2bue: Difference between revisions

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-{{Seed}}
-[[Image:2bue.png|left|200px]]
-<!--
+==Structure of AAC(6')-Ib in complex with Ribostamycin and Coenzyme A.==
-The line below this paragraph, containing "STRUCTURE_2bue", creates the "Structure Box" on the page.
+<StructureSection load='2bue' size='340' side='right'caption='[[2bue]], [[Resolution|resolution]] 1.70&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'>[[2bue]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BUE FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=RIO:RIBOSTAMYCIN'>RIO</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;'>[[2vqy|2vqy]], [[1v0c|1v0c]]</div></td></tr>
-{{STRUCTURE_2bue|  PDB=2bue  |  SCENE=  }}
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aminoglycoside_N(6')-acetyltransferase Aminoglycoside N(6')-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.82 2.3.1.82] </span></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=2bue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bue OCA], [https://pdbe.org/2bue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bue RCSB], [https://www.ebi.ac.uk/pdbsum/2bue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bue ProSAT]</span></td></tr>
+</table>
+== 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/bu/2bue_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=2bue ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Enzymatic modification of aminoglycoside antibiotics mediated by regioselective aminoglycoside N-acetyltransferases is the predominant cause of bacterial resistance to aminoglycosides. A recently discovered bifunctional aminoglycoside acetyltransferase (AAC(6')-Ib variant, AAC(6')-Ib-cr) has been shown to catalyze the acetylation of fluoroquinolones as well as aminoglycosides. We have expressed and purified AAC(6')-Ib-wt and its bifunctional variant AAC(6')-Ib-cr in Escherichia coli and characterized their kinetic and chemical mechanism. Initial velocity and dead-end inhibition studies support an ordered sequential mechanism for the enzyme(s). The three-dimensional structure of AAC(6')-Ib-wt was determined in various complexes with donor and acceptor ligands to resolutions greater than 2.2 A. Observation of the direct, and optimally positioned, interaction between the 6'-NH 2 and Asp115 suggests that Asp115 acts as a general base to accept a proton in the reaction. The structure of AAC(6')-Ib-wt permits the construction of a molecular model of the interactions of fluoroquinolones with the AAC(6')-Ib-cr variant. The model suggests that a major contribution to the fluoroquinolone acetylation activity comes from the Asp179Tyr mutation, where Tyr179 makes pi-stacking interactions with the quinolone ring facilitating quinolone binding. The model also suggests that fluoroquinolones and aminoglycosides have different binding modes. On the basis of kinetic properties, the pH dependence of the kinetic parameters, and structural information, we propose an acid/base-assisted reaction catalyzed by AAC(6')-Ib-wt and the AAC(6')-Ib-cr variant involving a ternary complex.
-===STRUCTURE OF AAC(6')-IB IN COMPLEX WITH RIBOSTAMYCIN AND COENZYME A.===
+Mechanistic and structural analysis of aminoglycoside N-acetyltransferase AAC(6')-Ib and its bifunctional, fluoroquinolone-active AAC(6')-Ib-cr variant.,Vetting MW, Park CH, Hegde SS, Jacoby GA, Hooper DC, Blanchard JS Biochemistry. 2008 Sep 16;47(37):9825-35. Epub 2008 Aug 19. PMID:18710261<ref>PMID:18710261</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_18710261}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2bue" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18710261 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18710261}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacillus coli migula 1895]]
-BUE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BUE OCA].
+[[Category: Large Structures]]
+[[Category: Blanchard, J S]]
-==Reference==
+[[Category: Hedge, S S]]
-Mechanistic and structural analysis of aminoglycoside N-acetyltransferase AAC(6')-Ib and its bifunctional, fluoroquinolone-active AAC(6')-Ib-cr variant., Vetting MW, Park CH, Hegde SS, Jacoby GA, Hooper DC, Blanchard JS, Biochemistry. 2008 Sep 16;47(37):9825-35. Epub 2008 Aug 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18710261 18710261]
+[[Category: Hooper, D C]]
-[[Category: Escherichia coli]]
+[[Category: Park, C H]]
-[[Category: Single protein]]
+[[Category: Vetting, M W]]
-[[Category: Blanchard, J S.]]
-[[Category: Hedge, S S.]]
-[[Category: Hooper, D C.]]
-[[Category: Park, C H.]]
-[[Category: Vetting, M W.]]
 [[Category: Acetyltransferase]]
 [[Category: Aminoglycoside]]
@@ Line 37: / Line 45: @@
 [[Category: Gnat]]
 [[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 17 13:09:24 2008''