Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38469.81 
• Atom Count: 2314 
• Residue Count: 330 
• Unique protein chains: 1

1A5Y

PROTEIN TYROSINE PHOSPHATASE 1B CYSTEINYL-PHOSPHATE INTERMEDIATE

• DOI: 10.2210/pdb1A5Y/pdb

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


• Deposited: 1998-02-19 Released: 1998-06-17 
• Deposition Author(s): Pannifer, A.D.P., Flint, A.J., Tonks, N.K., Barford, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.281 
• R-Value Work: 0.205 

Literature

Visualization of the cysteinyl-phosphate intermediate of a protein-tyrosine phosphatase by x-ray crystallography.

Pannifer, A.D., Flint, A.J., Tonks, N.K., Barford, D.

(1998) J.Biol.Chem. 273: 10454-10462

• PubMed: 9553104 
• DOI: 10.1074/jbc.273.17.10454


• PubMed Abstract: 
  

Protein-tyrosine phosphatases (PTPs) are signal transduction enzymes that catalyze the dephosphorylation of phosphotyrosine residues via the formation of a transient cysteinyl-phosphate intermediate. The mechanism of hydrolysis of this intermediate has been examined by generating a Gln-262 --> Ala mutant of PTP1B, which allows the accumulation and trapping of the intermediate within a PTP1B crystal. The structure of the intermediate at 2.5-A resolution reveals that a conformationally flexible loop (the WPD loop) is closed over the entrance to the catalytic site, sequestering the phosphocysteine intermediate and catalytic site water molecules and preventing nonspecific phosphoryltransfer reactions to extraneous phosphoryl acceptors. One of the catalytic site water molecules, the likely nucleophile, forms a hydrogen bond to the putative catalytic base, Asp-181. In the wild-type enzyme, the nucleophilic water molecule would be coordinated by the side chain of Gln-262. In combination with our previous structural data, we can now visualize each of the reaction steps of the PTP catalytic pathway. The hydrolysis of the cysteinyl-phosphate intermediate of PTPs is reminiscent of GTP hydrolysis by the GTPases, in that both families of enzymes utilize an invariant Gln residue to coordinate the attacking nucleophilic water molecule.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN TYROSINE PHOSPHATASE 1B	A	330	Homo sapiens	Mutation(s): 0  Gene Names: PTPN1 (PTP1B) EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens) Go to Gene View: PTPN1 Go to UniProtKB:  P18031

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSP	A	L-PEPTIDE LINKING	C3 H8 N O5 P S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.281 
• R-Value Work: 0.205 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 88.280	α = 90.00
b = 88.280	β = 90.00
c = 104.910	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
X-PLOR	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-19 
• Released Date: 1998-06-17 
• Deposition Author(s): Pannifer, A.D.P., Flint, A.J., Tonks, N.K., Barford, D.

Revision History 

• Version 1.0: 1998-06-17
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance