4JMK | pdb_00004jmk

Structure of dusp8

• PDB DOI: https://doi.org/10.2210/pdb4JMK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-03-14 Released: 2014-02-26 
• Deposition Author(s): Jeong, D.G., Kim, S.J., Ryu, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

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

• PubMed: 24531476 
• DOI: https://doi.org/10.1107/S1399004713029866
• Primary Citation 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.

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Organizational Affiliation: 
• Medical Proteomics Research Center, KRIBB, Daejeon, Republic of Korea.
Department of Bioengineering, College of Engineering, Hanyang University, Seoul, Republic of Korea.
Department of Industrial Engineering, College of Engineering, Hanyang University, Seoul, Republic of Korea.
Department of Bioscience and Biotechnology, Sejong University, Seoul, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.7 kDa 
• Atom Count: 2,522 
• Modeled Residue Count: 296 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase 8	A, B	152	Homo sapiens	Mutation(s): 1  Gene Names: DUSP8, C11orf81, VH5 EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13202 (Homo sapiens) Explore Q13202  Go to UniProtKB:  Q13202
PHAROS:  Q13202 GTEx:  ENSG00000184545

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.85	α = 90
b = 65.85	β = 90
c = 124.5	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Jeong, D.G., Kim, S.J., Ryu, S.E.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description