2ZOQ

Structural dissection of human mitogen-activated kinase ERK1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of human mono-phosphorylated ERK1 at Tyr204

Kinoshita, T., Yoshida, I., Nakae, S., Okita, K., Gouda, M., Matsubara, M., Yokota, K., Ishiguro, H., Tada, T.

(2008) Biochem Biophys Res Commun 377: 1123-1127

  • DOI: 10.1016/j.bbrc.2008.10.127
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Extracellular signal-regulated kinase (ERK) is a member of the MAP kinase family, and can regulate several cellular responses. The isoforms ERK1 and ERK2 have markedly similar amino acid sequences, but exhibit distinctive physiological functions. As ...

    Extracellular signal-regulated kinase (ERK) is a member of the MAP kinase family, and can regulate several cellular responses. The isoforms ERK1 and ERK2 have markedly similar amino acid sequences, but exhibit distinctive physiological functions. As well as ERK2, ERK1 was auto- and mono-phosphorylated at Tyr204 in the activation loop during Escherichia coli production, resulting in basal level activity, approximately 500-fold less compared with fully-active ERK1 dual-phosphorylated at Thr202 and Tyr204. Crystal structure demonstrated that the mono-phosphorylated ERK1 kinase possessed a novel conformation distinguishable from the un-phosphorylated (inactive) and the dual-phosphorylated (full-active) forms. The characteristic structural features in both the C-helix and the activation loop likely contribute to the basal activity of the mono-phosphorylated ERK1. The structural dissection of ERK1 compared to ERK2 suggests that the structural differences in the D-motif binding site and in the backside binding site are putative targets for development of selective ERK1/ERK2 inhibitors.

    Organizational Affiliation: 

    Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. kinotk@b.s.osakafu-u.ac.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 3A, B382Homo sapiensMutation(s): 0 
Gene Names: MAPK3, ERK1, PRKM3
EC: 2.7.11.24
Find proteins for P27361 (Homo sapiens)
Explore P27361 
Go to UniProtKB:  P27361
NIH Common Fund Data Resources
PHAROS  P27361
GTEx  ENSG00000102882
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5ID
Query on 5ID
Download CCD File 
A, B
(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL
C11 H13 I N4 O4
WHSIXKUPQCKWBY-IOSLPCCCSA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
NA
Query on NA
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		A,BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5IDIC50 :  900   nM  PDBBind
5IDKi:  530   nM  BindingDB
5IDIC50:  1200   nM  BindingDB
5IDIC50:  900   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.382α = 90
b = 91.54β = 91.5
c = 64.93γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance