2bgl: Difference between revisions
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==X- | |||
<StructureSection load='2bgl' size='340' side='right' caption='[[2bgl]], [[Resolution|resolution]] 2.80Å' scene=''> | ==X-Ray structure of binary-Secoisolariciresinol Dehydrogenase== | ||
<StructureSection load='2bgl' size='340' side='right'caption='[[2bgl]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2bgl]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2bgl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Podophyllum_peltatum Podophyllum peltatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BGL FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAJ:NICOTINAMIDE-ADENINE-DINUCLEOTIDE+(ACIDIC+FORM)'>NAJ</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bgl OCA], [https://pdbe.org/2bgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bgl RCSB], [https://www.ebi.ac.uk/pdbsum/2bgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bgl ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/SILD_PODPE SILD_PODPE] Oxidoreductase involved in lignan biosynthesis. Catalyzes the stereospecific conversion of (-)-secoisolariciresinol to (-)-matairesinol via a lactol intermediate.<ref>PMID:11278426</ref> <ref>PMID:16493463</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bg/2bgl_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bg/2bgl_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2bgl ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2bgl" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Podophyllum peltatum]] | [[Category: Podophyllum peltatum]] | ||
[[Category: Davin | [[Category: Davin LB]] | ||
[[Category: Kang | [[Category: Kang C]] | ||
[[Category: Lewis | [[Category: Lewis NG]] | ||
[[Category: Moinuddin | [[Category: Moinuddin SG]] | ||
[[Category: Youn | [[Category: Youn B]] | ||
Latest revision as of 16:35, 13 December 2023
X-Ray structure of binary-Secoisolariciresinol DehydrogenaseX-Ray structure of binary-Secoisolariciresinol Dehydrogenase
Structural highlights
FunctionSILD_PODPE Oxidoreductase involved in lignan biosynthesis. Catalyzes the stereospecific conversion of (-)-secoisolariciresinol to (-)-matairesinol via a lactol intermediate.[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(-)-Matairesinol is a central biosynthetic intermediate to numerous 8-8'-lignans, including the antiviral agent podophyllotoxin in Podophyllum species and its semi-synthetic anticancer derivatives teniposide, etoposide, and Etopophos. It is formed by action of an enantiospecific secoisolariciresinol dehydrogenase, an NAD(H)-dependent oxidoreductase that catalyzes the conversion of (-)-secoisolariciresinol. Matairesinol is also a plant-derived precursor of the cancer-preventative "mammalian" lignan or "phytoestrogen" enterolactone, formed in the gut following ingestion of high fiber dietary foodstuffs, for example. Additionally, secoisolariciresinol dehydrogenase is involved in pathways to important plant defense molecules, such as plicatic acid in the western red cedar (Thuja plicata) heartwood. To understand the molecular and enantiospecific basis of Podophyllum secoisolariciresinol dehydrogenase, crystal structures of the apo-form and binary/ternary complexes were determined at 1.6, 2.8, and 2.0 angstrom resolution, respectively. The enzyme is a homotetramer, consisting of an alpha/beta single domain monomer containing seven parallel beta-strands flanked by eight alpha-helices on both sides. Its overall monomeric structure is similar to that of NAD(H)-dependent short-chain dehydrogenases/reductases, with a conserved Asp47 forming a hydrogen bond with both hydroxyl groups of the adenine ribose of NAD(H), and thus specificity toward NAD(H) instead of NADP(H). The highly conserved catalytic triad (Ser153, Tyr167, and Lys171) is adjacent to both NAD(+) and substrate molecules, where Tyr167 functions as a general base. Following analysis of high resolution structures of the apo-form and two complex forms, the molecular basis for both the enantio-specificity and the reaction mechanism of secoisolariciresinol dehydrogenase is discussed and compared with that of pinoresinol-lariciresinol reductase. Crystal structures of apo-form and binary/ternary complexes of Podophyllum secoisolariciresinol dehydrogenase, an enzyme involved in formation of health-protecting and plant defense lignans.,Youn B, Moinuddin SG, Davin LB, Lewis NG, Kang C J Biol Chem. 2005 Apr 1;280(13):12917-26. Epub 2005 Jan 13. PMID:15653677[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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