3SME | pdb_00003sme

Structure of PTP1B inactivated by H2O2/bicarbonate

• PDB DOI: https://doi.org/10.2210/pdb3SME/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-27 Released: 2011-10-19 
• Deposition Author(s): Tanner, J.J., Singh, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.210 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

The Biological Buffer Bicarbonate/CO(2) Potentiates H(2)O(2)-Mediated Inactivation of Protein Tyrosine Phosphatases.

Zhou, H., Singh, H., Parsons, Z.D., Lewis, S.M., Bhattacharya, S., Seiner, D.R., Labutti, J.N., Reilly, T.J., Tanner, J.J., Gates, K.S.

(2011) J Am Chem Soc 133: 15803-15805

• PubMed: 21913686 
• DOI: https://doi.org/10.1021/ja2077137
• Primary Citation Related Structures: 
  3SME


• PubMed Abstract: 
  

  Hydrogen peroxide is a cell signaling agent that inactivates protein tyrosine phosphatases (PTPs) via oxidation of their catalytic cysteine residue. PTPs are inactivated rapidly during H(2)O(2)-mediated cellular signal transduction processes, but, paradoxically, hydrogen peroxide is a rather sluggish PTP inactivator in vitro. Here we present evidence that the biological buffer bicarbonate/CO(2) potentiates the ability of H(2)O(2) to inactivate PTPs. The results of biochemical experiments and high-resolution crystallographic analysis are consistent with a mechanism involving oxidation of the catalytic cysteine residue by peroxymonocarbonate generated via the reaction of H(2)O(2) with HCO(3)(-)/CO(2).

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Organizational Affiliation: 
• Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.94 kDa 
• Atom Count: 2,436 
• Modeled Residue Count: 282 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 1	A	300	Homo sapiens	Mutation(s): 0  Gene Names: PTP1B, PTPN1 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031  Go to UniProtKB:  P18031
PHAROS:  P18031 GTEx:  ENSG00000196396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.210 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88	α = 90
b = 88	β = 90
c = 104	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): Tanner, J.J., Singh, H.

Revision History  

• Version 1.0: 2011-10-19
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary