1I57

CRYSTAL STRUCTURE OF APO HUMAN PTP1B (C215S) MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of apo protein-tyrosine phosphatase 1B C215S mutant: more than just an S --> O change.

Scapin, G.Patel, S.Patel, V.Kennedy, B.Asante-Appiah, E.

(2001) Protein Sci. 10: 1596-1605

  • DOI: 10.1110/ps.11001

  • PubMed Abstract: 
  • Protein-tyrosine phosphatases catalyze the hydrolysis of phosphate monoesters via a two-step mechanism involving a covalent phospho-enzyme intermediate. Biochemical and site-directed mutagenesis experiments show that the invariant Cys residue present ...

    Protein-tyrosine phosphatases catalyze the hydrolysis of phosphate monoesters via a two-step mechanism involving a covalent phospho-enzyme intermediate. Biochemical and site-directed mutagenesis experiments show that the invariant Cys residue present in the PTPase signature motif (H/V)CX(5)R(S/T) (i.e., C215 in PTP1B) is absolutely required for activity. Mutation of the invariant Cys to Ser results in a catalytically inactive enzyme, which still is capable of binding substrates and inhibitors. Although it often is assumed that substrate-trapping mutants such as the C215S retain, in solution, the structural and binding properties of wild-type PTPases, significant differences have been found in the few studies that have addressed this issue, suggesting that the mutation may lead to structural/conformational alterations in or near the PTP1B binding site. Several crystal structures of apo-WT PTP1B, and of WT- and C215S-mutant PTP1B in complex with different ligands are available, but no structure of the apo-PTP1B C215S has ever been reported. In all previously reported structures, residues of the PTPase signature motif have an identical conformation, while residues of the WPD loop (a surface loop which includes the catalytic Asp) assume a different conformation in the presence or absence of ligand. These observations led to the hypothesis that the different spectroscopic and thermodynamic properties of the mutant protein may be the result of a different conformation for the WPD loop. We report here the structure of the apo-PTP1B C215S mutant, which reveals that, while the WPD loop is in the open conformation observed in the apo WT enzyme crystal structure, the residues of the PTPases signature motif are in a dramatically different conformation. These results provide a structural basis for the differences in spectroscopic properties and thermodynamic parameters in inhibitor binding observed for the wild-type and mutant enzymes.


    Related Citations: 
    • Conformational and Dynamic Changes of Yersinia Protein Tyrosine Phosphatase Induced by Ligand Binding and Active Site Mutation and Revealed by H/D Exchange and Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
      Wang, F.,Li, W.,Emmett, M.R.,Hendrickson, C.L.,Marshall, A.G.,Zhang, Y.L.,Wu, L.,Zhang, Z.Y.
      (1998) Biochemistry 37: 15289
    • The Single Sulfur to Oxygen Substitution in the Active Site Nucleofile of the Yersinia Protein-tyrosine Phosphatase Leads to Substantial Structural and Functional Perturbations
      Zhang, Z.Y.,Wu, L.
      (1997) Biochemistry 36: 1362
    • Rapid Loop Dynamics of Yersinia Protein-Tyrosine Phosphatase
      Juszczak, L.J.,Zhang, Z.Y.,Wu, L.,Gottfried, D.S.,Eads, D.D.
      (1997) Biochemistry 36: 2227
    • Thermodynamic Study of Ligand Binding to Protein-tyrosine Phosphatase 1B and its Substrate-trapping Mutants.
      Zhang, Y.L.,Yao, Z.J.,Sarmiento, M.,Wu, L.,Burke, T.R.,Zhang, Z.Y.
      (2000) J.Biol.Chem. 275: 34205


    Organizational Affiliation

    Department of Endocrinology and Chemical Biology, Merck Research Laboratories, Rahway, NJ 07065, USA. Giovanna_scapin@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHO-TYROSINE PHOSPHATASE 1B
A
310Homo sapiensGene 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
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.381α = 90.00
b = 87.381β = 90.00
c = 95.942γ = 120.00
Software Package:
Software NamePurpose
X-GENdata scaling
MAR345data collection
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description