› 1fyd

X-ray diffraction
2.25Å resolution

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION

Released:
DOI: 10.2210/pdb1fyd/pdb
PDB entry 1fyd coloured by chain, front view.
PDB entry 1fyd coloured by chain, side view.
PDB entry 1fyd coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.
Devedjiev Y, Symersky J, Singh R, Jedrzejas M, Brouillette C, Brouillette W, Muccio D, Chattopadhyay D, DeLucas L
Acta Crystallogr D Biol Crystallogr 57 806-12 (2001)
PMID: 11375500

Function and Biology Details

Reaction catalysed: 
ATP + deamido-NAD(+) + NH(3) = AMP + diphosphate + NAD(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139945 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NH(3)-dependent NAD(+) synthetase Chains: A, B
Molecule details ›
Chains: A, B
Length: 271 amino acids
Theoretical weight: 30.3 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: P08164 (Residues: 2-272; Coverage: 100%)
Gene names: BSU03130, nadE, outB
Sequence domains: NAD synthase
Structure domains: HUPs

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand AMP 1 x AMP
Ligand POP 1 x POP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 53.45Å b: 87.2Å c: 61.18Å
α: 90° β: 111.15° γ: 90°
R-values:
R R work R free
0.191 0.191 0.278
Expression system: Escherichia coli

Quick links

Citations

1 review citation

A structural perspective on the PP-loop ATP pyrophosphatase family.
Fellner et al. (2018)
16 other articles

2 mentions without citation

Protein subunit interfaces: heterodimers versus homodimers.
Zhanhua et al. (2005)
1 more