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| | <StructureSection load='2q3o' size='340' side='right'caption='[[2q3o]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='2q3o' size='340' side='right'caption='[[2q3o]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2q3o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2q3o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3O FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q45|1q45]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">OPR3, DDE1, At2g06050, F5K7.19 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/12-oxophytodienoate_reductase 12-oxophytodienoate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.42 1.3.1.42] </span></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=2q3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3o OCA], [https://pdbe.org/2q3o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3o RCSB], [https://www.ebi.ac.uk/pdbsum/2q3o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3o ProSAT]</span></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=2q3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3o OCA], [https://pdbe.org/2q3o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3o RCSB], [https://www.ebi.ac.uk/pdbsum/2q3o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3o ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/OPR3_ARATH OPR3_ARATH]] Specifically cleaves olefinic bonds in cyclic enones. Involved in the biosynthesis of jasmonic acid (JA) and perhaps in biosynthesis or metabolism of other oxylipin signaling moleclules. Required for the spatial and temporal regulation of JA levels during dehiscence of anthers, promoting the stomium degeneration program. In vitro, reduces 9S,13S-12-oxophytodienoic acid (9S,13S-OPDA) and 9R,13R-OPDA to 9S,13S-OPC-8:0 and 9R,13R-OPC-8:0, respectively. Can detoxify the explosive 2,4,6-trinitrotoluene (TNT) in vitro by catalyzing its nitroreduction to form hydroxylamino-dinitrotoluene (HADNT).<ref>PMID:10973494</ref> <ref>PMID:19605548</ref>
| + | [https://www.uniprot.org/uniprot/OPR3_ARATH OPR3_ARATH] Specifically cleaves olefinic bonds in cyclic enones. Involved in the biosynthesis of jasmonic acid (JA) and perhaps in biosynthesis or metabolism of other oxylipin signaling moleclules. Required for the spatial and temporal regulation of JA levels during dehiscence of anthers, promoting the stomium degeneration program. In vitro, reduces 9S,13S-12-oxophytodienoic acid (9S,13S-OPDA) and 9R,13R-OPDA to 9S,13S-OPC-8:0 and 9R,13R-OPC-8:0, respectively. Can detoxify the explosive 2,4,6-trinitrotoluene (TNT) in vitro by catalyzing its nitroreduction to form hydroxylamino-dinitrotoluene (HADNT).<ref>PMID:10973494</ref> <ref>PMID:19605548</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 12-oxophytodienoate reductase]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Arath]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Kondrashov DA]] |
| - | [[Category: Kondrashov, D A]] | + | [[Category: Levin EJ]] |
| - | [[Category: Levin, E J]] | + | [[Category: Phillips Jr GN]] |
| - | [[Category: Phillips, G N]] | + | [[Category: Wesenberg GE]] |
| - | [[Category: Wesenberg, G E]] | + | |
| - | [[Category: Cesg]]
| + | |
| - | [[Category: Ensemble refinement]]
| + | |
| - | [[Category: Flavoenzyme]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Old Yellow Enzyme]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Refinement methodology development]]
| + | |
| - | [[Category: Secondary messenger]]
| + | |
| - | [[Category: Xenobiotic reductase]]
| + | |
| Structural highlights
Function
OPR3_ARATH Specifically cleaves olefinic bonds in cyclic enones. Involved in the biosynthesis of jasmonic acid (JA) and perhaps in biosynthesis or metabolism of other oxylipin signaling moleclules. Required for the spatial and temporal regulation of JA levels during dehiscence of anthers, promoting the stomium degeneration program. In vitro, reduces 9S,13S-12-oxophytodienoic acid (9S,13S-OPDA) and 9R,13R-OPDA to 9S,13S-OPC-8:0 and 9R,13R-OPC-8:0, respectively. Can detoxify the explosive 2,4,6-trinitrotoluene (TNT) in vitro by catalyzing its nitroreduction to form hydroxylamino-dinitrotoluene (HADNT).[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.
Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Stintzi A, Browse J. The Arabidopsis male-sterile mutant, opr3, lacks the 12-oxophytodienoic acid reductase required for jasmonate synthesis. Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10625-30. PMID:10973494 doi:http://dx.doi.org/10.1073/pnas.190264497
- ↑ Beynon ER, Symons ZC, Jackson RG, Lorenz A, Rylott EL, Bruce NC. The role of oxophytodienoate reductases in the detoxification of the explosive 2,4,6-trinitrotoluene by Arabidopsis. Plant Physiol. 2009 Sep;151(1):253-61. doi: 10.1104/pp.109.141598. Epub 2009 Jul , 15. PMID:19605548 doi:http://dx.doi.org/10.1104/pp.109.141598
- ↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019
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