3dff: Difference between revisions

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-{{Seed}}
-[[Image:3dff.jpg|left|200px]]
-<!--
+==The crystal structure of teicoplanin pseudoaglycone deacetylase Orf2==
-The line below this paragraph, containing "STRUCTURE_3dff", creates the "Structure Box" on the page.
+<StructureSection load='3dff' size='340' side='right'caption='[[3dff]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3dff]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinoplanes_teichomyceticus Actinoplanes teichomyceticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DFF FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3dff|  PDB=3dff  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dff OCA], [https://pdbe.org/3dff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dff RCSB], [https://www.ebi.ac.uk/pdbsum/3dff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dff ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6ZZJ1_ACTTI Q6ZZJ1_ACTTI]
+== 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/df/3dff_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3dff ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Crystal Structures of Lipoglycopeptide Antibiotic Deacetylases: Implications for the Biosynthesis of A40926 and Teicoplanin===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18559264}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3dff" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18559264 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18559264}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DFF 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=3DFF OCA].
-==Reference==
-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]
 [[Category: Actinoplanes teichomyceticus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Brunzelle, J S.]]
+[[Category: Brunzelle JS]]
-[[Category: Nair, S K.]]
+[[Category: Nair SK]]
-[[Category: Zou, Y.]]
+[[Category: Zou Y]]
-[[Category: Deacetylase]]
-[[Category: Hydrolase]]
-[[Category: Lipoglycopeptide]]
-[[Category: Pseudoaglycone]]
-[[Category: Zinc dependent]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 11:52:32 2008''