1RNJ

Crystal structure of inactive mutant dUTPase complexed with substrate analogue imido-dUTP

Summary for 1RNJ

• Entry DOI: 10.2210/pdb1rnj/pdb
• Related: 1RN8 1RO1
• Descriptor: Deoxyuridine 5'-triphosphate nucleotidohydrolase, MAGNESIUM ION, 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: jelly roll, enzyme-ligand complex, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 17037.38

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: 2023-08-23)

Primary citation

Barabas, 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

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

Experimental method

X-RAY DIFFRACTION (1.7 Å)