1opr: Difference between revisions

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-[[Image:1opr.jpg|left|200px]]<br /><applet load="1opr" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1opr, resolution 2.3&Aring;" />
-'''THE CRYSTAL STRUCTURE OF THE OROTATE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH OROTATE AND ALPHA-D-5-PHOSPHORIBOSYL-1-PYROPHOSPHATE'''<br />
-==Overview==
+==THE CRYSTAL STRUCTURE OF THE OROTATE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH OROTATE AND ALPHA-D-5-PHOSPHORIBOSYL-1-PYROPHOSPHATE==
-The three-dimensional structure of Salmonella typhimurium orotate, phosphoribosyltransferase (OPRTase) in complex with the ribose 5-phosphate, donor alpha-D-5--phosphoribosyl-1-pyrophosphate (PRPP) and the nitrogenous, base orotic acid has been solved and refined with X-ray diffraction data, extending to 2.3 A resolution to a crystallographic R-factor of 18.7%. The, complex was generated by carrying out catalysis in the crystal. Comparison, of this structure with the previously reported structure of the orotidine, 5'-monophosphate (OMP) complex [Scapin, G., Grubmeyer, C., and, Sacchettini, J. C. (1994) Biochemistry 33, 1287-1294] revealed that the, enzyme backbone undergoes only small movements. The most significant, differences occur near the active site, at Ala71-Gly74, with the largest, difference involving the side chains of Lys73, Val127-Ala133, the, 5'-phosphate binding loop, and a long, solvent-exposed loop at the dimer, interface. The position of the ribose moiety is, on the other hand, very, different in the OMP and PRPP.orotate complexes, with its anomeric carbon, moving approximately 7 A across the binding cavity. In the PRPP.orotate, complex the highly conserved acidic side chain of Asp124 interacts with, the ribose of PRPP, whereas there are no interactions of this aspartate, with the substrate in the OMP complex.
+<StructureSection load='1opr' size='340' side='right'caption='[[1opr]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1opr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OPR 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]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ORO:OROTIC+ACID'>ORO</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</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=1opr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1opr OCA], [https://pdbe.org/1opr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1opr RCSB], [https://www.ebi.ac.uk/pdbsum/1opr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1opr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYRE_SALTY PYRE_SALTY] Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP) (By similarity).<ref>PMID:2271660</ref>
+== 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/op/1opr_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=1opr ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-OPR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with MG, ORO and PRP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Orotate_phosphoribosyltransferase Orotate phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.10 2.4.2.10] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OPR OCA].
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
+== References ==
-==Reference==
+<references/>
-The crystal structure of the orotate phosphoribosyltransferase complexed with orotate and alpha-D-5-phosphoribosyl-1-pyrophosphate., Scapin G, Ozturk DH, Grubmeyer C, Sacchettini JC, Biochemistry. 1995 Aug 29;34(34):10744-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7545004 7545004]
+__TOC__
-[[Category: Orotate phosphoribosyltransferase]]
+</StructureSection>
-[[Category: Salmonella typhimurium]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Sacchettini, J.C.]]
+[[Category: Sacchettini JC]]
-[[Category: Scapin, G.]]
+[[Category: Scapin G]]
-[[Category: MG]]
-[[Category: ORO]]
-[[Category: PRP]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:05:32 2007''