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PDBsum entry 2y9q

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2y9q
Jmol
Contents
Protein chains
350 a.a.
17 a.a.
Ligands
ANP
Waters ×546
PDB id:
2y9q
Name: Transferase
Title: Crystal structure of human erk2 complexed with a mapk dockin
Structure: Mitogen-activated protein kinase 1. Chain: a. Synonym: map kinase 1, mapk 1, ert1, extracellular signal-r kinase 2, erk-2, map kinase isoform p42, p42-mapk, mitogen-activated protein kinase 2, map kinase 2, mapk 2, engineered: yes. Map kinase-interacting serine/threonine-protein k chain: b. Fragment: c-terminal docking peptide, residues 434-451.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss. Synthetic: yes. Organism_taxid: 9606
Resolution:
1.55Å     R-factor:   0.155     R-free:   0.176
Authors: T.Barkai,A.Garai,I.Toeroe,A.Remenyi
Key ref: ..Garai et al. (2012). Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove. Sci Signal, 5, ra74. PubMed id: 23047924
Date:
16-Feb-11     Release date:   29-Feb-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28482  (MK01_HUMAN) -  Mitogen-activated protein kinase 1
Seq:
Struc:
360 a.a.
350 a.a.
Protein chain
Pfam   ArchSchema ?
Q9BUB5  (MKNK1_HUMAN) -  MAP kinase-interacting serine/threonine-protein kinase 1
Seq:
Struc:
465 a.a.
17 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: Chain A: E.C.2.7.11.24  - Mitogen-activated protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ phosphoprotein
   Enzyme class 2: Chain B: E.C.2.7.11.1  - Non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ phosphoprotein
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   21 terms 
  Biological process     viral reproduction   73 terms 
  Biochemical function     nucleotide binding     15 terms  

 

 
    reference    
 
 
Sci Signal 5:ra74 (2012)
PubMed id: 23047924  
 
 
Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove.
..Garai, A.Zeke, G.Gógl, I.Törő, F.Fördős, H.Blankenburg, T.Bárkai, J.Varga, A.Alexa, D.Emig, M.Albrecht, A.Reményi.
 
  ABSTRACT  
 
Mitogen-activated protein kinases (MAPKs) have a docking groove that interacts with linear "docking" motifs in binding partners. To determine the structural basis of binding specificity between MAPKs and docking motifs, we quantitatively analyzed the ability of 15 docking motifs from diverse MAPK partners to bind to c-Jun amino-terminal kinase 1 (JNK1), p38α, and extracellular signal-regulated kinase 2 (ERK2). Classical docking motifs mediated highly specific binding only to JNK1, and only those motifs with a sequence pattern distinct from the classical MAPK binding docking motif consensus differentiated between the topographically similar docking grooves of ERK and p38α. Crystal structures of four complexes of MAPKs with docking peptides, representing JNK-specific, ERK-specific, or ERK- and p38-selective binding modes, revealed that the regions located between consensus positions in the docking motifs showed conformational diversity. Although the consensus positions in the docking motifs served as anchor points that bound to common MAPK surface features and mostly contributed to docking in a nondiscriminatory fashion, the conformation of the intervening region between the anchor points mostly determined specificity. We designed peptides with tailored MAPK binding profiles by rationally changing the length and amino acid composition of intervening regions located between anchor points. These results suggest a coherent structural model for MAPK docking specificity that reveals how short linear motifs binding to a common kinase docking groove can mediate diverse interaction patterns and contribute to correct MAPK partner selection in signaling networks.