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PDBsum entry 1ctp
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Transferase/transferase inhibitor PDB id
1ctp

 

 

 

 

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Contents
Protein chains
333 a.a. *
18 a.a. *
Ligands
MYR
Waters ×2
* Residue conservation analysis
PDB id:
1ctp
Name: Transferase/transferase inhibitor
Title: Structure of the mammalian catalytic subunit of camp-dependent protein kinase and an inhibitor peptide displays an open conformation
Structure: Camp-dependent protein kinase. Chain: e. Engineered: yes. Camp-dependent protein kinase inhibitor, alpha form. Chain: i. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Tetramer (from PQS)
Resolution:
2.90Å     R-factor:   0.190    
Authors: R.Karlsson,J.Zheng,N.H.Xuong,S.S.Taylor,J.M.Sowadski
Key ref:
R.Karlsson et al. (1993). Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation. Acta Crystallogr D Biol Crystallogr, 49, 381-388. PubMed id: 15299513 DOI: 10.1107/S0907444993002306
Date:
08-Apr-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P36887  (KAPCA_PIG) -  cAMP-dependent protein kinase catalytic subunit alpha from Sus scrofa
Seq:
Struc: 		351 a.a.
333 a.a.*
Protein chain
Pfam   ArchSchema ?
P61926  (IPKA_RABIT) -  cAMP-dependent protein kinase inhibitor alpha from Oryctolagus cuniculus
Seq:
Struc: 		76 a.a.
18 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:
1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H+
2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H+
L-seryl-[protein]
 + ATP
 = O-phospho-L-seryl-[protein]
 + ADP
 + H(+)
L-threonyl-[protein]
 + ATP
 = O-phospho-L-threonyl-[protein]
 + ADP
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1107/S0907444993002306 Acta Crystallogr D Biol Crystallogr 49:381-388 (1993)
PubMed id: 15299513  
 
 
Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation.
R.Karlsson, J.Zheng, N.Xuong, S.S.Taylor, J.M.Sowadski.
 
  ABSTRACT  
 
The crystal structure of a binary complex of the porcine heart catalytic (C) subunit of cAMP-dependent protein kinase (space group P4(1)32; a = 171.5 A) complexed with a di-iodinated peptide inhibitor, PKI(5-24), has been solved and refined to 2.9 A resolution with an overall R of 21.1%. The r.m.s. deviations from ideal bond lengths and angles are 0.022 A and 4.3 degrees. A single isotropic B of 17 A(2) was used for all atoms. The structure solution was carried out initially by molecular replacement of electron density followed by refinement against atomic coordinates from orthorhombic crystals of a binary complex of the mouse recombinant enzyme previously described [Knighton, Zheng, Ten Eyck, Ashford, Xuong, Taylor & Sowadski (1991). Science, 253, 407-414]. The most striking difference between the two crystal structures is a large displacement of the small lobe of the enzyme. In the cubic crystal, the beta-sheet of the small lobe is rotated by 15 degrees and translated by 1.9 A with respect to the orthorhombic crystal. Possible explanations for why this binary complex crystallized in an open conformation in contrast to a similar binary complex of the recombinant enzyme are discussed. This study demonstrates that considerable information about parts of a crystal structure can be obtained without a complete crystal structure analysis. Specifically, the six rigid-group parameters of a poly alanine model of the beta-structure were obtained satisfactorily from a crystal structure by refinement of difference Fourier coefficients based on an approximate partial structure model.
 
  Selected figure(s)  
 
Figure 2.
ig. 2. Stereoview of the environ- ment of His87. The small lobe is indicated in red and the large lobe in blue. The inhibitor is indicated in black. (a) In the recombinant mouse C subunit, His87 of the small lobe interacts with the stble phosphoryation site of Thr197 of the large lobe and the carbonyl group of the main chain of Glu86 interacts with the side chain of Asng0. (b) In the pocine heart C subunit, His87 moves away from the phosphate of Thr197 and the side chain of Asng0 of the small lobe interacts with the carbonyl of Ala188 of the large lobe. istances are given in A.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 381-388) copyright 1993.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20626563 J.P.Covy, and B.I.Giasson (2010).
The G2019S pathogenic mutation disrupts sensitivity of leucine-rich repeat kinase 2 to manganese kinase inhibition.
  J Neurochem, 115, 36-46.  
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.  
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.  
18068628 S.Fröhling, C.Scholl, R.L.Levine, M.Loriaux, T.J.Boggon, O.A.Bernard, R.Berger, H.Döhner, K.Döhner, B.L.Ebert, S.Teckie, T.R.Golub, J.Jiang, M.M.Schittenhelm, B.H.Lee, J.D.Griffin, R.M.Stone, M.C.Heinrich, M.W.Deininger, B.J.Druker, and D.G.Gilliland (2007).
Identification of driver and passenger mutations of FLT3 by high-throughput DNA sequence analysis and functional assessment of candidate alleles.
  Cancer Cell, 12, 501-513.  
16640460 N.M.Levinson, O.Kuchment, K.Shen, M.A.Young, M.Koldobskiy, M.Karplus, P.A.Cole, and J.Kuriyan (2006).
A Src-like inactive conformation in the abl tyrosine kinase domain.
  PLoS Biol, 4, e144.
PDB codes: 2g1t 2g2f 2g2h 2g2i
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
15364937 Z.B.Xu, D.Chaudhary, S.Olland, S.Wolfrom, R.Czerwinski, K.Malakian, L.Lin, M.L.Stahl, D.Joseph-McCarthy, C.Benander, L.Fitz, R.Greco, W.S.Somers, and L.Mosyak (2004).
Catalytic domain crystal structure of protein kinase C-theta (PKCtheta).
  J Biol Chem, 279, 50401-50409.
PDB code: 1xjd
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
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
  12019230 P.J.Muhlrad, and S.Ward (2002).
Spermiogenesis initiation in Caenorhabditis elegans involves a casein kinase 1 encoded by the spe-6 gene.
  Genetics, 161, 143-155.  
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.  
10535933 M.Gangal, T.Clifford, J.Deich, X.Cheng, S.S.Taylor, and D.A.Johnson (1999).
Mobilization of the A-kinase N-myristate through an isoform-specific intermolecular switch.
  Proc Natl Acad Sci U S A, 96, 12394-12399.  
10450084 S.Hayward (1999).
Structural principles governing domain motions in proteins.
  Proteins, 36, 425-435.  
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.  
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
  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
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.  
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.  
  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
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.

 

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