› 4k2i

X-ray diffraction
2.22Å resolution

Crystal structure of ntda from bacillus subtilis with bound cofactor pmp

Released:
DOI: 10.2210/pdb4k2i/pdb
PDB entry 4k2i coloured by chain, front view.
PDB entry 4k2i coloured by chain, side view.
PDB entry 4k2i coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new subclass of aminotransferases.
van Straaten KE, Ko JB, Jagdhane R, Anjum S, Palmer DRJ, Sanders DAR
J Biol Chem 288 34121-34130 (2013)
PMID: 24097983

Function and Biology Details

Reaction catalysed: 
Kanosamine 6-phosphate + 2-oxoglutarate = 3-dehydro-D-glucose 6-phosphate + L-glutamate
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-126598 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-oxo-glucose-6-phosphate:glutamate aminotransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 443 amino acids
Theoretical weight: 50.33 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O07566 (Residues: 1-441; Coverage: 100%)
Gene names: BSU10550, ntdA, yhjL
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand PMP 2 x PMP
3 bound ligands:
Ligand ACT 4 x ACT
Ligand EDO 8 x EDO
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P21
Unit cell:
a: 50.109Å b: 106.979Å c: 99.177Å
α: 90° β: 95.96° γ: 90°
R-values:
R R work R free
0.161 0.158 0.211
Expression system: Escherichia coli BL21

Quick links

Citations

4 review citations

Overview of the Antimicrobial Compounds Produced by Members of the Bacillus subtilis Group.
Caulier et al. (2019)
3 more

2 mentions without citation

A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis.
Richts et al. (2019)
1 more