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| | <StructureSection load='5lal' size='340' side='right'caption='[[5lal]], [[Resolution|resolution]] 1.40Å' scene=''> | | <StructureSection load='5lal' size='340' side='right'caption='[[5lal]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5lal]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LAL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LAL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5lal]] 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=5LAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LAL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 1.4Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DIR6, At4g23690, F9D16.160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5lal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lal OCA], [http://pdbe.org/5lal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lal RCSB], [http://www.ebi.ac.uk/pdbsum/5lal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lal 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=5lal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lal OCA], [https://pdbe.org/5lal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lal RCSB], [https://www.ebi.ac.uk/pdbsum/5lal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lal ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DIR6_ARATH DIR6_ARATH]] Dirigent proteins impart stereoselectivity on the phenoxy radical-coupling reaction, yielding optically active lignans from two molecules of coniferyl alcohol in the biosynthesis of lignans, flavonolignans, and alkaloids and thus plays a central role in plant secondary metabolism. Enantiocomplementary dirigent protein that mediates the laccase-catalyzed enantioselective oxidative phenol coupling of (E)-coniferyl alcohol to (-)-pinoresinol.<ref>PMID:19946920</ref> <ref>PMID:22854967</ref> | + | [https://www.uniprot.org/uniprot/DIR6_ARATH DIR6_ARATH] Dirigent proteins impart stereoselectivity on the phenoxy radical-coupling reaction, yielding optically active lignans from two molecules of coniferyl alcohol in the biosynthesis of lignans, flavonolignans, and alkaloids and thus plays a central role in plant secondary metabolism. Enantiocomplementary dirigent protein that mediates the laccase-catalyzed enantioselective oxidative phenol coupling of (E)-coniferyl alcohol to (-)-pinoresinol.<ref>PMID:19946920</ref> <ref>PMID:22854967</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Effenberger, I]] | + | [[Category: Effenberger I]] |
| - | [[Category: Gasper, R]] | + | [[Category: Gasper R]] |
| - | [[Category: Hofmann, E]] | + | [[Category: Hofmann E]] |
| - | [[Category: Kolesinski, P]] | + | [[Category: Kolesinski P]] |
| - | [[Category: Schaller, A]] | + | [[Category: Schaller A]] |
| - | [[Category: Terlecka, B]] | + | [[Category: Terlecka B]] |
| - | [[Category: All beta]]
| + | |
| - | [[Category: Plant protein]]
| + | |
| - | [[Category: Protein binding]]
| + | |
| Structural highlights
5lal is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.4Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
DIR6_ARATH Dirigent proteins impart stereoselectivity on the phenoxy radical-coupling reaction, yielding optically active lignans from two molecules of coniferyl alcohol in the biosynthesis of lignans, flavonolignans, and alkaloids and thus plays a central role in plant secondary metabolism. Enantiocomplementary dirigent protein that mediates the laccase-catalyzed enantioselective oxidative phenol coupling of (E)-coniferyl alcohol to (-)-pinoresinol.[1] [2]
Publication Abstract from PubMed
Dirigent proteins impart stereoselectivity to phenoxy radical coupling reactions in plants and, thus, play an essential role in the biosynthesis of biologically active natural products. This includes the regioselective and enantioselective coupling and subsequent cyclization of two coniferyl alcohol radicals to pinoresinol as the committed step of lignan biosynthesis. The reaction is controlled by dirigent proteins, which, depending on the species and protein, direct the reaction to either (+)- or (-)-pinoresinol. We present the crystal structure of the (-)-pinoresinol forming DIRIGENT PROTEIN6 (AtDIR6) from Arabidopsis (Arabidopsis thaliana) with data to 1.4 A resolution. The structure shows AtDIR6 as an eight-stranded antiparallel beta-barrel that forms a trimer with spatially well-separated cavities for substrate binding. The binding cavities are two lobed, exhibiting two opposing pockets, each lined with a set of hydrophilic and potentially catalytic residues, including essential aspartic acids. These residues are conserved between (+) and (-)-pinoresinol-forming DIRs and required for activity. The structure supports a model in which two substrate radicals bind to each of the DIR monomers. With the aromatic rings fixed in the two pockets, the propionyl side chains face each other for radical-radical coupling, and stereoselectivity is determined by the exact positioning of the side chains. Extensive mutational analysis supports a previously unrecognized function for DIRs in catalyzing the cyclization of the bis-quinone methide reaction intermediate to yield (+)- or (-)-pinoresinol.
Dirigent Protein Mode of Action Revealed by the Crystal Structure of AtDIR6.,Gasper R, Effenberger I, Kolesinski P, Terlecka B, Hofmann E, Schaller A Plant Physiol. 2016 Dec;172(4):2165-2175. Epub 2016 Oct 17. PMID:27756822[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Pickel B, Constantin MA, Pfannstiel J, Conrad J, Beifuss U, Schaller A. An enantiocomplementary dirigent protein for the enantioselective laccase-catalyzed oxidative coupling of phenols. Angew Chem Int Ed Engl. 2010;49(1):202-4. doi: 10.1002/anie.200904622. PMID:19946920 doi:http://dx.doi.org/10.1002/anie.200904622
- ↑ Kim KW, Moinuddin SG, Atwell KM, Costa MA, Davin LB, Lewis NG. Opposite stereoselectivities of dirigent proteins in Arabidopsis and schizandra species. J Biol Chem. 2012 Oct 5;287(41):33957-72. doi: 10.1074/jbc.M112.387423. Epub 2012, Aug 1. PMID:22854967 doi:http://dx.doi.org/10.1074/jbc.M112.387423
- ↑ Gasper R, Effenberger I, Kolesinski P, Terlecka B, Hofmann E, Schaller A. Dirigent Protein Mode of Action Revealed by the Crystal Structure of AtDIR6. Plant Physiol. 2016 Dec;172(4):2165-2175. Epub 2016 Oct 17. PMID:27756822 doi:http://dx.doi.org/10.1104/pp.16.01281
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