2FYS | pdb_00002fys

Crystal structure of Erk2 complex with KIM peptide derived from MKP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.175 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural basis of docking interactions between ERK2 and MAP kinase phosphatase 3

Liu, S.Sun, J.P.Zhou, B.Zhang, Z.Y.

(2006) Proc Natl Acad Sci U S A 103: 5326-5331

  • DOI: https://doi.org/10.1073/pnas.0510506103
  • Primary Citation Related Structures: 
    2FYS

  • PubMed Abstract: 

    Mitogen-activated protein (MAP) kinases are central components of signal transduction pathways for cell proliferation, stress responses, and differentiation. Signaling efficiency and specificity are modulated in large part by docking interactions between individual MAP kinase and the kinase interaction motif (KIM), (R/K)(2-3)-X(1-6)-Phi(A)-X-Phi(B), in its cognate kinases, phosphatases, scaffolding proteins, and substrates. We have determined the crystal structure of extracellular signal-regulated protein kinase 2 bound to the KIM peptide from MAP kinase phosphatase 3, an extracellular signal-regulated protein kinase 2-specific phosphatase. The structure reveals that the KIM docking site, situated in a noncatalytic region opposite of the kinase catalytic pocket, is comprised of a highly acidic patch and a hydrophobic groove, which engage the basic and Phi(A)-X-Phi(B) residues, respectively, in the KIM sequence. The specific docking interactions observed in the structure consolidate all known biochemical data. In addition, structural comparison indicates that the KIM docking site is conserved in all MAP kinases. The results establish a structural model for understanding how MAP kinases interact with their regulators and substrates and provide new insights into how MAP kinase docking specificity can be achieved.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.

Macromolecule Content 

  • Total Structure Weight: 88.2 kDa 
  • Atom Count: 6,253 
  • Modeled Residue Count: 708 
  • Deposited Residue Count: 762 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1A [auth B],
B [auth A]
364Rattus norvegicusMutation(s): 0 
Gene Names: Mapk1Erk2MapkPrkm1
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt
Find proteins for P63086 (Rattus norvegicus)
Explore P63086 
Go to UniProtKB:  P63086
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63086
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual specificity protein phosphatase 6C [auth D],
D [auth C]
17N/AMutation(s): 0 
EC: 3.1.3.48 (PDB Primary Data), 3.1.3.16 (PDB Primary Data)
UniProt
Find proteins for Q64346 (Rattus norvegicus)
Explore Q64346 
Go to UniProtKB:  Q64346
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64346
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.377α = 90
b = 67.478β = 99.55
c = 86.605γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description