4ERC

Structure of VHZ bound to metavanadate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

New Aspects of the Phosphatase VHZ Revealed by a High-Resolution Structure with Vanadate and Substrate Screening.

Kuznetsov, V.I.Hengge, A.C.Johnson, S.J.

(2012) Biochemistry 51: 9869-9879

  • DOI: 10.1021/bi300908y

  • PubMed Abstract: 
  • The recently discovered 150-residue human VHZ (VH1-related protein, Z member) is one of the smallest protein tyrosine phosphatases (PTPs) known and contains only the minimal structural elements common to all PTPs. We report a substrate screening anal ...

    The recently discovered 150-residue human VHZ (VH1-related protein, Z member) is one of the smallest protein tyrosine phosphatases (PTPs) known and contains only the minimal structural elements common to all PTPs. We report a substrate screening analysis and a crystal structure of the VHZ complex with vanadate at 1.1 Å resolution, with a detailed structural comparison with other members of the protein tyrosine phosphatase family, including classical tyrosine-specific protein tyrosine phosphatases (PTPs) and dual-specificity phosphatases (DSPs). A screen with 360 phosphorylated peptides shows VHZ efficiently catalyzes the hydrolysis of phosphotyrosine (pY)-containing peptides but exhibits no activity toward phosphoserine (pS) or phosphothreonine (pT) peptides. The new structure reveals a deep and narrow active site more typical of the classical tyrosine-specific PTPs. Despite the high degrees of structural and sequence similarity between VHZ and classical PTPs, its general acid IPD-loop is most likely conformationally rigid, in contrast to the flexible WPD counterpart of classical PTPs. VHZ also lacks substrate recognition domains and other domains typically found on classical PTPs. It is therefore proposed that VHZ is more properly classified as an atypical PTP rather than an atypical DSP, as has been suggested.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity protein phosphatase 23
A, B
150Homo sapiensMutation(s): 0 
Gene Names: DUSP23 (LDP3, VHZ)
EC: 3.1.3.16, 3.1.3.48
Find proteins for Q9BVJ7 (Homo sapiens)
Go to Gene View: DUSP23
Go to UniProtKB:  Q9BVJ7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VN4
Query on VN4

Download SDF File 
Download CCD File 
A, B
oxido(dioxo)vanadium
O3 V
ALTWGIIQPLQAAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.128 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.992α = 90.00
b = 79.970β = 90.00
c = 99.718γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
X-PLORmodel building
HKL-2000data scaling
PHENIXrefinement
X-PLORphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references