1KNC

Structure of AhpD from Mycobacterium tuberculosis, a novel enzyme with thioredoxin-like activity.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein.

Bryk, R.Lima, C.D.Erdjument-Bromage, H.Tempst, P.Nathan, C.

(2002) Science 295: 1073-1077

  • DOI: 10.1126/science.1067798

  • PubMed Abstract: 
  • Mycobacterium tuberculosis (Mtb) mounts a stubborn defense against oxidative and nitrosative components of the immune response. Dihydrolipoamide dehydrogenase (Lpd) and dihydrolipoamide succinyltransferase (SucB) are components of alpha-ketoacid dehy ...

    Mycobacterium tuberculosis (Mtb) mounts a stubborn defense against oxidative and nitrosative components of the immune response. Dihydrolipoamide dehydrogenase (Lpd) and dihydrolipoamide succinyltransferase (SucB) are components of alpha-ketoacid dehydrogenase complexes that are central to intermediary metabolism. We find that Lpd and SucB support Mtb's antioxidant defense. The peroxiredoxin alkyl hydroperoxide reductase (AhpC) is linked to Lpd and SucB by an adaptor protein, AhpD. The 2.0 angstrom AhpD crystal structure reveals a thioredoxin-like active site that is responsive to lipoamide. We propose that Lpd, SucB (the only lipoyl protein detected in Mtb), AhpD, and AhpC together constitute a nicotinamide adenine dinucleotide (reduced)-dependent peroxidase and peroxynitrite reductase. AhpD thus represents a class of thioredoxin-like molecules that enables an antioxidant defense.


    Organizational Affiliation

    Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AhpD protein
A, B, C
177Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: ahpD
EC: 1.11.1.15
Find proteins for P9WQB5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WQB5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.318α = 90.00
b = 108.318β = 90.00
c = 233.582γ = 120.00
Software Package:
Software NamePurpose
andmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance