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3dfk

From Proteopedia

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{{Seed}}
 
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[[Image:3dfk.png|left|200px]]
 
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<!--
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==The crystal structure of teicoplanin pseudoaglycone deacetylase Orf2* bound to one of its products decanoic acid==
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The line below this paragraph, containing "STRUCTURE_3dfk", creates the "Structure Box" on the page.
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<StructureSection load='3dfk' size='340' side='right'caption='[[3dfk]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3dfk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinoplanes_teichomyceticus"_parenti_et_al._1978 "actinoplanes teichomyceticus" parenti et al. 1978]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DFK FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DKA:DECANOIC+ACID'>DKA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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-->
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_3dfk| PDB=3dfk | SCENE= }}
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dff|3dff]], [[3dfi|3dfi]], [[3dfm|3dfm]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tcp14 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1867 "Actinoplanes teichomyceticus" Parenti et al. 1978])</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=3dfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dfk OCA], [https://pdbe.org/3dfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dfk RCSB], [https://www.ebi.ac.uk/pdbsum/3dfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dfk ProSAT]</span></td></tr>
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</table>
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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/df/3dfk_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=3dfk 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 lipoglycopeptide antibiotics teicoplanin and A40926 have proven efficacy against Gram-positive pathogens. These drugs are distinguished from glycopeptide antibiotics by N-linked long chain acyl-D-glucosamine decorations that contribute to antibacterial efficacy. During the biosynthesis of lipoglycopeptides, tailoring glycosyltransferases attach an N-acetyl-D-glucosamine to the aglycone, and this N-acetyl-glucosaminyl pseudoaglycone is deacetylated prior to long chain hydrocarbon attachment. Here we present several high-resolution crystal structures of the pseudoaglycone deacetylases from the biosynthetic pathways of teicoplanin and A40926. The cocrystal structure of the teicoplanin pseudoaglycone deacetylase with a fatty acid product provides further insights into the roles of active-site residues, and suggests mechanistic similarities with structurally distinct zinc deacetylases, such as peptidoglycan deacetylase and LpxC. A unique, structurally mobile capping lid, located at the apex of these pseudoaglycone deacetylases, likely serves as a determinant of substrate specificity.
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===The crystal structure of teicoplanin pseudoaglycone deacetylase Orf2* bound to one of its products decanoic acid===
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Crystal structures of lipoglycopeptide antibiotic deacetylases: implications for the biosynthesis of A40926 and teicoplanin.,Zou Y, Brunzelle JS, Nair SK Chem Biol. 2008 Jun;15(6):533-45. PMID:18559264<ref>PMID:18559264</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<!--
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18559264}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3dfk" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18559264 is the PubMed ID number.
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== References ==
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-->
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<references/>
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{{ABSTRACT_PUBMED_18559264}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Actinoplanes teichomyceticus parenti et al. 1978]]
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3DFK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Actinoplanes_teichomyceticus Actinoplanes teichomyceticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DFK OCA].
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[[Category: Large Structures]]
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[[Category: Brunzelle, J S]]
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==Reference==
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[[Category: Nair, S K]]
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Crystal structures of lipoglycopeptide antibiotic deacetylases: implications for the biosynthesis of A40926 and teicoplanin., Zou Y, Brunzelle JS, Nair SK, Chem Biol. 2008 Jun;15(6):533-45. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18559264 18559264]
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[[Category: Zou, Y]]
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[[Category: Actinoplanes teichomyceticus]]
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[[Category: Single protein]]
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[[Category: Brunzelle, J S.]]
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[[Category: Nair, S K.]]
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[[Category: Zou, Y.]]
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[[Category: Alpha-beta single domain]]
[[Category: Alpha-beta single domain]]
[[Category: Bound to decanoic acid]]
[[Category: Bound to decanoic acid]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 30 09:33:34 2008''
 

Current revision

The crystal structure of teicoplanin pseudoaglycone deacetylase Orf2* bound to one of its products decanoic acid

PDB ID 3dfk

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