2PY4

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.

Summary for 2PY4

• Entry DOI: 10.2210/pdb2py4/pdb
• Related: 1MQ7 1SIX
• 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: Mycobacterium tuberculosis
• Total number of polymer chains: 1
• Total formula weight: 18605.92

Authors

Barabas, O.,Nagy, N.,Takacs, E.,Vertessy, B.G. (deposition date: 2007-05-15, release date: 2007-05-22, Last modification date: 2023-08-30)

Primary citation

Varga, B.,Barabas, O.,Takacs, E.,Nagy, N.,Nagy, P.,Vertessy, B.G.
Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor.
Biochem.Biophys.Res.Commun., 373:8-13, 2008

PubMed Abstract: dUTPases are essential to eliminate dUTP for DNA integrity and provide dUMP for thymidylate biosynthesis. Mycobacterium tuberculosis apparently lacks any other thymidylate biosynthesis pathway, therefore dUTPase is a promising antituberculotic drug target. Crystal structure of the mycobacterial enzyme in complex with the isosteric substrate analog, alpha,beta-imido-dUTP and Mg(2+) at 1.5A resolution was determined that visualizes the full-length C-terminus, previously not localized. Interactions of a conserved motif important in catalysis, the Mycobacterium-specific five-residue-loop insert and C-terminal tetrapeptide could now be described in detail. Stacking of C-terminal histidine upon the uracil moiety prompted replacement with tryptophan. The resulting sensitive fluorescent sensor enables fast screening for binding of potential inhibitors to the active site. K(d) for alpha,beta-imido-dUTP binding to mycobacterial dUTPase is determined to be 10-fold less than for human dUTPase, which is to be considered in drug optimization. A robust continuous activity assay for kinetic screening is proposed.

PubMed: 18519027
DOI: 10.1016/j.bbrc.2008.05.130

Experimental method

X-RAY DIFFRACTION (1.49 Å)