› 3ghh

X-ray diffraction
1.94Å resolution

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

Released:
DOI: 10.2210/pdb3ghh/pdb
PDB entry 3ghh coloured by chain, front view.
PDB entry 3ghh coloured by chain, side view.
PDB entry 3ghh coloured by chain, top view.
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
PLoS One 7 e34918 (2012)
PMID: 22529956

Function and Biology Details

Reactions catalysed: 
(1a) NADP(+) = 2'-phospho-cyclic ADP-ribose + nicotinamide
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193579 (preferred)
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 5 x SO4
Ligand 2NF 1 x 2NF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 46.399Å b: 79.411Å c: 156.297Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.206 0.24
Expression system: Komagataella pastoris

Quick links

Citations

1 review citation

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

1 mention 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)