› 2ri0

X-ray diffraction
1.6Å resolution

Crystal Structure of glucosamine 6-phosphate deaminase (NagB) from S. mutans

Released:
DOI: 10.2210/pdb2ri0/pdb
PDB entry 2ri0 coloured by chain, front view.
PDB entry 2ri0 coloured by chain, side view.
PDB entry 2ri0 coloured by chain, top view.
Source organism: Streptococcus mutans
Primary publication:
Ring-opening mechanism revealed by crystal structures of NagB and its ES intermediate complex.
Liu C, Li D, Liang YH, Li LF, Su XD
J Mol Biol 379 73-81 (2008)
PMID: 18436239

Function and Biology Details

Reaction catalysed: 
Alpha-D-glucosamine 6-phosphate + H(2)O = D-fructose 6-phosphate + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184238 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glucosamine-6-phosphate deaminase Chains: A, B
Molecule details ›
Chains: A, B
Length: 234 amino acids
Theoretical weight: 25.59 KDa
Source organism: Streptococcus mutans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8DV70 (Residues: 1-233; Coverage: 100%)
Gene names: SMU_636, nagB
Sequence domains: Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand BTB 2 x BTB
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 54Å b: 82.17Å c: 134.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.177 0.199
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 citation in other articles

GlmS and NagB regulate amino sugar metabolism in opposing directions and affect Streptococcus mutans virulence.
Kawada-Matsuo et al. (2012)
5 more

1 mention without citation

Diaryl Urea Derivative Molecule Inhibits Cariogenic Streptococcus mutans by Affecting Exopolysaccharide Synthesis, Stress Response, and Nitrogen Metabolism.
Liao et al. (2022)