3v0n: Difference between revisions

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 ==Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-GalNAc derived inhibitor (3GW and 4GW)==
-<StructureSection load='3v0n' size='340' side='right' caption='[[3v0n]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='3v0n' size='340' side='right'caption='[[3v0n]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3v0n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V0N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V0N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3v0n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V0N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GW:5-(5-FORMYLTHIOPHEN-2-YL)URIDINE-5(2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GALACTOSYL)-DIPHOSPHATE'>3GW</scene>, <scene name='pdbligand=4GW:5-(5-FORMYLTHIOPHEN-2-YL)URIDINE+5-(TRIHYDROGEN+DIPHOSPHATE)'>4GW</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.75&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ioh|3ioh]], [[3ioi|3ioi]], [[3ioj|3ioj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GW:5-(5-FORMYLTHIOPHEN-2-YL)URIDINE-5(2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GALACTOSYL)-DIPHOSPHATE'>3GW</scene>, <scene name='pdbligand=4GW:5-(5-FORMYLTHIOPHEN-2-YL)URIDINE+5-(TRIHYDROGEN+DIPHOSPHATE)'>4GW</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AB0, ABO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3v0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v0n OCA], [https://pdbe.org/3v0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v0n RCSB], [https://www.ebi.ac.uk/pdbsum/3v0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v0n 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=3v0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v0n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v0n RCSB], [http://www.ebi.ac.uk/pdbsum/3v0n PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BGAT_HUMAN BGAT_HUMAN]] This protein is the basis of the ABO blood group system. The histo-blood group ABO involves three carbohydrate antigens: A, B, and H. A, B, and AB individuals express a glycosyltransferase activity that converts the H antigen to the A antigen (by addition of UDP-GalNAc) or to the B antigen (by addition of UDP-Gal), whereas O individuals lack such activity.
+[https://www.uniprot.org/uniprot/BGAT_HUMAN BGAT_HUMAN] This protein is the basis of the ABO blood group system. The histo-blood group ABO involves three carbohydrate antigens: A, B, and H. A, B, and AB individuals express a glycosyltransferase activity that converts the H antigen to the A antigen (by addition of UDP-GalNAc) or to the B antigen (by addition of UDP-Gal), whereas O individuals lack such activity.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Glycosyltransferases (GTs) are enzymes that are involved, as Nature's ''glycosylation reagents'', in many fundamental biological processes including cell adhesion and blood group biosynthesis. Although of similar importance as other large enzyme families such as protein kinases and proteases, the undisputed potential of GTs for chemical biology and drug discovery has remained largely unrealized to date. This is due, at least in part, to a relative lack of GT inhibitors and tool compounds for structural, mechanistic and cellular studies. In this study, we have used a novel class of GT donor analogues to obtain new structural and enzymological information for a representative blood group GT. These analogues interfere with the folding of an internal loop and the C-terminus which are essential for catalysis. Our experiments have led to the discovery of an entirely new active site folding mode for this enzyme family, which can be targeted in inhibitor development, similar to the DFG motif in protein kinases. Taken together, our results provide new insights into substrate binding, dynamics and utilization in this important enzyme family, which can very likely be harnessed for the rational development of new GT inhibitors and probes.
-Base-modified donor analogues reveal novel dynamic features of a glycosyltransferase.,Jorgensen R, Pesnot T, Lee HJ, Palcic MM, Wagner GK J Biol Chem. 2013 Jul 8. PMID:23836908<ref>PMID:23836908</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Jorgensen, R]]
+[[Category: Large Structures]]
-[[Category: Palcic, M M]]
+[[Category: Jorgensen R]]
-[[Category: Closed conformation]]
+[[Category: Palcic MM]]
-[[Category: Abo]]
-[[Category: Blood group antigen]]
-[[Category: Cisab mutant]]
-[[Category: Glycoprotein]]
-[[Category: Glycosylation]]
-[[Category: Glycosyltransferase]]
-[[Category: Golgi apparatus]]
-[[Category: Gta]]
-[[Category: Manganese]]
-[[Category: Metal-binding]]
-[[Category: Rossmann fold]]
-[[Category: Secreted]]
-[[Category: Signal-anchor]]
-[[Category: Transferase-transferase inhibitor complex]]
-[[Category: Transmembrane]]
-[[Category: Udp-galnac]]