4WOH

Structure of of human dual-specificity phosphatase 22 (E24A/K28A/K30A/C88S) complexed with 4-nitrophenolphosphate

• PDB DOI: https://doi.org/10.2210/pdb4WOH/pdb

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


• Deposited: 2014-10-15 Released: 2015-02-18 
• Deposition Author(s): Lountos, G.T., Cherry, S., Tropea, J.E., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate.

Lountos, G.T., Cherry, S., Tropea, J.E., Waugh, D.S.

(2015) Acta Crystallogr F Struct Biol Commun 71: 199-205

• PubMed: 25664796 
• DOI: https://doi.org/10.1107/S2053230X15000217
• Primary Citation of Related Structures:  
  4WOH


• PubMed Abstract: 
  

  4-Nitrophenyl phosphate (p-nitrophenyl phosphate, pNPP) is widely used as a small molecule phosphotyrosine-like substrate in activity assays for protein tyrosine phosphatases. It is a colorless substrate that upon hydrolysis is converted to a yellow 4-nitrophenolate ion that can be monitored by absorbance at 405 nm. Therefore, the pNPP assay has been widely adopted as a quick and simple method to assess phosphatase activity and is also commonly used in assays to screen for inhibitors. Here, the first crystal structure is presented of a dual-specificity phosphatase, human dual-specificity phosphatase 22 (DUSP22), in complex with pNPP. The structure illuminates the molecular basis for substrate binding and may also facilitate the structure-assisted development of DUSP22 inhibitors.

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Organizational Affiliation: 

Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.94 kDa 
• Atom Count: 1,543 
• Modelled Residue Count: 158 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase 22	A	166	Homo sapiens	Mutation(s): 4  Gene Names: DUSP22, JSP1, LMWDSP2, MKPX EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRW4 (Homo sapiens) Explore Q9NRW4  Go to UniProtKB:  Q9NRW4
PHAROS:  Q9NRW4 GTEx:  ENSG00000112679

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4NP	B [auth A]	4-NITROPHENYL PHOSPHATE C6 H6 N O6 P XZKIHKMTEMTJQX-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.816	α = 90
b = 49.632	β = 94.88
c = 39.899	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Lountos, G.T., Cherry, S., Tropea, J.E., Waugh, D.S.

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy