1rn8: Difference between revisions

Revision as of 15:52, 21 February 2008

Crystal structure of dUTPase complexed with substrate analogue imido-dUTP

OverviewOverview

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.

About this StructureAbout this Structure

1RN8 is a Single protein structure of sequence from Escherichia coli with , , and as ligands. Active as dUTP diphosphatase, with EC number 3.6.1.23 Full crystallographic information is available from OCA.

ReferenceReference

Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase., Barabas O, Pongracz V, Kovari J, Wilmanns M, Vertessy BG, J Biol Chem. 2004 Oct 8;279(41):42907-15. Epub 2004 Jun 17. PMID:15208312

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OCA

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-[[Image:1rn8.gif|left|200px]]<br /><applet load="1rn8" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1rn8.gif|left|200px]]<br /><applet load="1rn8" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1rn8, resolution 1.93&Aring;" />
 '''Crystal structure of dUTPase complexed with substrate analogue imido-dUTP'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-RN8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG, ACT, DUP and TRS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RN8 OCA].
+RN8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=ACT:'>ACT</scene>, <scene name='pdbligand=DUP:'>DUP</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RN8 OCA].
 ==Reference==
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 [[Category: Kovari, J.]]
 [[Category: Pongracz, V.]]
-[[Category: Vertessy, B.G.]]
+[[Category: Vertessy, B G.]]
 [[Category: Wilmanns, M.]]
 [[Category: ACT]]
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 [[Category: jelly roll]]
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