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| | ==Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with uridine-diphosphate (UDP) - GpgS*UDP== | | ==Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with uridine-diphosphate (UDP) - GpgS*UDP== |
| - | <StructureSection load='5jud' size='340' side='right' caption='[[5jud]], [[Resolution|resolution]] 2.59Å' scene=''> | + | <StructureSection load='5jud' size='340' side='right'caption='[[5jud]], [[Resolution|resolution]] 2.59Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5jud]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycbo Mycbo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JUD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JUD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5jud]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_variant_bovis_AF2122/97 Mycobacterium tuberculosis variant bovis AF2122/97]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JUD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 2.59Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5juc|5juc]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gpgS, Mb1240 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=233413 MYCBO])</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=5jud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jud OCA], [https://pdbe.org/5jud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jud RCSB], [https://www.ebi.ac.uk/pdbsum/5jud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jud ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucosyl-3-phosphoglycerate_synthase Glucosyl-3-phosphoglycerate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.266 2.4.1.266] </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=5jud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jud OCA], [http://pdbe.org/5jud PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jud RCSB], [http://www.ebi.ac.uk/pdbsum/5jud PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jud ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GPGS_MYCBO GPGS_MYCBO]] Involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs). Catalyzes the condensation of NDP-glucose and 3-phospho-glycerate (3-PGA) to yield glucosyl-3-phosphoglycerate (GPG). It can use UDP-glucose, ADP-glucose and GDP-glucose as donor substrates with decreasing affinity, and 3-PGA as an acceptor. D-glycerate could only be the acceptor with ADP-glucose and at a very low rate.<ref>PMID:18221489</ref> | + | [https://www.uniprot.org/uniprot/GPGS_MYCBO GPGS_MYCBO] Involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs). Catalyzes the condensation of NDP-glucose and 3-phospho-glycerate (3-PGA) to yield glucosyl-3-phosphoglycerate (GPG). It can use UDP-glucose, ADP-glucose and GDP-glucose as donor substrates with decreasing affinity, and 3-PGA as an acceptor. D-glycerate could only be the acceptor with ADP-glucose and at a very low rate.<ref>PMID:18221489</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: Glucosyl-3-phosphoglycerate synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Mycbo]] | + | [[Category: Mycobacterium tuberculosis variant bovis AF2122/97]] |
| - | [[Category: Albesa-Jove, D]] | + | [[Category: Albesa-Jove D]] |
| - | [[Category: Arrasate, P]] | + | [[Category: Arrasate P]] |
| - | [[Category: Carreras-Gonzalez, A]] | + | [[Category: Carreras-Gonzalez A]] |
| - | [[Category: Comino, N]] | + | [[Category: Comino N]] |
| - | [[Category: Guerin, M E]] | + | [[Category: Guerin ME]] |
| - | [[Category: Rodrigo-Unzueta, A]] | + | [[Category: Rodrigo-Unzueta A]] |
| - | [[Category: Sancho-Vaello, E]] | + | [[Category: Sancho-Vaello E]] |
| - | [[Category: Urresti, S]] | + | [[Category: Urresti S]] |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
GPGS_MYCBO Involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs). Catalyzes the condensation of NDP-glucose and 3-phospho-glycerate (3-PGA) to yield glucosyl-3-phosphoglycerate (GPG). It can use UDP-glucose, ADP-glucose and GDP-glucose as donor substrates with decreasing affinity, and 3-PGA as an acceptor. D-glycerate could only be the acceptor with ADP-glucose and at a very low rate.[1]
Publication Abstract from PubMed
Glycosyltransferases (GTs) play a central role in nature. They catalyze the transfer of a sugar moiety to a broad range of acceptor substrates. GTs are highly selective enzymes, allowing the recognition of subtle structural differences in the sequences and stereochemistry of their sugar and acceptor substrates. We report here a series of structural snapshots of the reaction center of the retaining glucosyl-3-phosphoglycerate synthase (GpgS). During this sequence of events, we visualize how the enzyme guides the substrates into the reaction center where the glycosyl transfer reaction takes place, and unveil the mechanism of product release, involving multiple conformational changes not only in the substrates/products but also in the enzyme. The structural data are further complemented by metadynamics free-energy calculations, revealing how the equilibrium of loop conformations is modulated along these itineraries. The information reported here represent an important contribution for the understanding of GT enzymes at the molecular level.
Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS.,Albesa-Jove D, Romero-Garcia J, Sancho-Vaello E, Contreras FX, Rodrigo-Unzueta A, Comino N, Carreras-Gonzalez A, Arrasate P, Urresti S, Biarnes X, Planas A, Guerin ME Structure. 2017 Jul 5;25(7):1034-1044.e3. doi: 10.1016/j.str.2017.05.009. Epub, 2017 Jun 15. PMID:28625787[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Empadinhas N, Albuquerque L, Mendes V, Macedo-Ribeiro S, da Costa MS. Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase. FEMS Microbiol Lett. 2008 Mar;280(2):195-202. Epub 2008 Jan 24. PMID:18221489 doi:10.1111/j.1574-6968.2007.01064.x
- ↑ Albesa-Jove D, Romero-Garcia J, Sancho-Vaello E, Contreras FX, Rodrigo-Unzueta A, Comino N, Carreras-Gonzalez A, Arrasate P, Urresti S, Biarnes X, Planas A, Guerin ME. Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS. Structure. 2017 Jul 5;25(7):1034-1044.e3. doi: 10.1016/j.str.2017.05.009. Epub, 2017 Jun 15. PMID:28625787 doi:http://dx.doi.org/10.1016/j.str.2017.05.009
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