1eu5: Difference between revisions

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OCA

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-[[Image:1eu5.gif|left|200px]]<br /><applet load="1eu5" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1eu5, resolution 1.45&Aring;" />
-'''STRUCTURE OF E. COLI DUTPASE AT 1.45 A'''<br />
-==Overview==
+==STRUCTURE OF E. COLI DUTPASE AT 1.45 A==
-Cryocooled crystals of a mercury complex of Escherichia coli dUTPase, diffract to atomic resolution. Data to 1.05 A resolution were collected, from a derivative crystal and the structure model was derived from a, Fourier map with phases calculated from the coordinates of the Hg atom, (one site per subunit of the trimeric enzyme) using the program ARP/wARP., After refinement with anisotropic temperature factors a highly accurate, model of the bacterial dUTPase was obtained. Data to 1.45 A from a native, crystal were also collected and the 100 K structures were compared., Inspection of the refined models reveals that a large part of the dUTPase, remains rather mobile upon freezing, with 14% of the main chain being, totally disordered and with numerous side chains containing disordered, atoms in multiple discrete conformations. A large number of those residues, surround the active-site cavity. Two glycerol molecules (the cryosolvent), occupy the deoxyribose-binding site. Comparison between the native enzyme, and the mercury complex shows that the active site is not adversely, affected by the binding of mercury. An unexpected effect seems to be a, stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of, inhibitor-substrate-analogue complexes of this protein at very high, resolution.
+<StructureSection load='1eu5' size='340' side='right'caption='[[1eu5]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1eu5]] 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=1EU5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EU5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1eu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eu5 OCA], [https://pdbe.org/1eu5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eu5 RCSB], [https://www.ebi.ac.uk/pdbsum/1eu5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eu5 ProSAT]</span></td></tr>
+</table>
+== 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/eu/1eu5_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=1eu5 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-EU5 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 GOL 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=1EU5 OCA].
+*[[DUTPase 3D structures|DUTPase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Atomic resolution structure of Escherichia coli dUTPase determined ab initio., Gonzalez A, Larsson G, Persson R, Cedergren-Zeppezauer E, Acta Crystallogr D Biol Crystallogr. 2001 Jun;57(Pt 6):767-74. Epub 2001, May 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11375495 11375495]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: dUTP diphosphatase]]
+[[Category: Cedergren-Zeppezauer E]]
-[[Category: Cedergren-Zeppezauer, E.]]
+[[Category: Gonzalez A]]
-[[Category: Gonzalez, A.]]
+[[Category: Larsson G]]
-[[Category: Larsson, G.]]
+[[Category: Persson R]]
-[[Category: Persson, R.]]
-[[Category: GOL]]
-[[Category: distorted jelly roll]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:19:08 2007''