› 3gh3

X-ray diffraction
1.8Å resolution

Structural insights into the catalytic mechanism of CD38: Evidence for a conformationally flexible covalent enzyme-substrate complex.

Released:
DOI: 10.2210/pdb3gh3/pdb
PDB 3gh3 coloured by chain and viewed from the front.
PDB 3gh3 coloured by chain and viewed from the side.
PDB 3gh3 coloured by chain and viewed from the top.
Source organism: Bos taurus
Primary publication:
Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates.
Egea PF, Muller-Steffner H, Kuhn I, Cakir-Kiefer C, Oppenheimer NJ, Stroud RM, Kellenberger E, Schuber F
OpenAccess logo PLoS One 7 e34918 (2012)
PMID: 22529956

Function and Biology Details

Reactions catalysed: 
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
(1a) NADP(+) = 2'-phospho-cyclic ADP-ribose + nicotinamide
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 247 amino acids
Theoretical weight: 28.3 KDa
Source organism: Bos taurus
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q9TTF5 (Residues: 32-278; Coverage: 98%)
Gene name: CD38
Sequence domains: ADP-ribosyl cyclase
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand SO4 2 x SO4
Ligand CAC 1 x CAC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 47.483Å b: 80.879Å c: 151.79Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.177 0.223
Expression system: Komagataella pastoris

Quick links

Citations

1 review citation

Sirtuins: NAD(+)-dependent deacetylase mechanism and regulation.
Sauve et al. (2012)
9 other articles

2 mentions without citation

Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates.
Egea et al. (2012)
1 more