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| | <StructureSection load='1rrv' size='340' side='right'caption='[[1rrv]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='1rrv' size='340' side='right'caption='[[1rrv]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1rrv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_orientalis"_pittenger_and_brigham_1956 "streptomyces orientalis" pittenger and brigham 1956] and [http://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1RRV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1rrv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RRV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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]] 2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3FG:(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC+ACID'>3FG</scene>, <scene name='pdbligand=GHP:(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC+ACID'>GHP</scene>, <scene name='pdbligand=MLU:N-METHYL-D-LEUCINE'>MLU</scene>, <scene name='pdbligand=OMY:(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE'>OMY</scene>, <scene name='pdbligand=OMZ:(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE'>OMZ</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3FG:(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC+ACID'>3FG</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GHP:(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC+ACID'>GHP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MLU:N-METHYL-D-LEUCINE'>MLU</scene>, <scene name='pdbligand=OMY:(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE'>OMY</scene>, <scene name='pdbligand=OMZ:(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE'>OMZ</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aa5|1aa5]], [[1c0q|1c0q]], [[1c0r|1c0r]], [[1fvm|1fvm]], [[1gac|1gac]], [[1ghg|1ghg]], [[1pn3|1pn3]], [[1pnv|1pnv]], [[1qd8|1qd8]], [[1sho|1sho]]</div></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=1rrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrv OCA], [https://pdbe.org/1rrv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rrv RCSB], [https://www.ebi.ac.uk/pdbsum/1rrv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrv ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GTFD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31958 "Streptomyces orientalis" Pittenger and Brigham 1956])</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=1rrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rrv OCA], [http://pdbe.org/1rrv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rrv RCSB], [http://www.ebi.ac.uk/pdbsum/1rrv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rrv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GTFD_AMYOR GTFD_AMYOR] Catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of glycopeptide antibiotic vancomycin biosynthesis.<ref>PMID:11294642</ref> <ref>PMID:15122882</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Streptomyces orientalis pittenger and brigham 1956]] | |
| | [[Category: Amycolatopsis orientalis]] | | [[Category: Amycolatopsis orientalis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Garavito, R M]] | + | [[Category: Garavito RM]] |
| - | [[Category: Losey, H C]] | + | [[Category: Losey HC]] |
| - | [[Category: Lu, W]] | + | [[Category: Lu W]] |
| - | [[Category: Mulichak, A M]] | + | [[Category: Mulichak AM]] |
| - | [[Category: Walsh, C T]] | + | [[Category: Walsh CT]] |
| - | [[Category: Antibiotic]]
| + | |
| - | [[Category: Glycopeptide]]
| + | |
| - | [[Category: Glycosyltransferase]]
| + | |
| - | [[Category: Gt-b]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Transferase-antibiotic complex]]
| + | |
| - | [[Category: Vacosamycin]]
| + | |
| Structural highlights
1rrv is a 4 chain structure with sequence from Amycolatopsis orientalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2Å |
| Ligands: | , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
GTFD_AMYOR Catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of glycopeptide antibiotic vancomycin biosynthesis.[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
The TDP-vancosaminyltransferase GtfD catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of vancomycin biosynthesis. Glycosyltransferases from this and similar antibiotic pathways are potential tools for the design of new compounds that are effective against vancomycin resistant bacterial strains. We have determined the X-ray crystal structure of GtfD as a complex with TDP and the natural glycopeptide substrate at 2.0 A resolution. GtfD, a member of the bidomain GT-B glycosyltransferase superfamily, binds TDP in the interdomain cleft, while the aglycone acceptor binds in a deep crevice in the N-terminal domain. However, the two domains are more interdependent in terms of substrate binding and overall structure than was evident in the structures of closely related glycosyltransferases GtfA and GtfB. Structural and kinetic analyses support the identification of Asp13 as a catalytic general base, with a possible secondary role for Thr10. Several residues have also been identified as being involved in donor sugar binding and recognition.
Crystal structure of vancosaminyltransferase GtfD from the vancomycin biosynthetic pathway: interactions with acceptor and nucleotide ligands.,Mulichak AM, Lu W, Losey HC, Walsh CT, Garavito RM Biochemistry. 2004 May 11;43(18):5170-80. PMID:15122882[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Losey HC, Peczuh MW, Chen Z, Eggert US, Dong SD, Pelczer I, Kahne D, Walsh CT. Tandem action of glycosyltransferases in the maturation of vancomycin and teicoplanin aglycones: novel glycopeptides. Biochemistry. 2001 Apr 17;40(15):4745-55. PMID:11294642 doi:10.1021/bi010050w
- ↑ Mulichak AM, Lu W, Losey HC, Walsh CT, Garavito RM. Crystal structure of vancosaminyltransferase GtfD from the vancomycin biosynthetic pathway: interactions with acceptor and nucleotide ligands. Biochemistry. 2004 May 11;43(18):5170-80. PMID:15122882 doi:10.1021/bi036130c
- ↑ Mulichak AM, Lu W, Losey HC, Walsh CT, Garavito RM. Crystal structure of vancosaminyltransferase GtfD from the vancomycin biosynthetic pathway: interactions with acceptor and nucleotide ligands. Biochemistry. 2004 May 11;43(18):5170-80. PMID:15122882 doi:10.1021/bi036130c
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