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› 1w19

X-ray diffraction
2Å resolution

Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)propane 1-phosphate

Released:
DOI: 10.2210/pdb1w19/pdb
Model geometry
Fit model/data
PDB entry 1w19 coloured by chain, front view.
PDB entry 1w19 coloured by chain, side view.
PDB entry 1w19 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Crystal structure of lumazine synthase from Mycobacterium tuberculosis as a target for rational drug design: binding mode of a new class of purinetrione inhibitors.
Morgunova E, Meining W, Illarionov B, Haase I, Jin G, Bacher A, Cushman M, Fischer M, Ladenstein R
Biochemistry 44 2746-58 (2005)
PMID: 15723519

Function and Biology Details

Reaction catalysed: 
(2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil =6,7-dimethyl-8-(1-D-ribityl)lumazine + phosphate + 2 H2O + H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161544 (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

9 bound ligands:
Ligand ACY 5 x ACY
Ligand DTU 2 x DTU
Ligand T1P 1 x T1P
Ligand K 13 x K
Ligand T2P 1 x T2P
Ligand DTV 3 x DTV
Ligand T5P 1 x T5P
Ligand T4P 2 x T4P
Ligand D1D 1 x D1D
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: C2
Unit cell:
a: 131.267Å b: 80.688Å c: 86.188Å
α: 90° β: 120.29° γ: 90°
R-values:
R R work R free
0.151 0.149 0.194
Expression system: Escherichia coli

Quick links

Citations

16 review citations

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

5 mentions without citation

Stretching to understand proteins - a survey of the protein data bank.
Sułkowska et al. (2008)
4 more