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PDBsum entry 1cmk

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protein ligands metals Protein-protein interface(s) links
Transferase/transferase inhibitor PDB id
1cmk
Jmol
Contents
Protein chains
350 a.a. *
20 a.a. *
Ligands
MYR
Metals
IOD ×2
* Residue conservation analysis
PDB id:
1cmk
Name: Transferase/transferase inhibitor
Title: Crystal structures of the myristylated catalytic subunit of dependent protein kinase reveal open and closed conformatio
Structure: Camp-dependent protein kinase catalytic subunit. Chain: e. Engineered: yes. Camp-dependent protein kinase inhibitor, alpha fo chain: i. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: heart. Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Dodecamer (from PQS)
Resolution:
2.90Å     R-factor:   0.233    
Authors: J.Zheng,D.R.Knighton,N.-H.Xuong,S.S.Taylor,J.M.Sowadski,L.F.
Key ref:
J.Zheng et al. (1993). Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Protein Sci, 2, 1559-1573. PubMed id: 8251932 DOI: 10.1002/pro.5560021003
Date:
18-Nov-93     Release date:   31-May-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P36887  (KAPCA_PIG) -  cAMP-dependent protein kinase catalytic subunit alpha
Seq:
Struc:
351 a.a.
350 a.a.*
Protein chain
Pfam   ArchSchema ?
P61925  (IPKA_HUMAN) -  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     membrane   5 terms 
  Biological process     phosphorylation   3 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
DOI no: 10.1002/pro.5560021003 Protein Sci 2:1559-1573 (1993)
PubMed id: 8251932  
 
 
Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations.
J.Zheng, D.R.Knighton, N.H.Xuong, S.S.Taylor, J.M.Sowadski, L.F.Ten Eyck.
 
  ABSTRACT  
 
Three crystal structures, representing two distinct conformational states, of the mammalian catalytic subunit of cAMP-dependent protein kinase were solved using molecular replacement methods starting from the refined structure of the recombinant catalytic subunit ternary complex (Zheng, J., et al., 1993a, Biochemistry 32, 2154-2161). These structures correspond to the free apoenzyme, a binary complex with an iodinated inhibitor peptide, and a ternary complex with both ATP and the unmodified inhibitor peptide. The apoenzyme and the binary complex crystallized in an open conformation, whereas the ternary complex crystallized in a closed conformation similar to the ternary complex of the recombinant enzyme. The model of the binary complex, refined at 2.9 A resolution, shows the conformational changes associated with the open conformation. These can be described by a rotation of the small lobe and a displacement of the C-terminal 30 residues. This rotation of the small lobe alters the cleft interface in the active-site region surrounding the glycine-rich loop and Thr 197, a critical phosphorylation site. In addition to the conformational changes, the myristylation site, absent in the recombinant enzyme, was clearly defined in the binary complex. The myristic acid binds in a deep hydrophobic pocket formed by four segments of the protein that are widely dispersed in the linear sequence. The N-terminal 40 residues that lie outside the conserved catalytic core are anchored by the N-terminal myristylate plus an amphipathic helix that spans both lobes and is capped by Trp 30. Both posttranslational modifications, phosphorylation and myristylation, contribute directly to the stable structure of this enzyme.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Active-siteregionin the open conformational state. A: Theactive regionof the binary complex from the mamma- lian enzyme(red)issuperimposedinstereowith the correspondingregionfrom the ternary complexof therecombinantenzyme (blue). The ATP in the ternary complex is shon in black. B: Some f the distances that hangemostgoing to open confor- mation of the mammalian binary complex are indicated. Distancesin A betweenseveralkey residuesin the two structures are as follows (numbers in parentheses correspond to the closed conformation): Asp 184 to Gly 52 or, 10.5 (6.5); sp 184 to Lys 72 NZ, 6. (3.7); 54 CZ to His 87 ND1, 7.4 His 87 NE2 to P-Thr 197 OE2,6.0 (2.7); lu 91 OEl to Lys 72 HZ, 4.1
Figure 6.
Fig. 6. The Ca-backbone of heclosedand open conformations, highlightingcriticalchangesathe cleft interface.The binary complex of therecombinantC-subunit,representingthe closed conformation, isshown on heright.The open conformation associatedwiththemamalianbinarycomplexisshown on the left. TheN-terminalregions(1-127inthemammalianC-subunit and 9-127 in therecombinantenzymeareshowninred.TheC-terminalregions(resiues128-350)areshowninblue.Thepep- tidesare shown inblack. The fattyacidinthemammaliancomplexandtheMEGA-8detergentintherecombinantcomlex areshowningreen. Key residues at he cleft interface(His87, Asn 90, Thr 197),whoseenironmentchangesasaconsequence of cleft opening,are also indicated in reen.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (1993, 2, 1559-1573) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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Conformational diversity of catalytic cores of protein kinases.
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Fatty acylation of proteins: new insights into membrane targeting of myristoylated and palmitoylated proteins.
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Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase.
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PDB code: 1bx6
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Determinants of ligand binding to cAMP-dependent protein kinase.
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Protein tyrosine kinases: structure, substrate specificity, and drug discovery.
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SRPK2: a differentially expressed SR protein-specific kinase involved in mediating the interaction and localization of pre-mRNA splicing factors in mammalian cells.
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2H NMR studies of a myristoylated peptide in neutral and acidic phospholipid bicelles.
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Effect of mutating the regulatory phosphoserine and conserved threonine on the activity of the expressed catalytic domain of Acanthamoeba myosin I heavy chain kinase.
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PDB code: 1a6o
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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.  
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.  
9174341 M.Kovalenko, L.Rönnstrand, C.H.Heldin, M.Loubtchenkov, A.Gazit, A.Levitzki, and F.D.Böhmer (1997).
Phosphorylation site-specific inhibition of platelet-derived growth factor beta-receptor autophosphorylation by the receptor blocking tyrphostin AG1296.
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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
9667861 S.S.Taylor, and E.Radzio-Andzelm (1997).
Protein kinase inhibition: natural and synthetic variations on a theme.
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9043657 T.F.Gallagher, G.L.Seibel, S.Kassis, J.T.Laydon, M.J.Blumenthal, J.C.Lee, D.Lee, J.C.Boehm, S.M.Fier-Thompson, J.W.Abt, M.E.Soreson, J.M.Smietana, R.F.Hall, R.S.Garigipati, P.E.Bender, K.F.Erhard, A.J.Krog, G.A.Hofmann, P.L.Sheldrake, P.C.McDonnell, S.Kumar, P.R.Young, and J.L.Adams (1997).
Regulation of stress-induced cytokine production by pyridinylimidazoles; inhibition of CSBP kinase.
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  9385635 V.Helms, and J.A.McCammon (1997).
Kinase conformations: a computational study of the effect of ligand binding.
  Protein Sci, 6, 2336-2343.  
8610175 C.P.Hill, D.Worthylake, D.P.Bancroft, A.M.Christensen, and W.I.Sundquist (1996).
Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: implications for membrane association and assembly.
  Proc Natl Acad Sci U S A, 93, 3099-3104.
PDB code: 1hiw
  8670794 F.Hanakam, R.Albrecht, C.Eckerskorn, M.Matzner, and G.Gerisch (1996).
Myristoylated and non-myristoylated forms of the pH sensor protein hisactophilin II: intracellular shuttling to plasma membrane and nucleus monitored in real time by a fusion with green fluorescent protein.
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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.  
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Detergent binding to unmyristylated protein kinase A--structural implications for the role of myristate.
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8958442 M.D.Resh (1996).
Regulation of cellular signalling by fatty acid acylation and prenylation of signal transduction proteins.
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8692801 R.Murali, P.J.Brennan, T.Kieber-Emmons, and M.I.Greene (1996).
Structural analysis of p185c-neu and epidermal growth factor receptor tyrosine kinases: oligomerization of kinase domains.
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8952507 S.J.Mansour, J.M.Candia, J.E.Matsuura, M.C.Manning, and N.G.Ahn (1996).
Interdependent domains controlling the enzymatic activity of mitogen-activated protein kinase kinase 1.
  Biochemistry, 35, 15529-15536.  
  7767386 C.A.Buser, J.Kim, S.McLaughlin, and R.M.Peitzsch (1995).
Does the binding of clusters of basic residues to acidic lipids induce domain formation in membranes?
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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.
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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.
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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.  
  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.  
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.  
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