1pn3: Difference between revisions

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<StructureSection load='1pn3' size='340' side='right'caption='[[1pn3]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='1pn3' size='340' side='right'caption='[[1pn3]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1pn3]] 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=1PN3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PN3 FirstGlance]. <br>
<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>
</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=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]] 2.8&#8491;</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=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]], [[1pnv|1pnv]], [[1qd8|1qd8]], [[1rrv|1rrv]], [[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=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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GTFA ([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=1pn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pn3 OCA], [http://pdbe.org/1pn3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pn3 RCSB], [http://www.ebi.ac.uk/pdbsum/1pn3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pn3 ProSAT]</span></td></tr>
</table>
</table>
== 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1pn3 ConSurf].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:12874381<ref>PMID:12874381</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1pn3" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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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: Wawrzak, Z]]
[[Category: Wawrzak Z]]
[[Category: Antibiotic]]
[[Category: Glycopeptide]]
[[Category: Gt-b glycosyltransferase]]
[[Category: Rossmann fold]]
[[Category: Transferase-antibiotic complex]]
[[Category: Vancomycin]]

Latest revision as of 08:57, 17 April 2024

Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV.Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV.

Structural highlights

1pn3 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 2.8Å
Ligands:, , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] [3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Lu W, Oberthür M, Leimkuhler C, Tao J, Kahne D, Walsh CT. Characterization of a regiospecific epivancosaminyl transferase GtfA and enzymatic reconstitution of the antibiotic chloroeremomycin. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4390-5. PMID:15070728 doi:10.1073/pnas.0400277101
  2. ↑ Truman AW, Dias MV, Wu S, Blundell TL, Huang F, Spencer JB. Chimeric glycosyltransferases for the generation of hybrid glycopeptides. Chem Biol. 2009 Jun 26;16(6):676-85. PMID:19549605 doi:S1074-5521(09)00178-1
  3. ↑ Solenberg PJ, Matsushima P, Stack DR, Wilkie SC, Thompson RC, Baltz RH. Production of hybrid glycopeptide antibiotics in vitro and in Streptomyces toyocaensis. Chem Biol. 1997 Mar;4(3):195-202. PMID:9115410 doi:10.1016/s1074-5521(97)90288-x

1pn3, resolution 2.80Å

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