› 1vlp

X-ray diffraction
1.75Å resolution

Crystal structure of a putative nicotinate phosphoribosyltransferase (yor209c, npt1) from saccharomyces cerevisiae at 1.75 A resolution

Released:
DOI: 10.2210/pdb1vlp/pdb
PDB entry 1vlp coloured by chain, front view.
PDB entry 1vlp coloured by chain, side view.
PDB entry 1vlp coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases.
Chappie JS, Cànaves JM, Han GW, Rife CL, Xu Q, Stevens RC
Structure 13 1385-96 (2005)
PMID: 16154095

Function and Biology Details

Reaction catalysed: 
Nicotinate + 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H(2)O = beta-nicotinate D-ribonucleotide + diphosphate + ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153927 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nicotinate phosphoribosyltransferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 441 amino acids
Theoretical weight: 51.01 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P39683 (Residues: 1-429; Coverage: 100%)
Gene names: NPT1, YOR209C
Sequence domains:
Structure domains: nicotinate phosphoribosyltransferase

Ligands and Environments

4 bound ligands:
Ligand PO4 4 x PO4
Ligand CL 3 x CL
Ligand MES 1 x MES
Ligand EDO 3 x EDO
1 modified residue:
Ligand MSE 40 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1, ALS BEAMLINE 8.2.2
Spacegroup: P1
Unit cell:
a: 54.406Å b: 83.103Å c: 107.237Å
α: 97.35° β: 95.67° γ: 97.99°
R-values:
R R work R free
0.172 0.17 0.21
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going?
Hassa et al. (2006)
4 more

4 mentions without citation

Recent Progress on the Versatility of Virus-Like Particles.
Qian et al. (2020)
3 more