1XVW

Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys Peroxiredoxin

Li, S.Peterson, N.A.Kim, M.Y.Kim, C.Y.Hung, L.W.Yu, M.Lekin, T.Segelke, B.W.Lott, J.S.Baker, E.N.

(2005) J Mol Biol 346: 1035-1046

  • DOI: 10.1016/j.jmb.2004.12.046
  • Primary Citation of Related Structures:  
    1XVW, 1XXU

  • PubMed Abstract: 
  • All living systems require protection against the damaging effects of reactive oxygen species. The genome of Mycobacterium tuberculosis, the cause of TB, encodes a number of peroxidases that are thought to be active against organic and inorganic pero ...

    All living systems require protection against the damaging effects of reactive oxygen species. The genome of Mycobacterium tuberculosis, the cause of TB, encodes a number of peroxidases that are thought to be active against organic and inorganic peroxides, and are likely to play a key role in the ability of this organism to survive within the phagosomes of macrophages. The open reading frame Rv2238c in M.tuberculosis encodes a 153-residue protein AhpE, which is a peroxidase of the 1-Cys peroxiredoxin (Prx) family. The crystal structure of AhpE, determined at 1.87 A resolution (R(cryst)=0.179, R(free)=0.210), reveals a compact single-domain protein with a thioredoxin fold. AhpE forms both dimers and octamers; a tightly-associated dimer and a ring-like octamer, generated by crystallographic 4-fold symmetry. In this native structure, the active site Cys45 is in its oxidized, sulfenic acid (S-O-H) state. A second crystal form of AhpE, obtained after soaking in sodium bromide and refined at 1.90 A resolution (R(cryst)=0.242, R(free)=0.286), reveals the reduced structure. In this structure, a conformational change in an external loop, in two of the four molecules in the asymmetric unit, allows Arg116 to stabilise the Cys45 thiolate ion, and concomitantly closes a surface channel. This channel is identified as the likely binding site for a physiological reductant, and the conformational change is inferred to be important for the reaction cycle of AhpE.


    Organizational Affiliation

    Centre of Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical protein Rv2238c/MT2298AB160Mycobacterium tuberculosisMutation(s): 1 
Gene Names: Rv2238c
EC: 1.8.1 (PDB Primary Data), 1.11.1.29 (UniProt)
Find proteins for P9WIE3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIE3 
Go to UniProtKB:  P9WIE3
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A,BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.994α = 90
b = 147.994β = 90
c = 33.711γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance