› 5eso

X-ray diffraction
2.05Å resolution

Crystal Structure of M. tuberculosis MenD with ThDP, Mg2+ and Isochorismate bound

Released:
DOI: 10.2210/pdb5eso/pdb
PDB entry 5eso coloured by chain, front view.
PDB entry 5eso coloured by chain, side view.
PDB entry 5eso coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Jirgis EN, Bashiri G, Bulloch EM, Johnston JM, Baker EN
Structure 24 1167-77 (2016)
PMID: 27291649

Function and Biology Details

Reaction catalysed: 
Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161714 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 574 amino acids
Theoretical weight: 60.07 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: P9WK11 (Residues: 1-554; Coverage: 100%)
Gene names: Rv0555, menD
Sequence domains: Thiamine pyrophosphate enzyme, N-terminal TPP binding domain

Ligands and Environments


Cofactor: Ligand TPP 2 x TPP
5 bound ligands:
Ligand MG 4 x MG
Ligand ISC 2 x ISC
Ligand FMT 6 x FMT
Ligand GOL 3 x GOL
Ligand BME 2 x BME
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 101.444Å b: 139.592Å c: 181.768Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.192 0.219
Expression system: Mycolicibacterium smegmatis

Quick links

Citations

6 citation in other articles

Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogen Mycobacterium tuberculosis.
Bashiri et al. (2020)
5 more

1 mention without citation

Sulfur-bridged chromophores for photofunctional materials: using sulfur oxidation state to tune electronic and structural properties.
Yuan et al. (2022)