2wof: Difference between revisions

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-{{Seed}}
-[[Image:2wof.jpg|left|200px]]
-<!--
+==EDTA treated E. coli copper amine oxidase==
-The line below this paragraph, containing "STRUCTURE_2wof", creates the "Structure Box" on the page.
+<StructureSection load='2wof' size='340' side='right'caption='[[2wof]], [[Resolution|resolution]] 2.25&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'>[[2wof]] is a 2 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=2WOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WOF 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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPQ:5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE'>TPQ</scene></td></tr>
-{{STRUCTURE_2wof|  PDB=2wof  |  SCENE=  }}
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dyu|1dyu]], [[2wo0|2wo0]], [[1oac|1oac]], [[1qak|1qak]], [[2wgq|2wgq]], [[1qal|1qal]], [[1d6u|1d6u]], [[1spu|1spu]], [[2w0q|2w0q]], [[1jrq|1jrq]], [[1qaf|1qaf]], [[1d6y|1d6y]], [[1lvn|1lvn]], [[1d6z|1d6z]]</div></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </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=2wof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wof OCA], [https://pdbe.org/2wof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wof RCSB], [https://www.ebi.ac.uk/pdbsum/2wof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wof ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/AMO_ECOLI AMO_ECOLI]] The enzyme prefers aromatic over aliphatic amines.
+== 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/wo/2wof_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=2wof ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+To investigate the role of the active site copper in Escherichia coli copper amine oxidase (ECAO), we initiated a metal-substitution study. Copper reconstitution of ECAO (Cu-ECAO) restored only approximately 12% wild-type activity as measured by k(cat(amine)). Treatment with EDTA, to remove exogenous divalent metals, increased Cu-ECAO activity but reduced the activity of wild-type ECAO. Subsequent addition of calcium restored wild-type ECAO and further enhanced Cu-ECAO activities. Cobalt-reconstituted ECAO (Co-ECAO) showed lower but significant activity. These initial results are consistent with a direct electron transfer from TPQ to oxygen stabilized by the metal. If a Cu(I)-TPQ semiquinone mechanism operates, then an alternative outer-sphere electron transfer must also exist to account for the catalytic activity of Co-ECAO. The positive effect of calcium on ECAO activity led us to investigate the peripheral calcium binding sites of ECAO. Crystallographic analysis of wild-type ECAO structures, determined in the presence and absence of EDTA, confirmed that calcium is the normal ligand of these peripheral sites. The more solvent exposed calcium can be easily displaced by mono- and divalent cations with no effect on activity, whereas removal of the more buried calcium ion with EDTA resulted in a 60-90% reduction in ECAO activity and the presence of a lag phase, which could be overcome under oxygen saturation or by reoccupying the buried site with various divalent cations. Our studies indicate that binding of metal ions in the peripheral sites, while not essential, is important for maximal enzymatic activity in the mature enzyme.
-===EDTA TREATED E. COLI COPPER AMINE OXIDASE===
+Exploring the roles of the metal ions in Escherichia coli copper amine oxidase.,Smith MA, Pirrat P, Pearson AR, Kurtis CR, Trinh CH, Gaule TG, Knowles PF, Phillips SE, McPherson MJ Biochemistry. 2010 Feb 16;49(6):1268-80. PMID:20052994<ref>PMID:20052994</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2wof" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20052994}}, adds the Publication Abstract to the page
+*[[Copper amine oxidase 3D structures|Copper amine oxidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20052994 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20052994}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacillus coli migula 1895]]
-WOF is a 2 chains structure with sequences 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=2WOF OCA].
+[[Category: Large Structures]]
+[[Category: Oxidoreductase]]
-==Reference==
+[[Category: Knowles, P F]]
-<ref group="xtra">PMID:20052994</ref><references group="xtra"/>
+[[Category: McPherson, M J]]
-[[Category: Escherichia coli]]
+[[Category: Pearson, A R]]
-[[Category: Knowles, P F.]]
+[[Category: Phillips, S E.V]]
-[[Category: McPherson, M J.]]
+[[Category: Pirrat, P]]
-[[Category: Pearson, A R.]]
+[[Category: Smith, M A]]
-[[Category: Phillips, S E.V.]]
-[[Category: Pirrat, P.]]
-[[Category: Smith, M A.]]
 [[Category: Amine oxidation]]
 [[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
 [[Category: Tpq]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May  5 12:01:31 2010''