4TVM | pdb_00004tvm

Structure of Citrate Synthase from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4TVM/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-27 Released: 2015-01-14 
• Deposition Author(s): Ferraris, D.M., Rizzi, M.
• Funding Organization(s): European Union FP7 Program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structures of citrate synthase and malate dehydrogenase of Mycobacterium tuberculosis.

Ferraris, D.M., Spallek, R., Oehlmann, W., Singh, M., Rizzi, M.

(2015) Proteins 83: 389-394

• PubMed: 25524525 
• DOI: https://doi.org/10.1002/prot.24743
• Primary Citation Related Structures: 
  4TVM, 4TVO


• PubMed Abstract: 
  

  The tricarboxylic acid (TCA) cycle is a central metabolic pathway of all aerobic organisms and is responsible for the synthesis of many important precursors and molecules. TCA cycle plays a key role in the metabolism of Mycobacterium tuberculosis and is involved in the adaptation process of the bacteria to the host immune response. We present here the first crystal structures of M. tuberculosis malate dehydrogenase and citrate synthase, two consecutive enzymes of the TCA, at 2.6 Å and 1.5 Å resolution, respectively. General analogies and local differences with the previously reported homologous protein structures are described.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, Università del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100, Novara, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 48.13 kDa 
• Atom Count: 3,011 
• Modeled Residue Count: 380 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	A	431	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: RVBD_0896 EC: 2.3.3.1 (PDB Primary Data), 2.3.3.16 (UniProt)
UniProt
Find proteins for P9WPD5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPD5  Go to UniProtKB:  P9WPD5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAA	B [auth A]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.767	α = 90
b = 148.767	β = 90
c = 182.797	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Ferraris, D.M., Rizzi, M.

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Funding Organization	Location	Grant Number
European Union FP7 Program	Italy	SysteMTb HEALTH-F4-2010-241587

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Refinement description