1dud: Difference between revisions

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-[[Image:1dud.gif|left|200px]]<br /><applet load="1dud" size="450" color="white" frame="true" align="right" spinBox="true"
+==DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE (D-UTPASE) COMPLEXED WITH THE SUBSTRATE ANALOGUE DEOXYURIDINE 5'-DIPHOSPHATE (D-UDP)==
-caption="1dud, resolution 2.3&Aring;" />
+<StructureSection load='1dud' size='340' side='right' caption='[[1dud]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-'''DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE (D-UTPASE) COMPLEXED WITH THE SUBSTRATE ANALOGUE DEOXYURIDINE 5'-DIPHOSPHATE (D-UDP)'''<br />
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dud]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DUD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DUD FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUD:DEOXYURIDINE-5-DIPHOSPHATE'>DUD</scene></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dud OCA], [http://pdbe.org/1dud PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dud RCSB], [http://www.ebi.ac.uk/pdbsum/1dud PDBsum]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/DUT_ECOLI DUT_ECOLI]] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.[HAMAP-Rule:MF_00116]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/1dud_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dud ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have determined the structure of the homotrimeric dUTPase from Escherichia coli, completed with an inhibitor and substrate analogue, dUDP. Three molecules of dUDP are found symmetrically bound per trimer, each in a shallow cleft between adjacent subunits, interacting with evolutionary conserved residues. The interactions of the uracil ring and the deoxypentose with the protein are consistent with the high specificity of the enzyme with respect to these groups. The positions of the two phosphate groups and adjacent water molecules are discussed in relation to the mechanism and kinetics of catalysis. The role that dUTPase plays in DNA metabolism makes the enzyme a potential target for chemotherapeutic drugs: the results presented here will aid in the design and development of inhibitory compounds.
-==Overview==
+Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP).,Larsson G, Svensson LA, Nyman PO Nat Struct Biol. 1996 Jun;3(6):532-8. PMID:8646539<ref>PMID:8646539</ref>
-We have determined the structure of the homotrimeric dUTPase from, Escherichia coli, completed with an inhibitor and substrate analogue, dUDP. Three molecules of dUDP are found symmetrically bound per trimer, each in a shallow cleft between adjacent subunits, interacting with, evolutionary conserved residues. The interactions of the uracil ring and, the deoxypentose with the protein are consistent with the high specificity, of the enzyme with respect to these groups. The positions of the two, phosphate groups and adjacent water molecules are discussed in relation to, the mechanism and kinetics of catalysis. The role that dUTPase plays in, DNA metabolism makes the enzyme a potential target for chemotherapeutic, drugs: the results presented here will aid in the design and development, of inhibitory compounds.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-DUD 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 DUD as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1DUD OCA].
+</div>
+<div class="pdbe-citations 1dud" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP)., Larsson G, Svensson LA, Nyman PO, Nat Struct Biol. 1996 Jun;3(6):532-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8646539 8646539]
+*[[Deoxyuridine 5'-triphosphate nucleotidohydrolase|Deoxyuridine 5'-triphosphate nucleotidohydrolase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: DUTP diphosphatase]]
-[[Category: dUTP diphosphatase]]
+[[Category: Larsson, G]]
-[[Category: Larsson, G.]]
+[[Category: Nyman, P O]]
-[[Category: Nyman, P.O.]]
+[[Category: Svensson, L A]]
-[[Category: Svensson, L.A.]]
+[[Category: D-udp complex]]
-[[Category: DUD]]
+[[Category: D-utpase]]
-[[Category: d-udp complex]]
+[[Category: Hydrolase]]
-[[Category: d-utpase]]
+[[Category: Nucleotide metabolism]]
-[[Category: hydrolase]]
+[[Category: Substrate analogue]]
-[[Category: nucleotide metabolism]]
-[[Category: substrate analogue]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:35:35 2007''