8OSC

Structure of Homo sapiens 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) bound to deoxyuridine 5'- monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Literature

Human 2'-Deoxynucleoside 5'-Phosphate N -Hydrolase 1: Mechanism of 2'-Deoxyuridine 5'-Monophosphate Hydrolysis.

Devi, S.Carberry, A.E.Zickuhr, G.M.Dickson, A.L.Harrison, D.J.da Silva, R.G.

(2023) Biochemistry 62: 2658-2668

  • DOI: https://doi.org/10.1021/acs.biochem.3c00369
  • Primary Citation of Related Structures:  
    8OS9, 8OSC

  • PubMed Abstract: 

    The enzyme 2'-deoxynucleoside 5'-phosphate N -hydrolase 1 (DNPH1) catalyzes the N -ribosidic bond cleavage of 5-hydroxymethyl-2'-deoxyuridine 5'-monophosphate to generate 2-deoxyribose 5-phosphate and 5-hydroxymethyluracil. DNPH1 accepts other 2'-deoxynucleoside 5'-monophosphates as slow-reacting substrates. DNPH1 inhibition is a promising strategy to overcome resistance to and potentiate anticancer poly(ADP-ribose) polymerase inhibitors. We solved the crystal structure of unliganded human DNPH1 and took advantage of the slow reactivity of 2'-deoxyuridine 5'-monophosphate (dUMP) as a substrate to obtain a crystal structure of the DNPH1:dUMP Michaelis complex. In both structures, the carboxylate group of the catalytic Glu residue, proposed to act as a nucleophile in covalent catalysis, forms an apparent low-barrier hydrogen bond with the hydroxyl group of a conserved Tyr residue. The crystal structures are supported by functional data, with liquid chromatography-mass spectrometry analysis showing that DNPH1 incubation with dUMP leads to slow yet complete hydrolysis of the substrate. A direct UV-vis absorbance-based assay allowed characterization of DNPH1 kinetics at low dUMP concentrations. A bell-shaped pH-rate profile indicated that acid-base catalysis is operational and that for maximum k cat / K M , two groups with an average p K a of 6.4 must be deprotonated, while two groups with an average p K a of 8.2 must be protonated. A modestly inverse solvent viscosity effect rules out diffusional processes involved in dUMP binding to and possibly uracil release from the enzyme as rate limiting to k cat / K M . Solvent deuterium isotope effects on k cat / K M and k cat were inverse and unity, respectively. A reaction mechanism for dUMP hydrolysis is proposed.


  • Organizational Affiliation

    School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2'-deoxynucleoside 5'-phosphate N-hydrolase 1
A, B
145Homo sapiensMutation(s): 0 
Gene Names: DNPH1C6orf108RCL
EC: 3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for O43598 (Homo sapiens)
Explore O43598 
Go to UniProtKB:  O43598
PHAROS:  O43598
GTEx:  ENSG00000112667 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43598
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UMP (Subject of Investigation/LOI)
Query on UMP

Download Ideal Coordinates CCD File 
C [auth B]2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.354α = 90
b = 38.772β = 120.29
c = 66.195γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited KingdomIBioIC 2021-01-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Database references