1pn3: Difference between revisions

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-[[Image:1pn3.gif|left|200px]]
- {{Structure
+==Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV.==
-|PDB= 1pn3 |SIZE=350|CAPTION= <scene name='initialview01'>1pn3</scene>, resolution 2.8&Aring;
+<StructureSection load='1pn3' size='340' side='right'caption='[[1pn3]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DVV:DESVANCOSAMINYL+VANCOMYCIN'>DVV</scene>, <scene name='pdbligand=TYD:THYMIDINE-5&#39;-+DIPHOSPHATE'>TYD</scene>
+<table><tr><td colspan='2'>[[1pn3]] 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=1PN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PN3 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-|GENE= gtfA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31958 Amycolatopsis orientalis])
+<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=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>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pn3 OCA], [https://pdbe.org/1pn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pn3 RCSB], [https://www.ebi.ac.uk/pdbsum/1pn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pn3 ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pn3 OCA], [http://www.ebi.ac.uk/pdbsum/1pn3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pn3 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/GTFA_AMYOR GTFA_AMYOR] Catalyzes the attachment of 4-epi-vancosamine from a TDP donor to the beta-OH-Tyr-6 of the aglycone cosubstrate in the biosynthesis of glycopeptide antibiotic chloroeremomycin, a member of the vancomycin group of antibiotics. Strongly prefers devancoaminyl-vancomycin (DVV) as substrate rather than the heptapeptide vancomycin aglycone (AGV). Acts downstream of GtfB.<ref>PMID:15070728</ref> <ref>PMID:19549605</ref> <ref>PMID:9115410</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pn/1pn3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1pn3 ConSurf].
+<div style="clear:both"></div>
-'''Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV.'''
+==See Also==
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
+== References ==
-==Overview==
+<references/>
-During the biosynthesis of the vancomycin-class antibiotic chloroeremomycin, TDP-epi-vancosaminyltransferase GtfA catalyzes the attachment of 4-epi-vancosamine from a TDP donor to the beta-OHTyr-6 of the aglycone cosubstrate. Glycosyltransferases from this pathway are potential tools for the combinatorial design of new antibiotics that are effective against vancomycin-resistant bacterial strains. These enzymes are members of the GT-B glycosyltransferase superfamily, which share a homologous bidomain topology. We present the 2.8-A crystal structures of GtfA complexes with vancomycin and the natural monoglycosylated peptide substrate, representing the first direct observation of acceptor substrate binding among closely related glycosyltransferases. The acceptor substrates bind to the N-terminal domain such that the aglycone substrate's reactive hydroxyl group hydrogen bonds to the side chains of Ser-10 and Asp-13, thus identifying these as residues of potential catalytic importance. As well as an open form of the enzyme, the crystal structures have revealed a closed form in which a TDP ligand is bound at a donor substrate site in the interdomain cleft, thereby illustrating not only binding interactions, but the conformational changes in the enzyme that accompany substrate binding.
+__TOC__
+</StructureSection>
-==About this Structure==
-PN3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PN3 OCA].
-==Reference==
-Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway., Mulichak AM, Losey HC, Lu W, Wawrzak Z, Walsh CT, Garavito RM, Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9238-43. Epub 2003 Jul 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12874381 12874381]
 [[Category: Amycolatopsis orientalis]]
-[[Category: Single protein]]
+[[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: Wawrzak, Z.]]
+[[Category: Wawrzak Z]]
-[[Category: gt-b glycosyltransferase]]
-[[Category: rossmann fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:01:50 2008''