1KNC

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

• PDB DOI: https://doi.org/10.2210/pdb1KNC/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-12-18 Released: 2002-01-23 
• Deposition Author(s): Bryk, R., Lima, C.D., Erdjument-Bromage, H., Tempst, P., Nathan, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.216 

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

• PubMed: 11799204 
• DOI: https://doi.org/10.1126/science.1067798
• Primary Citation of Related Structures:  
  1KNC


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.04 kDa 
• Atom Count: 4,311 
• Modelled Residue Count: 521 
• Deposited Residue Count: 531 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AhpD protein	A, B, C	177	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for P9WQB5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQB5  Go to UniProtKB:  P9WQB5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.216 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.318	α = 90
b = 108.318	β = 90
c = 233.582	γ = 120

Software Package:

Software Name	Purpose
and	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-23 
Deposition Author(s): Bryk, R., Lima, C.D., Erdjument-Bromage, H., Tempst, P., Nathan, C.

Revision History  

• Version 1.0: 2002-01-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations