ArticleThe Biochemical journal2025
The energy landscape of N-ribosidic bond cleavage catalysed by 2'-deoxynucleoside 5'-phosphate N-hydrolase 1.
Article in The Biochemical journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The human enzyme 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (HsDNPH1) catalyses the N-ribosidic bond hydrolysis of the non-canonical nucleotide 5-hydroxymethyl-2'-deoxyuridine 5'-monophosphate (5hmdUMP), producing 5-hydroxymethyluracil and 2-deoxyribose 5-phosphate, preventing 5hmdUMP incorporation into DNA. This reaction is unusual for a nucleoside/nucleotide N-hydrolase as it proceeds by a double-displacement mechanism whereby Glu104 nucleophilically attacks 5hmdUMP to form a covalent 5-phospho-2-deoxyribosylated enzyme intermediate, which is subsequently hydrolysed. Here, we used site-directed mutagenesis and UV-VIS differential spectroscopy to show a shift in the 5hmdUMP absorbance spectrum upon binding to HsDNPH1 before N-ribosidic bond cleavage. This spectral shift can be monitored independently in different wavelengths to characterise the kinetics of HsDNPH1-5hmdUMP binary complex formation. The one-step binding mechanism produces a calculated equilibrium dissociation constant in agreement with that obtained by isothermal titration calorimetry. Pre-steady-state kinetics under multipleturnover conditions revealed absence of a burst of substrate consumption at a wavelength where binding does not lead to change in absorbance. This indicates steps after N-ribosidic bond cleavage are fast. Single-turnover kinetics, where the signal comes solely from the first half-reaction, indicate N-ribosidic bond cleavage in the first half-reaction is rate-determining for kcat. Linear free energy relationships between leaving groups with increased pKa and kcat/KM suggest a late transition state with significant negative charge accumulation in the leaving group during N-ribosidic bond cleavage. These results were complemented by on-enzyme QM/MM calculations of the first half-reaction to reveal an anionic leaving group in an SN2-like transition state with C1'-N1 bond cleavage more advanced than C1-O bond formation with Glu104.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.