› 2gru

X-ray diffraction
2.15Å resolution

Crystal structure of 2-deoxy-scyllo-inosose synthase complexed with carbaglucose-6-phosphate, NAD+ and Co2+

Released:
DOI: 10.2210/pdb2gru/pdb
PDB entry 2gru coloured by chain, front view.
PDB entry 2gru coloured by chain, side view.
PDB entry 2gru coloured by chain, top view.
Source organism: Niallia circulans
Primary publication:
Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+.
Nango E, Kumasaka T, Hirayama T, Tanaka N, Eguchi T
Proteins 70 517-27 (2008)
PMID: 17879343

Function and Biology Details

Reaction catalysed: 
D-glucose-6-phosphate = 2-deoxy-L-scyllo-inosose + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193404 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-deoxy-scyllo-inosose synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 368 amino acids
Theoretical weight: 40.79 KDa
Source organism: Niallia circulans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9S5E2 (Residues: 1-368; Coverage: 100%)
Gene name: btrC
Sequence domains: 3-dehydroquinate synthase
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
6 bound ligands:
Ligand CO 2 x CO
Ligand SO3 2 x SO3
Ligand PO4 1 x PO4
Ligand EXO 1 x EXO
Ligand MPD 2 x MPD
Ligand CAK 1 x CAK
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P21
Unit cell:
a: 79.569Å b: 70.108Å c: 81.569Å
α: 90° β: 117.61° γ: 90°
R-values:
R R work R free
0.176 0.174 0.223
Expression system: Escherichia coli

Quick links

Citations

2 review citations

2-Deoxystreptamine-containing aminoglycoside antibiotics: recent advances in the characterization and manipulation of their biosynthetic pathways.
Park et al. (2013)
1 more

3 mentions without citation

Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase.
Carbone et al. (2015)
2 more