4XIH

Crystal structure of the R116A mutant AhpE from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The active site architecture in peroxiredoxins: a case study on Mycobacterium tuberculosis AhpE.

Pedre, B.van Bergen, L.A.Pallo, A.Rosado, L.A.Dufe, V.T.Molle, I.V.Wahni, K.Erdogan, H.Alonso, M.Proft, F.D.Messens, J.

(2016) Chem Commun (Camb) 52: 10293-10296

  • DOI: 10.1039/c6cc02645a
  • Primary Citation of Related Structures:  
    4XIH, 5C04

  • PubMed Abstract: 
  • Peroxiredoxins catalyze the reduction of peroxides, a process of vital importance to survive oxidative stress. A nucleophilic cysteine, also known as the peroxidatic cysteine, is responsible for this catalytic process. We used the Mycobacterium tuberculosis alkyl hydroperoxide reductase E (MtAhpE) as a model to investigate the effect of the chemical environment on the specificity of the reaction ...

    Peroxiredoxins catalyze the reduction of peroxides, a process of vital importance to survive oxidative stress. A nucleophilic cysteine, also known as the peroxidatic cysteine, is responsible for this catalytic process. We used the Mycobacterium tuberculosis alkyl hydroperoxide reductase E (MtAhpE) as a model to investigate the effect of the chemical environment on the specificity of the reaction. Using an integrative structural (R116A - PDB ; F37H - PDB ), kinetic and computational approach, we explain the mutational effects of key residues in its environment. This study shows that the active site residues are specifically oriented to create an environment which selectively favours a reaction with peroxides.


    Organizational Affiliation

    Structural Biology Research Center, Oxidative Stress Signaling lab, VIB, Pleinlaan 2, 1050 Brussels, Belgium. joris.messens@vib-vub.be and Brussels Center for Redox Biology, 1050 Brussels, Belgium and Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AhpC/TSA family proteinA, B153Mycobacterium tuberculosis CCDC5079Mutation(s): 1 
Gene Names: ahpECCDC5079_2075CFBS_2371
EC: 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.26α = 90
b = 147.26β = 90
c = 33.303γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG030512N

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2016-08-10
    Changes: Database references
  • Version 1.3: 2016-08-24
    Changes: Database references
  • Version 2.0: 2020-03-25
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations