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PDBsum entry 1jbp

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1jbp
Jmol
Contents
Protein chains
342 a.a. *
20 a.a. *
Ligands
ADP
OCT
Waters ×168
* Residue conservation analysis
PDB id:
1jbp
Name: Transferase
Title: Crystal structure of the catalytic subunit of camp- dependent protein kinase complexed with a substrate peptide, adp and detergent
Structure: Camp-dependent protein kinase, alpha-catalytic subunit. Chain: e. Synonym: pka c-alpha. Engineered: yes. Camp-dependent protein kinase inhibitor, muscle/brain form. Chain: s. Fragment: residues 5-24.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in mus musculus (mouse).
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.175    
Authors: Madhusudan,E.A.Trafny,N.H.Xuong,J.A.Adams,L.F.Ten Eyck, S.S.Taylor,J.M.Sowadski
Key ref:
Madhusudan et al. (1994). cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer. Protein Sci, 3, 176-187. PubMed id: 8003955 DOI: 10.1002/pro.5560030203
Date:
06-Jun-01     Release date:   27-Jun-01    
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.
342 a.a.*
Protein chain
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 4 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
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     sperm midpiece   14 terms 
  Biological process     regulation of proteasomal protein catabolic process   18 terms 
  Biochemical function     nucleotide binding     13 terms  

 

 
    reference    
 
 
DOI no: 10.1002/pro.5560030203 Protein Sci 3:176-187 (1994)
PubMed id: 8003955  
 
 
cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer.
Madhusudan, E.A.Trafny, N.H.Xuong, J.A.Adams, L.F.Ten Eyck, S.S.Taylor, J.M.Sowadski.
 
  ABSTRACT  
 
The crystal structure of ternary and binary substrate complexes of the catalytic subunit of cAMP-dependent protein kinase has been refined at 2.2 and 2.25 A resolution, respectively. The ternary complex contains ADP and a 20-residue substrate peptide, whereas the binary complex contains the phosphorylated substrate peptide. These 2 structures were refined to crystallographic R-factors of 17.5 and 18.1%, respectively. In the ternary complex, the hydroxyl oxygen OG of the serine at the P-site is 2.7 A from the OD1 atom of Asp 166. This is the first crystallographic evidence showing the direct interaction of this invariant carboxylate with a peptide substrate, and supports the predicted role of Asp 166 as a catalytic base and as an agent to position the serine -OH for nucleophilic attack. A comparison of the substrate and inhibitor ternary complexes places the hydroxyl oxygen of the serine 2.7 A from the gamma-phosphate of ATP and supports a direct in-line mechanism for phosphotransfer. In the binary complex, the phosphate on the Ser interacts directly with the epsilon N of Lys 168, another conserved residue. In the ternary complex containing ATP and the inhibitor peptide, Lys 168 interacts electrostatically with the gamma-phosphate of ATP (Zheng J, Knighton DR, Ten Eyck LF, Karlsson R, Xuong NH, Taylor SS, Sowadski JM, 1993, Biochemistry 32:2154-2161). Thus, Lys 168 remains closely associated with the phosphate in both complexes. A comparison of this binary complex structure with the recently solved structure of the ternary complex containing ATP and inhibitor peptide also reveals that the phosphate atom traverses a distance of about 1.5 A following nucleophilic attack by serine and transfer to the peptide. No major conformational changes of active site residues are seen when the substrate and product complexes are compared, although the binary complex with the phosphopeptide reveals localized changes in conformation in the region corresponding to the glycine-rich loop. The high B-factors for this loop support the conclusion that this structural motif is a highly mobile segment of the protein.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. Diagramofesentialresiduesthatcontribtetonucleotidebindingndcatalysis. A: Inhibitorternarycomplex. Dis- tancesaretakenfromtheternarycomplexof C:IPZO:ATP (Zhengetal.,1993~).Thecrystalsweresoaked in MnZ*, andboth theinhibitorandtheactivatingmetalsareshown (++) (Zhengetal., 1993~).The activating metal bridges the p- andy-phosphates, whereastheinhibitorymetalbridgesthe Y- andy-phospates.Thearrowbridgesthemethylsidechain f theP-siteAlaand they-phosphate of ATP. B: Substrateternarycomplex. C: Phosphorylatedsubstratebinarycomplex.
Figure 8.
ig. 8. Stereoviewshowingthesuperimposition f inaryandternarycomplexesandhigh- lighting localized chagesin the glycine-rich loop. Overallcomparison of the a-carbon back- bone of the pper omain(residues 15-127) of the ternary complexwith MnATP (red),thebi- nary withproductpeptide (blue), and the mammalianC-subunitbinarycomplexwih di-iodinated Tyr 7 PKI(5-24) (green). In hese 3 structures,thelargelobesaresuperimposedand are omitted from thedrawing, as theysho no major conformational changes.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1994, 3, 176-187) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23064647 S.Hughes, F.Elustondo, A.Di Fonzo, F.G.Leroux, A.C.Wong, A.P.Snijders, S.J.Matthews, and P.Cherepanov (2012).
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PDB codes: 4f99 4f9a 4f9b 4f9c
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  J Biol Chem, 285, 16330-16340.
PDB codes: 3feg 3g15 3lq3
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PDB code: 3lmg
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19886670 I.V.Khavrutskii, B.Grant, S.S.Taylor, and J.A.McCammon (2009).
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  Proc Natl Acad Sci U S A, 104, 19802-19807.
PDB code: 3b2t
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PDB codes: 2chw 2chx 2chz
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11329267 D.Wang, X.Y.Huang, and P.A.Cole (2001).
Molecular determinants for Csk-catalyzed tyrosine phosphorylation of the Src tail.
  Biochemistry, 40, 2004-2010.  
  11152133 M.C.Hutter, and V.Helms (2000).
Phosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase.
  Protein Sci, 9, 2225-2231.  
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Insights into nucleotide binding in protein kinase A using fluorescent adenosine derivatives.
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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.  
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.  
9889150 D.M.Daigle, G.A.McKay, P.R.Thompson, and G.D.Wright (1999).
Aminoglycoside antibiotic phosphotransferases are also serine protein kinases.
  Chem Biol, 6, 11-18.  
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.  
10220345 J.Shaffer, and J.A.Adams (1999).
An ATP-linked structural change in protein kinase A precedes phosphoryl transfer under physiological magnesium concentrations.
  Biochemistry, 38, 5572-5581.  
  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.  
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
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
9425036 D.Sondhi, W.Xu, Z.Songyang, M.J.Eck, and P.A.Cole (1998).
Peptide and protein phosphorylation by protein tyrosine kinase Csk: insights into specificity and mechanism.
  Biochemistry, 37, 165-172.  
9817025 F.A.al-Obeidi, J.J.Wu, and K.S.Lam (1998).
Protein tyrosine kinases: structure, substrate specificity, and drug discovery.
  Biopolymers, 47, 197-223.  
9843424 J.Lisnock, A.Tebben, B.Frantz, E.A.O'Neill, G.Croft, S.J.O'Keefe, B.Li, C.Hacker, S.de Laszlo, A.Smith, B.Libby, N.Liverton, J.Hermes, and P.LoGrasso (1998).
Molecular basis for p38 protein kinase inhibitor specificity.
  Biochemistry, 37, 16573-16581.  
9539704 J.Szczepanowska, U.Ramachandran, C.J.Herring, J.M.Gruschus, J.Qin, E.D.Korn, and H.Brzeska (1998).
Effect of mutating the regulatory phosphoserine and conserved threonine on the activity of the expressed catalytic domain of Acanthamoeba myosin I heavy chain kinase.
  Proc Natl Acad Sci U S A, 95, 4146-4151.  
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.  
  9528799 P.R.Romano, M.T.Garcia-Barrio, X.Zhang, Q.Wang, D.R.Taylor, F.Zhang, C.Herring, M.B.Mathews, J.Qin, and A.G.Hinnebusch (1998).
Autophosphorylation in the activation loop is required for full kinase activity in vivo of human and yeast eukaryotic initiation factor 2alpha kinases PKR and GCN2.
  Mol Cell Biol, 18, 2282-2297.  
9730835 P.Saylor, C.Wang, T.J.Hirai, and J.A.Adams (1998).
A second magnesium ion is critical for ATP binding in the kinase domain of the oncoprotein v-Fps.
  Biochemistry, 37, 12624-12630.  
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.  
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
9184152 J.Lew, S.S.Taylor, and J.A.Adams (1997).
Identification of a partially rate-determining step in the catalytic mechanism of cAMP-dependent protein kinase: a transient kinetic study using stopped-flow fluorescence spectroscopy.
  Biochemistry, 36, 6717-6724.  
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.  
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
  8819164 B.D.Grant, I.Tsigelny, J.A.Adams, and S.S.Taylor (1996).
Examination of an active-site electrostatic node in the cAMP-dependent protein kinase catalytic subunit.
  Protein Sci, 5, 1316-1324.  
8639687 B.D.Grant, and J.A.Adams (1996).
Pre-steady-state kinetic analysis of cAMP-dependent protein kinase using rapid quench flow techniques.
  Biochemistry, 35, 2022-2029.  
8718888 J.A.Adams (1996).
Insight into tyrosine phosphorylation in v-Fps using proton inventory techniques.
  Biochemistry, 35, 10949-10956.  
  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.  
  8657148 M.P.Wymann, G.Bulgarelli-Leva, M.J.Zvelebil, L.Pirola, B.Vanhaesebroeck, M.D.Waterfield, and G.Panayotou (1996).
Wortmannin inactivates phosphoinositide 3-kinase by covalent modification of Lys-802, a residue involved in the phosphate transfer reaction.
  Mol Cell Biol, 16, 1722-1733.  
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.  
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.