4f96: Difference between revisions

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 ==Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP==
-<StructureSection load='4f96' size='340' side='right' caption='[[4f96]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+<StructureSection load='4f96' size='340' side='right'caption='[[4f96]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4f96]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_hygroscopicus_subsp._limoneus"_shibata_et_al._1973 "streptomyces hygroscopicus subsp. limoneus" shibata et al. 1973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F96 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4f96]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_hygroscopicus_subsp._limoneus Streptomyces hygroscopicus subsp. limoneus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F96 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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]] 2.152&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vdm|3vdm]], [[3vdn|3vdn]], [[4f97|4f97]], [[4f9f|4f9f]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vldE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264445 "Streptomyces hygroscopicus subsp. limoneus" Shibata et al. 1973])</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=4f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f96 OCA], [https://pdbe.org/4f96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f96 RCSB], [https://www.ebi.ac.uk/pdbsum/4f96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f96 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4f96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f96 OCA], [http://pdbe.org/4f96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f96 RCSB], [http://www.ebi.ac.uk/pdbsum/4f96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f96 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/VLDE_STRHL VLDE_STRHL] Involved in the biosynthesis of the antifungal agent validamycin A (PubMed:16725283). Catalyzes the condensation between GDP-valienol and validamine 7-phosphate via a nonglycosidic C-N bond formation to yield validoxylamine A 7'-phosphate (PubMed:21766819).<ref>PMID:16725283</ref> <ref>PMID:21766819</ref>
-The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7'-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7'-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an "open" and "closed" conformation is also described. With these structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol.
-Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex.,Cavalier MC, Yim YS, Asamizu S, Neau D, Almabruk KH, Mahmud T, Lee YH PLoS One. 2012;7(9):e44934. doi: 10.1371/journal.pone.0044934. Epub 2012 Sep 13. PMID:23028689<ref>PMID:23028689</ref>
+==See Also==
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4f96" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Streptomyces hygroscopicus subsp. limoneus shibata et al. 1973]]
+[[Category: Large Structures]]
-[[Category: Almabruk, K H]]
+[[Category: Streptomyces hygroscopicus subsp. limoneus]]
-[[Category: Asamizu, S]]
+[[Category: Almabruk KH]]
-[[Category: Cavalier, M C]]
+[[Category: Asamizu S]]
-[[Category: Lee, Y H]]
+[[Category: Cavalier MC]]
-[[Category: Mahmud, T]]
+[[Category: Lee Y-H]]
-[[Category: Neau, D]]
+[[Category: Mahmud T]]
-[[Category: Yim, Y S]]
+[[Category: Neau D]]
-[[Category: Transferase]]
+[[Category: Yim Y-S]]
-[[Category: Twin rossman fold]]