4WOH | pdb_00004woh

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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.165 (Depositor), 0.174 (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 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.

---

Organizational Affiliation: 
• Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, 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 
• Modeled 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), 0.174 (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