1icq: Difference between revisions

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-{{Seed}}
-[[Image:1icq.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO COMPLEXED WITH 9R,13R-OPDA==
-The line below this paragraph, containing "STRUCTURE_1icq", creates the "Structure Box" on the page.
+<StructureSection load='1icq' size='340' side='right'caption='[[1icq]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1icq]] 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=1ICQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ICQ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#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>, <scene name='pdbligand=OPD:9R,13R-12-OXOPHYTODIENOIC+ACID'>OPD</scene></td></tr>
-{{STRUCTURE_1icq|  PDB=1icq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1icq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1icq OCA], [https://pdbe.org/1icq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1icq RCSB], [https://www.ebi.ac.uk/pdbsum/1icq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1icq 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/1icq_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=1icq 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.
-===CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO COMPLEXED WITH 9R,13R-OPDA===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1icq" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11377202}}, adds the Publication Abstract to the page
+*[[12-oxophytodienoate reductase|12-oxophytodienoate reductase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11377202 is the PubMed ID number.
+*[[12-oxophytodienoate reductase 3D structures|12-oxophytodienoate reductase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_11377202}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-ICQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ICQ OCA].
+[[Category: Large Structures]]
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/11377202 11377202]
-[[Category: 12-oxophytodienoate reductase]]
-[[Category: Single protein]]
 [[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: Beta-alpha-barrel]]
-[[Category: Fmn-substrate-complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 10:46:09 2008''