1rrv

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(New page: 200px<br /><applet load="1rrv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rrv, resolution 2.0&Aring;" /> '''X-ray crystal structu...)
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[[Image:1rrv.gif|left|200px]]<br /><applet load="1rrv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rrv, resolution 2.0&Aring;" />
 
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'''X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.'''<br />
 
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==Overview==
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==X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.==
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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.
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<StructureSection load='1rrv' size='340' side='right'caption='[[1rrv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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&#8491;</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rr/1rrv_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1rrv ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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<ref>PMID:15122882</ref>
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1RRV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis] with K, DVV, TYD and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RRV OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15122882 15122882]
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</div>
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[[Category: Amycolatopsis orientalis]]
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<div class="pdbe-citations 1rrv" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Garavito, R.M.]]
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[[Category: Losey, H.C.]]
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[[Category: Lu, W.]]
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[[Category: Mulichak, A.M.]]
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[[Category: Walsh, C.T.]]
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[[Category: DVV]]
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[[Category: GOL]]
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[[Category: K]]
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[[Category: TYD]]
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[[Category: glycosyltransferase]]
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[[Category: gt-b]]
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[[Category: rossmann fold]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:10:24 2007''
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==See Also==
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*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Amycolatopsis orientalis]]
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[[Category: Large Structures]]
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[[Category: Garavito RM]]
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[[Category: Losey HC]]
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[[Category: Lu W]]
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[[Category: Mulichak AM]]
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[[Category: Walsh CT]]

Current revision

X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.

PDB ID 1rrv

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