4OTK | pdb_00004otk

A structural characterization of the isoniazid Mycobacterium tuberculosis drug target, Rv2971, in its unliganded form

• PDB DOI: https://doi.org/10.2210/pdb4OTK/pdb

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


• Deposited: 2014-02-13 Released: 2014-05-07 
• Deposition Author(s): Shahine, A., Beddoe, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

A structural characterization of the isoniazid Mycobacterium tuberculosis drug target, Rv2971, in its unliganded form

Shahine, A., Prasetyoputri, A., Rossjohn, J., Beddoe, T.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 572-577

• PubMed: 24817712 
• DOI: https://doi.org/10.1107/S2053230X14007158
• Primary Citation Related Structures: 
  4OTK


• PubMed Abstract: 
  

  Aldo-keto reductases (AKR) are a large superfamily of NADPH-dependent oxidoreductases and play a role in detoxification of toxic metabolites. Rv2971, an AKR in Mycobacterium tuberculosis, has recently been identified as a target of isoniazid, a key first-line drug against tuberculosis. Here, the cloning, expression, purification, crystallization and structural characterization of Rv2971 are described. To gain insight into its function, the crystal structure of Rv2971 was successfully determined to 1.60 Å resolution in its unliganded form. The structure exhibits a TIM-barrel fold typical of AKRs, revealing structural characteristics essential for function and substrate specificities, allowing a structural comparison between Rv2971 and other mycobacterial AKRs.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 34.43 kDa 
• Atom Count: 2,454 
• Modeled Residue Count: 276 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycobacterial Enzyme Rv2971	A	318	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv2971, MT3049 EC: 1 (PDB Primary Data), 1.1.1 (UniProt)
UniProt
Find proteins for P9WQA5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQA5  Go to UniProtKB:  P9WQA5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	B [auth A], C [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.27	α = 90
b = 86.27	β = 90
c = 86.29	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Shahine, A., Beddoe, T.

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-05-14
  Changes: Database references
• Version 1.2: 2014-06-04
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Refinement description, Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description