1rn8: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1rn8.gif|left|200px]]
- {{Structure
+==Crystal structure of dUTPase complexed with substrate analogue imido-dUTP==
-|PDB= 1rn8 |SIZE=350|CAPTION= <scene name='initialview01'>1rn8</scene>, resolution 1.93&Aring;
+<StructureSection load='1rn8' size='340' side='right'caption='[[1rn8]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DUP:2&#39;-DEOXYURIDINE+5&#39;-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
+<table><tr><td colspan='2'>[[1rn8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RN8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RN8 FirstGlance]. <br>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</td></tr>
-|GENE= DUT, DNAS, SOF, B3640 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rn8 OCA], [https://pdbe.org/1rn8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rn8 RCSB], [https://www.ebi.ac.uk/pdbsum/1rn8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rn8 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1rnj|1RNJ]], [[1ro1|1RO1]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rn8 OCA], [http://www.ebi.ac.uk/pdbsum/1rn8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rn8 RCSB]</span>
+== Function ==
-}}
+[https://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/rn/1rn8_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=1rn8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-'''Crystal structure of dUTPase complexed with substrate analogue imido-dUTP'''
+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<ref>PMID:15208312</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1rn8" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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 3D structures|DUTPase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-RN8 is a [[Single protein]] structure of 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=1RN8 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/15208312 15208312]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: dUTP diphosphatase]]
+[[Category: Barabas O]]
-[[Category: Barabas, O.]]
+[[Category: Kovari J]]
-[[Category: Kovari, J.]]
+[[Category: Pongracz V]]
-[[Category: Pongracz, V.]]
+[[Category: Vertessy BG]]
-[[Category: Vertessy, B G.]]
+[[Category: Wilmanns M]]
-[[Category: Wilmanns, M.]]
-[[Category: enzyme-ligand complex]]
-[[Category: jelly roll]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:30:24 2008''