1seh: Difference between revisions

Revision as of 16:00, 21 February 2008

Crystal structure of E. coli dUTPase complexed with the product dUMP

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

1SEH 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

Page seeded by OCA on Thu Feb 21 15:00:36 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1seh.gif|left|200px]]<br /><applet load="1seh" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1seh.gif|left|200px]]<br /><applet load="1seh" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1seh, resolution 1.47&Aring;" />
 '''Crystal structure of E. coli dUTPase complexed with the product dUMP'''<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==
-SEH 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 UMP 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=1SEH OCA].
+SEH 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=UMP:'>UMP</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=1SEH OCA].
 ==Reference==
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 [[Category: Kovari, J.]]
 [[Category: Pongracz, V.]]
-[[Category: Vertessy, B.G.]]
+[[Category: Vertessy, B G.]]
 [[Category: Wilmanns, M.]]
 [[Category: TRS]]
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 [[Category: jelly roll]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:19:08 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:00:36 2008''