8QHQ

Crystal structure of human DNPH1 bound to hmdUMP

Summary for 8QHQ

• Entry DOI: 10.2210/pdb8qhq/pdb
• Related: 8QHR
• Descriptor: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1, 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: dnph1 n-glycosidase hmdump, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 6
• Total formula weight: 100549.98

Authors

Rzechorzek, N.J.,West, S.C. (deposition date: 2023-09-09, release date: 2023-11-08)

Primary citation

Rzechorzek, N.J.,Kunzelmann, S.,Purkiss, A.G.,Silva Dos Santos, M.,MacRae, J.I.,Taylor, I.A.,Fugger, K.,West, S.C.
Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1.
Nat Commun, 14:6809-6809, 2023

PubMed Abstract: Poly(ADP-ribose) polymerase (PARP) inhibitors are used in the clinic to treat BRCA-deficient breast, ovarian and prostate cancers. As their efficacy is potentiated by loss of the nucleotide salvage factor DNPH1 there is considerable interest in the development of highly specific small molecule DNPH1 inhibitors. Here, we present X-ray crystal structures of dimeric DNPH1 bound to its substrate hydroxymethyl deoxyuridine monophosphate (hmdUMP). Direct interaction with the hydroxymethyl group is important for substrate positioning, while conserved residues surrounding the base facilitate target discrimination. Glycosidic bond cleavage is driven by a conserved catalytic triad and proceeds via a two-step mechanism involving formation and subsequent disruption of a covalent glycosyl-enzyme intermediate. Mutation of a previously uncharacterised yet conserved glutamate traps the intermediate in the active site, demonstrating its role in the hydrolytic step. These observations define the enzyme's catalytic site and mechanism of hydrolysis, and provide important insights for inhibitor discovery.

PubMed: 37884503
DOI: 10.1038/s41467-023-42544-4

Experimental method

X-RAY DIFFRACTION (1.78 Å)