1ics: Difference between revisions

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-[[Image:1ics.jpg|left|200px]]<br /><applet load="1ics" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ics, resolution 2.3&Aring;" />
-'''CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO==
-BACKGROUND: 12-Oxophytodienoate reductase (OPR) is a flavin mononucleotide, (FMN)-dependent oxidoreductase in plants that belongs to the family of Old, Yellow Enzyme (OYE). It was initially characterized as an enzyme involved, in the biosynthesis of the plant hormone jasmonic acid, where it catalyzes, the reduction of the cyclic fatty acid derivative, 9S,13S-12-oxophytodienoate (9S,13S-OPDA) to, 1S,2S-3-oxo-2(2'[Z]-pentenyl)-cyclopentane-1-octanoate. Several isozymes, of OPR are now known that show different stereoselectivities with regard, to the four stereoisomers of OPDA. RESULTS: Here, we report the, high-resolution crystal structure of OPR1 from Lycopersicon esculentum and, its complex structures with the substrate 9R,13R-OPDA and with, polyethylene glycol 400. OPR1 crystallizes as a monomer and folds into a, (betaalpha)(8) barrel with an overall structure similar to OYE. The, cyclopentenone ring of 9R,13R-OPDA is stacked above the flavin and, activated by two hydrogen bonds to His187 and His190. The olefinic bond is, properly positioned for hydride transfer from the FMN N(5) and proton, transfer from Tyr192 to Cbeta and Calpha, respectively. Comparison of the, OPR1 and OYE structures reveals striking differences in the loops, responsible for binding 9R,13R-OPDA in OPR1. CONCLUSIONS: Despite, extensive biochemical characterization, the physiological function of OYE, still remains unknown. The similar catalytic cavity structures and the, substrate binding mode in OPR1 strongly support the assumption that, alpha,beta-unsaturated carbonyl compounds are physiological substrates of, the OYE family. The specific binding of 9R,13R-OPDA by OPR1 explains the, experimentally observed stereoselectivity and argues in favor of, 9R,13R-OPDA or a structurally related oxylipin as natural substrate of, OPR1.
+<StructureSection load='1ics' size='340' side='right'caption='[[1ics]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ics]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ICS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ICS 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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=1ics FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ics OCA], [https://pdbe.org/1ics PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ics RCSB], [https://www.ebi.ac.uk/pdbsum/1ics PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ics ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OPR1_SOLLC OPR1_SOLLC] Specifically cleaves olefinic bonds in alpha,beta-unsaturated carbonyls and may be involved in detoxification or modification of these reactive compounds. May be involved in the biosynthesis or metabolism of oxylipin signaling molecules. In vitro, reduces 9R,13R-12-oxophyodienoic acid (9R,13R-OPDA) to 9R,13R-OPC-8:0, but not 9S,13S-OPDA, the natural precursor of jasmonic acid. Also reduces N-ethylmaleimide and maleic acid.<ref>PMID:12445129</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/ic/1ics_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=1ics ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: 12-Oxophytodienoate reductase (OPR) is a flavin mononucleotide (FMN)-dependent oxidoreductase in plants that belongs to the family of Old Yellow Enzyme (OYE). It was initially characterized as an enzyme involved in the biosynthesis of the plant hormone jasmonic acid, where it catalyzes the reduction of the cyclic fatty acid derivative 9S,13S-12-oxophytodienoate (9S,13S-OPDA) to 1S,2S-3-oxo-2(2'[Z]-pentenyl)-cyclopentane-1-octanoate. Several isozymes of OPR are now known that show different stereoselectivities with regard to the four stereoisomers of OPDA. RESULTS: Here, we report the high-resolution crystal structure of OPR1 from Lycopersicon esculentum and its complex structures with the substrate 9R,13R-OPDA and with polyethylene glycol 400. OPR1 crystallizes as a monomer and folds into a (betaalpha)(8) barrel with an overall structure similar to OYE. The cyclopentenone ring of 9R,13R-OPDA is stacked above the flavin and activated by two hydrogen bonds to His187 and His190. The olefinic bond is properly positioned for hydride transfer from the FMN N(5) and proton transfer from Tyr192 to Cbeta and Calpha, respectively. Comparison of the OPR1 and OYE structures reveals striking differences in the loops responsible for binding 9R,13R-OPDA in OPR1. CONCLUSIONS: Despite extensive biochemical characterization, the physiological function of OYE still remains unknown. The similar catalytic cavity structures and the substrate binding mode in OPR1 strongly support the assumption that alpha,beta-unsaturated carbonyl compounds are physiological substrates of the OYE family. The specific binding of 9R,13R-OPDA by OPR1 explains the experimentally observed stereoselectivity and argues in favor of 9R,13R-OPDA or a structurally related oxylipin as natural substrate of OPR1.
-==About this Structure==
+X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.,Breithaupt C, Strassner J, Breitinger U, Huber R, Macheroux P, Schaller A, Clausen T Structure. 2001 May 9;9(5):419-29. PMID:11377202<ref>PMID:11377202</ref>
-ICS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum] with FMN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/12-oxophytodienoate_reductase 12-oxophytodienoate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.42 1.3.1.42] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ICS OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE., Breithaupt C, Strassner J, Breitinger U, Huber R, Macheroux P, Schaller A, Clausen T, Structure. 2001 May 9;9(5):419-29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11377202 11377202]
+</div>
-[[Category: 12-oxophytodienoate reductase]]
+<div class="pdbe-citations 1ics" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+==See Also==
+*[[12-oxophytodienoate reductase 3D structures|12-oxophytodienoate reductase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Solanum lycopersicum]]
-[[Category: Breithaupt, C.]]
+[[Category: Breithaupt C]]
-[[Category: Breitinger, U.]]
+[[Category: Breitinger U]]
-[[Category: Clausen, T.]]
+[[Category: Clausen T]]
-[[Category: Huber, R.]]
+[[Category: Huber R]]
-[[Category: Macheroux, P.]]
+[[Category: Macheroux P]]
-[[Category: Schaller, A.]]
+[[Category: Schaller A]]
-[[Category: Strassner, J.]]
+[[Category: Strassner J]]
-[[Category: FMN]]
-[[Category: beta-alpha-barrel]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:17:27 2007''