4TVO | pdb_00004tvo

Structure of Malate Dehydrogenase from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb4TVO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.193 (Depositor), 0.190 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.24743
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 69.48 kDa
Atom Count: 5,233
Modeled Residue Count: 645
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	330	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: mdh, RVBD_1240 EC: 1.1.1.37
UniProt
Find proteins for P9WK13 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK13 Go to UniProtKB: P9WK13
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WK13
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain R [auth B]	C [auth A], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain U [auth B] SDF format, chain X [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B] mmCIF format, chain X [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.193 (Depositor), 0.190 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.606	α = 90
b = 79.307	β = 90
c = 155.513	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Ferraris, D.M.

Rizzi, M.

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

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2015-01-28
Changes: Database references
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Refinement description