6EDR image
Deposition Date 2018-08-10
Release Date 2018-11-21
Last Version Date 2024-11-20
Entry Detail
PDB ID:
6EDR
Title:
Crystal Structure of Human CD38 in Complex with 4'-Thioribose NAD+
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Gene (Uniprot):CD38
Mutations:N100D, N164A, N209D, N219D
Chain IDs:A, B
Chain Length:257
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Facile chemoenzymatic synthesis of a novel stable mimic of NAD.
Chem Sci 9 8337 8342 (2018)
PMID: 30568770 DOI: 10.1039/c8sc03899f

Abstact

Nicotinamide adenine dinucleotide (NAD+) is an essential cofactor participating in a variety of important enzyme-catalyzed physiological and pathophysiological processes. Analogues of NAD+ provide key and valuable agents for investigating NAD+-dependent enzymes. In this study, we report the preparation of a novel stable NAD+ mimic, 4'-thioribose NAD+ (S-NAD+), using a facile and efficient chemoenzymatic approach. Substrate activity assays indicated the resulting S-NAD+ is chemically inert to human CD38 and sirtuin 2 enzymes, but capable of participating in redox reactions in a manner similar to NAD+. X-ray crystallographic analysis revealed binding of S-NAD+ to the active site of human CD38 and critical residues involved in leaving group activation and catalysis. By more closely mimicking NAD+ in geometry and electrostatics, the generated S-NAD+ offers a unique and important tool that can be extended to study enzymes utilizing NAD+.

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