8qhr
From Proteopedia
Crystal structure of the human DNPH1 glycosyl-enzyme intermediate
Structural highlights
FunctionDNPH1_HUMAN Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases (By similarity).[HAMAP-Rule:MF_03036] Publication Abstract from PubMedPoly(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. Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1.,Rzechorzek NJ, Kunzelmann S, Purkiss AG, Silva Dos Santos M, MacRae JI, Taylor IA, Fugger K, West SC Nat Commun. 2023 Oct 26;14(1):6809. doi: 10.1038/s41467-023-42544-4. PMID:37884503[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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