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1RN8

Crystal structure of dUTPase complexed with substrate analogue imido-dUTP

Summary for 1RN8
Entry DOI10.2210/pdb1rn8/pdb
Related1RNJ 1RO1
DescriptorDeoxyuridine 5'-triphosphate nucleotidohydrolase, MAGNESIUM ION, ACETATE ION, ... (6 entities in total)
Functional Keywordsjelly roll, enzyme-ligand complex, hydrolase
Biological sourceEscherichia coli
Total number of polymer chains1
Total formula weight16975.26
Authors
Barabas, O.,Pongracz, V.,Kovari, J.,Wilmanns, M.,Vertessy, B.G. (deposition date: 2003-12-01, release date: 2004-09-07, Last modification date: 2023-09-20)
Primary citationBarabas, O.,Pongracz, V.,Kovari, J.,Wilmanns, M.,Vertessy, B.G.
Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase.
J.Biol.Chem., 279:42907-42915, 2004
Cited by
PubMed Abstract: dUTPase is essential to keep uracil out of DNA. Crystal structures of substrate (dUTP and alpha,beta-imino-dUTP) and product complexes of wild type and mutant dUTPases were determined to reveal how an enzyme responsible for DNA integrity functions. A kinetic analysis of wild type and mutant dUTPases was performed to obtain relevant mechanistic information in solution. Substrate hydrolysis is shown to be initiated via in-line nucleophile attack of a water molecule oriented by an activating conserved aspartate residue. Substrate binding in a catalytically competent conformation is achieved by (i) multiple interactions of the triphosphate moiety with catalysis-assisting Mg2+, (ii) a concerted motion of residues from three conserved enzyme motifs as compared with the apoenzyme, and (iii) an intricate hydrogen-bonding network that includes several water molecules in the active site. Results provide an understanding for the catalytic role of conserved residues in dUTPases.
PubMed: 15208312
DOI: 10.1074/jbc.M406135200
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.93 Å)
Structure validation

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