3F6Y image
Deposition Date 2008-11-07
Release Date 2008-11-18
Last Version Date 2024-10-09
Entry Detail
PDB ID:
3F6Y
Keywords:
Title:
Conformational Closure of the Catalytic Site of Human CD38 Induced by Calcium
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.45 Å
R-Value Free:
0.18
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ADP-ribosyl cyclase 1
Gene (Uniprot):CD38
Mutations:R45F, Q49T, N100D, N164D, N209D, N219D
Chain IDs:A
Chain Length:262
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Conformational Closure of the Catalytic Site of Human CD38 Induced by Calcium
Biochemistry 47 13966 13973 (2008)
PMID: 19117080 DOI: 10.1021/bi801642q

Abstact

First identified on the surface of lymphoids as a type II transmembrane protein, CD38 has now been established to have dual functions not only as a receptor but also as a multifunctional enzyme,catalyzing the synthesis of and hydrolysis of a general calcium messenger molecule, cyclic ADP-ribose(cADPR). The receptorial functions of CD38 include the induction of cell adhesion, differentiation,apoptosis, and cytokine production upon antibody ligation. Here we determined the crystal structure of calcium-loaded human CD38 at 1.45 A resolution which reveals that CD38 undergoes dramatic structural changes to an inhibited conformation in the presence of calcium. The structural changes are highly localized and occur in only two regions. The first region is part of the active site and consists of residues 121-141.In the presence of calcium, W125 moves 5 A into the active site and forms hydrophobic interactions with W189. The movement closes the active site pocket and reduces entry of substrates, resulting in inhibition of the enzymatic activity. The structural role of calcium in inducing these conformational changes is readily visualized in the crystal structure. The other region that undergoes calcium-induced changes is at the receptor region, where a highly ordered helix is unraveled to a random coil. The results suggest a novel conformational coupling mechanism, whereby protein interaction targeted at the receptor region can effectively regulate the enzymatic activity of CD38.

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Primary Citation of related structures