› 2c97

X-ray diffraction
2Å resolution

LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 4-(6- chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl phosphate

Released:
DOI: 10.2210/pdb2c97/pdb
PDB entry 2c97 coloured by chain, front view.
PDB entry 2c97 coloured by chain, side view.
PDB entry 2c97 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Structural and thermodynamic insights into the binding mode of five novel inhibitors of lumazine synthase from Mycobacterium tuberculosis.
Morgunova E, Illarionov B, Sambaiah T, Haase I, Bacher A, Cushman M, Fischer M, Ladenstein R
FEBS J 273 4790-804 (2006)
PMID: 16984393

Function and Biology Details

Reaction catalysed: 
1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H(2)O + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161545 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6,7-dimethyl-8-ribityllumazine synthase Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 160 amino acids
Theoretical weight: 16.39 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WHE9 (Residues: 1-160; Coverage: 100%)
Gene names: MTCY21B4.34, Rv1416, ribH
Sequence domains: 6,7-dimethyl-8-ribityllumazine synthase
Structure domains: Lumazine/riboflavin synthase

Ligands and Environments

5 bound ligands:
Ligand JCL 5 x JCL
Ligand K 16 x K
Ligand ACT 5 x ACT
Ligand MPD 6 x MPD
Ligand DTD 1 x DTD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: C2
Unit cell:
a: 131.64Å b: 82.244Å c: 86.346Å
α: 90° β: 120.53° γ: 90°
R-values:
R R work R free
0.15 0.146 0.215
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers.
Abbas et al. (2011)
6 more

2 mentions without citation

Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase.
Talukdar et al. (2010)
1 more