, N.Shenoy, M.Stanke, V.Ter-Hovhannisyan, A.Tunlid, R.Velagapudi, T.J.Vision, Q.Zeng, M.E.Zolan, and P.J.Pukkila (2010).
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).
  Proc Natl Acad Sci U S A, 107, 11889-11894.  
20192289 J.Jung, Y.Sugita, and S.Ten-no (2010).
Møller-Plesset perturbation theory gradient in the generalized hybrid orbital quantum mechanical and molecular mechanical method.
  J Chem Phys, 132, 084106.  
20022944 J.Monsey, W.Shen, P.Schlesinger, and R.Bose (2010).
Her4 and Her2/neu tyrosine kinase domains dimerize and activate in a reconstituted in vitro system.
  J Biol Chem, 285, 7035-7044.  
  20180991 J.Zhang, C.A.King, K.Dalby, and P.Ren (2010).
Conformational preference of ChaK1 binding peptides: a molecular dynamics study.
  PMC Biophys, 3, 2.  
20072606 M.Röttig, C.Rausch, and O.Kohlbacher (2010).
Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families.
  PLoS Comput Biol, 6, e1000636.  
20209159 Y.H.Hsu, and J.A.Traugh (2010).
Reciprocally coupled residues crucial for protein kinase Pak2 activity calculated by statistical coupling analysis.
  PLoS One, 5, e9455.  
19610074 E.E.Thompson, A.P.Kornev, N.Kannan, C.Kim, L.F.Ten Eyck, and S.S.Taylor (2009).
Comparative surface geometry of the protein kinase family.
  Protein Sci, 18, 2016-2026.
PDB code: 3fjq
19425109 J.D.Knight, D.Hamelberg, J.A.McCammon, and R.Kothary (2009).
The role of conserved water molecules in the catalytic domain of protein kinases.
  Proteins, 76, 527-535.  
19180449 K.S.Keating, S.C.Flores, M.B.Gerstein, and L.A.Kuhn (2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
  Protein Sci, 18, 359-371.  
19060928 M.Scaltriti, C.Verma, M.Guzman, J.Jimenez, J.L.Parra, K.Pedersen, D.J.Smith, S.Landolfi, S.Ramon y Cajal, J.Arribas, and J.Baselga (2009).
Lapatinib, a HER2 tyrosine kinase inhibitor, induces stabilization and accumulation of HER2 and potentiates trastuzumab-dependent cell cytotoxicity.
  Oncogene, 28, 803-814.  
19225111 S.Yang, N.K.Banavali, and B.Roux (2009).
Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories.
  Proc Natl Acad Sci U S A, 106, 3776-3781.  
18381623 A.Scholten, T.T.Aye, and A.J.Heck (2008).
A multi-angular mass spectrometric view at cyclic nucleotide dependent protein kinases: in vivo characterization and structure/function relationships.
  Mass Spectrom Rev, 27, 331-353.  
18339619 P.Singh, B.Wang, T.Maeda, K.Palczewski, and J.J.Tesmer (2008).
Structures of rhodopsin kinase in different ligand states reveal key elements involved in G protein-coupled receptor kinase activation.
  J Biol Chem, 283, 14053-14062.
PDB codes: 3c4w 3c4x 3c4y 3c4z 3c50 3c51
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
18056630 E.D.Lew, J.H.Bae, E.Rohmann, B.Wollnik, and J.Schlessinger (2007).
Structural basis for reduced FGFR2 activity in LADD syndrome: Implications for FGFR autoinhibition and activation.
  Proc Natl Acad Sci U S A, 104, 19802-19807.
PDB code: 3b2t
17409557 H.Sugiyama, M.Yoshida, K.Mori, T.Kawamoto, S.Sogabe, T.Takagi, H.Oki, T.Tanaka, H.Kimura, and Y.Ikeura (2007).
Synthesis and structure activity relationship studies of benzothieno[3,2-b]furan derivatives as a novel class of IKKbeta inhibitors.
  Chem Pharm Bull (Tokyo), 55, 613-624.  
17585314 J.A.Ubersax, and J.E.Ferrell (2007).
Mechanisms of specificity in protein phosphorylation.
  Nat Rev Mol Cell Biol, 8, 530-541.  
17912359 J.D.Knight, B.Qian, D.Baker, and R.Kothary (2007).
Conservation, variability and the modeling of active protein kinases.
  PLoS ONE, 2, e982.  
17932298 J.Wu, S.H.Brown, S.von Daake, and S.S.Taylor (2007).
PKA type IIalpha holoenzyme reveals a combinatorial strategy for isoform diversity.
  Science, 318, 274-279.
PDB code: 2qvs
17913888 M.H.Cho, X.Cao, D.Wang, and J.Z.Tsien (2007).
Dentate gyrus-specific manipulation of beta-Ca2+/calmodulin-dependent kinase II disrupts memory consolidation.
  Proc Natl Acad Sci U S A, 104, 16317-16322.  
17380483 N.K.Banavali, and B.Roux (2007).
Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck.
  Proteins, 67, 1096-1112.  
17335005 S.Ranganathan, Y.Wang, F.G.Kern, Z.Qu, and R.Li (2007).
Activation loop phosphorylation-independent kinase activity of human protein kinase C zeta.
  Proteins, 67, 709-719.  
17522047 S.Y.Ku, P.Yip, K.A.Cornell, M.K.Riscoe, J.B.Behr, G.Guillerm, and P.L.Howell (2007).
Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding.
  J Biol Chem, 282, 22195-22206.
PDB codes: 2pu8 2pui 2pul 2pun 2pup
17914234 V.S.Gowri, K.Anamika, S.Gore, and N.Srinivasan (2007).
Analysis on sliding helices and strands in protein structural comparisons: a case study with protein kinases.
  J Biosci, 32, 921-928.  
16758442 A.D.Hegeman, M.Rodriguez, B.W.Han, Y.Uno, G.N.Phillips, E.M.Hrabak, J.C.Cushman, J.F.Harper, A.C.Harmon, and M.R.Sussman (2006).
A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases.
  Proteomics, 6, 3649-3664.  
16365849 M.U.Ung, B.Lu, and J.A.McCammon (2006).
E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor.
  Biopolymers, 81, 428-439.  
17055412 N.Foloppe, N.Matassova, and F.Aboul-Ela (2006).
Towards the discovery of drug-like RNA ligands?
  Drug Discov Today, 11, 1019-1027.  
15543157 J.F.Ohren, H.Chen, A.Pavlovsky, C.Whitehead, E.Zhang, P.Kuffa, C.Yan, P.McConnell, C.Spessard, C.Banotai, W.T.Mueller, A.Delaney, C.Omer, J.Sebolt-Leopold, D.T.Dudley, I.K.Leung, C.Flamme, J.Warmus, M.Kaufman, S.Barrett, H.Tecle, and C.A.Hasemann (2004).
Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition.
  Nat Struct Mol Biol, 11, 1192-1197.
PDB codes: 1s9i 1s9j
12493833 M.S.Yousef, S.A.Clark, P.K.Pruett, T.Somasundaram, W.R.Ellington, and M.S.Chapman (2003).
Induced fit in guanidino kinases--comparison of substrate-free and transition state analog structures of arginine kinase.
  Protein Sci, 12, 103-111.
PDB code: 1m80
12191613 A.V.Velentza, A.M.Schumacher, and D.M.Watterson (2002).
Structure, activity, regulation, and inhibitor discovery for a protein kinase associated with apoptosis and neuronal death.
  Pharmacol Ther, 93, 217-224.  
12465028 M.C.Hutter, J.Krebs, J.Meiler, C.Griesinger, E.Carafoli, and V.Helms (2002).
A structural model of the complex formed by phospholamban and the calcium pump of sarcoplasmic reticulum obtained by molecular mechanics.
  Chembiochem, 3, 1200-1208.  
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
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.  
11468361 G.Pujadas, and J.Palau (2001).
Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
  Protein Sci, 10, 1645-1657.  
11573098 V.Tereshko, M.Teplova, J.Brunzelle, D.M.Watterson, and M.Egli (2001).
Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression.
  Nat Struct Biol, 8, 899-907.
PDB codes: 1ig1 1jkk 1jkl 1jks 1jkt
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.  
10454194 J.M.Sowadski, L.F.Epstein, L.Lankiewicz, and R.Karlsson (1999).
Conformational diversity of catalytic cores of protein kinases.
  Pharmacol Ther, 82, 157-164.  
  10631989 M.C.Hutter, and V.Helms (1999).
Influence of key residues on the reaction mechanism of the cAMP-dependent protein kinase.
  Protein Sci, 8, 2728-2733.  
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
10450084 S.Hayward (1999).
Structural principles governing domain motions in proteins.
  Proteins, 36, 425-435.  
10360180 T.Schindler, F.Sicheri, A.Pico, A.Gazit, A.Levitzki, and J.Kuriyan (1999).
Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor.
  Mol Cell, 3, 639-648.
PDB code: 1qcf
9857185 M.E.Cunningham, and L.A.Greene (1998).
A function-structure model for NGF-activated TRK.
  EMBO J, 17, 7282-7293.  
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.  
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
9434895 F.Sicheri, and J.Kuriyan (1997).
Structures of Src-family tyrosine kinases.
  Curr Opin Struct Biol, 7, 777-785.  
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
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
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
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
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.  
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.  
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.  
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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.