4IF2

Structure of the phosphotriesterase from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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This is version 1.2 of the entry. See complete history


Literature

The crystal structure of the phosphotriesterase from M. tuberculosis, another member of phosphotriesterase-like lactonase family.

Zhang, L.Wang, H.Liu, X.Zhou, W.Rao, Z.

(2019) Biochem Biophys Res Commun 510: 224-229

  • DOI: https://doi.org/10.1016/j.bbrc.2019.01.069
  • Primary Citation of Related Structures:  
    4IF2

  • PubMed Abstract: 

    Organophosphates (OPs) have been used widely as insecticides for protecting the agricultural crops from the pests. These compounds are highly toxic because they can cause the irreversible damage to human nervous system. Phosphotriesterases (PTEs), widely exist in many different kinds of bacteria, insects and mammals, can hydrolyze phosphotriesters (one major kind of OP) sufficiently. The phosphotriesterase-activities of PTEs are considered to derive from the lactonase-activities during the evolution, and phosphotriesterase-like lactonase family (PLL), is the closest protein family to PTE family based on protein-protein blast results. But members of PLL family exhibit higher lactonase activities than the phosphotriesterase activities, while the best substrates for PTEs are phosphotriesters. In this paper, the X-ray crystal structure of phosphotriesterase from M. tuberculosis (mPHP) was solved at a resolution of 2.3 Å. The structure reveals that the mPHP is a dimer with a typical distorted (β/α) 8 barrel structure like other structures of PLL family and PTE family. The architecture of active pocket of mPHP coordinates with 2 metal ions which is also similar to other PLLs and PTEs. The activity assay proved the mPHP is biological active form and the Atomic Absorption Spectroscopy assay gave the evidence that the two metal ions bound to the active pocket were Zinc cations. The structural comparison between mPHP and other homologues concluded that the mPHP should belong to PLL family, not PTE family.


  • Organizational Affiliation

    College of Life Sciences, Nankai University, Tianjin, 30071, China. Electronic address: liang.zhang3@nih.gov.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphotriesterase homology protein326Mycobacterium tuberculosisMutation(s): 0 
Gene Names: phpRv0230cMT0240MTCY08D5.26c
UniProt
Find proteins for P9WHN9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHN9 
Go to UniProtKB:  P9WHN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHN9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.032α = 90
b = 149.596β = 90
c = 74.23γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations