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Transferase(phosphotransferase) PDB id
1apm
Jmol
Contents
Protein chains
341 a.a. *
20 a.a. *
Ligands
OCT
Waters ×207
* Residue conservation analysis
PDB id:
1apm
Name: Transferase(phosphotransferase)
Title: 2.0 angstrom refined crystal structure of the catalytic subunit of camp-dependent protein kinase complexed with a peptide inhibitor and detergent
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)
Resolution:
2.00Å     R-factor:   0.186    
Authors: D.R.Knighton,S.M.Bell,J.Zheng,L.F.Teneyck,N.-H.Xuong, S.S.Taylor,J.M.Sowadski
Key ref:
D.R.Knighton et al. (1993). 2.0 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with a peptide inhibitor and detergent. Acta Crystallogr D Biol Crystallogr, 49, 357-361. PubMed id: 15299526 DOI: 10.1107/S0907444993000502
Date:
18-Jan-93     Release date:   15-Apr-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05132  (KAPCA_MOUSE) -  cAMP-dependent protein kinase catalytic subunit alpha
Seq:
Struc: 		351 a.a.
341 a.a.*
Protein chain
Pfam   ArchSchema ?
P63248  (IPKA_MOUSE) -  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: Chain E: E.C.2.7.11.11  - cAMP-dependent protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
 + protein
 = ADP
 + phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     neuromuscular junction   16 terms 
  Biological process     positive regulation of cell cycle arrest   14 terms 
  Biochemical function     nucleotide binding     12 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444993000502 Acta Crystallogr D Biol Crystallogr 49:357-361 (1993)
PubMed id: 15299526  
 
 
2.0 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with a peptide inhibitor and detergent.
D.R.Knighton, S.M.Bell, J.Zheng, L.F.Ten Eyck, N.H.Xuong, S.S.Taylor, J.M.Sowadski.
 
  ABSTRACT  
 
. A mutant (Serl39Ala) of the mouse recombinant catalytic (C) subunit of cAMP-dependent protein kinase was co-crystallized with a peptide inhibitor, PKI(5-24), and MEGA-8 (octanoyl-N-methylglucamide) detergent. This structure was refined using all observed data (30 248 reflections) between 30 and 1.95 A resolution to an R factor of 0.186. R.m.s. deviations of bond lengths and bond angles are 0.013 A and 2.3 degrees, respectively. The final model has 3075 atoms (207 solvent) with a mean B factor of 31.9 A(2). The placement of invariant protein-kinase residues and most C:PKI(5-24) interactions were confirmed, but register errors affecting residues 55-64 and 309-339 were corrected during refinement by shifting the affected sequences toward the C terminus along the previously determined backbone path. New details of C:PKI(5-24) interactions and the Ser338 autophosphorylation site are described, and the acyl group binding site near the catalytic subunit NH(2) terminus is identified.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. C:PKI(5-24) C a backbone trace. The PKI(5-24) peptide inhibitor is shown in red. The MEGA-8 detergent, modeled as n-octane, is shown in blue in the lower left. In green is the superimposed C a trace of the superseded 2.7 ,/k 1CPK model for residues 54-67 and 307-341.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 357-361) copyright 1993.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19204278 C.Hyeon, P.A.Jennings, J.A.Adams, and J.N.Onuchic (2009).
Ligand-induced global transitions in the catalytic domain of protein kinase A.
  Proc Natl Acad Sci U S A, 106, 3023-3028.  
18361454 M.A.Dolan, M.Keil, and D.S.Baker (2008).
Comparison of composer and ORCHESTRAR.
  Proteins, 72, 1243-1258.  
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
17585314 J.A.Ubersax, and J.E.Ferrell (2007).
Mechanisms of specificity in protein phosphorylation.
  Nat Rev Mol Cell Biol, 8, 530-541.  
16674218 P.H.Nguyen, E.Mittag, A.E.Torda, and G.Stock (2006).
Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces.
  J Chem Phys, 124, 154107.  
16253959 J.Wu, J.Yang, N.Kannan, Madhusudan, N.H.Xuong, L.F.Ten Eyck, and S.S.Taylor (2005).
Crystal structure of the E230Q mutant of cAMP-dependent protein kinase reveals an unexpected apoenzyme conformation and an extended N-terminal A helix.
  Protein Sci, 14, 2871-2879.
PDB code: 1syk
15185335 P.A.Sims, C.F.Wong, and J.A.McCammon (2004).
Charge optimization of the interface between protein kinases and their ligands.
  J Comput Chem, 25, 1416-1429.  
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.  
  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.  
  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.  
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.  
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.  
9302280 K.Schiebel, M.Winkelmann, A.Mertz, X.Xu, D.C.Page, D.Weil, C.Petit, and G.A.Rappold (1997).
Abnormal XY interchange between a novel isolated protein kinase gene, PRKY, and its homologue, PRKX, accounts for one third of all (Y+)XX males and (Y-)XY females.
  Hum Mol Genet, 6, 1985-1989.  
  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
  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.  
  7795524 D.B.Glass, J.Trewhella, R.D.Mitchell, and D.A.Walsh (1995).
Conformationally constrained analogs of protein kinase inhibitor (6-22)amide: effect of turn structures in the center of the peptide on inhibition of cAMP-dependent protein kinase.
  Protein Sci, 4, 405-415.  
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.  
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.  
  8336738 M.J.Marcote, D.R.Knighton, G.Basi, J.M.Sowadski, P.Brambilla, G.Draetta, and S.S.Taylor (1993).
A three-dimensional model of the Cdc2 protein kinase: localization of cyclin- and Suc1-binding regions and phosphorylation sites.
  Mol Cell Biol, 13, 5122-5131.  
7504272 M.Veron, E.Radzio-Andzelm, I.Tsigelny, L.F.Ten Eyck, and S.S.Taylor (1993).
A conserved helix motif complements the protein kinase core.
  Proc Natl Acad Sci U S A, 90, 10618-10622.  
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 code is shown on the right.