4KI9

Crystal structure of the catalytic domain of human DUSP12 at 2.0 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The family-wide structure and function of human dual-specificity protein phosphatases

Jeong, D.G.Wei, C.H.Ku, B.Jeon, T.J.Chien, P.N.Kim, J.K.Park, S.Y.Hwang, H.S.Ryu, S.Y.Park, H.Kim, D.S.Kim, S.J.Ryu, S.E.

(2014) Acta Crystallogr D Biol Crystallogr 70: 421-435

  • DOI: https://doi.org/10.1107/S1399004713029866
  • Primary Citation of Related Structures:  
    4JMJ, 4JMK, 4JNB, 4KI9

  • PubMed Abstract: 

    Dual-specificity protein phosphatases (DUSPs), which dephosphorylate both phosphoserine/threonine and phosphotyrosine, play vital roles in immune activation, brain function and cell-growth signalling. A family-wide structural library of human DUSPs was constructed based on experimental structure determination supplemented with homology modelling. The catalytic domain of each individual DUSP has characteristic features in the active site and in surface-charge distribution, indicating substrate-interaction specificity. The active-site loop-to-strand switch occurs in a subtype-specific manner, indicating that the switch process is necessary for characteristic substrate interactions in the corresponding DUSPs. A comprehensive analysis of the activity-inhibition profile and active-site geometry of DUSPs revealed a novel role of the active-pocket structure in the substrate specificity of DUSPs. A structure-based analysis of redox responses indicated that the additional cysteine residues are important for the protection of enzyme activity. The family-wide structures of DUSPs form a basis for the understanding of phosphorylation-mediated signal transduction and the development of therapeutics.


  • Organizational Affiliation

    Medical Proteomics Research Center, KRIBB, Daejeon, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein phosphatase 12163Homo sapiensMutation(s): 2 
Gene Names: DUSP12
EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNI6 (Homo sapiens)
Explore Q9UNI6 
Go to UniProtKB:  Q9UNI6
PHAROS:  Q9UNI6
GTEx:  ENSG00000081721 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNI6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.55α = 90
b = 50.55β = 90
c = 128.63γ = 90
Software Package:
Software NamePurpose
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Database references, Experimental preparation
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations