1gyc: Difference between revisions

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-[[Image:1gyc.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE DETERMINATION AT ROOM TEMPERATURE OF A LACCASE FROM TRAMETES VERSICOLOR IN ITS OXIDISED FORM CONTAINING A FULL COMPLEMENT OF COPPER IONS==
-The line below this paragraph, containing "STRUCTURE_1gyc", creates the "Structure Box" on the page.
+<StructureSection load='1gyc' size='340' side='right'caption='[[1gyc]], [[Resolution|resolution]] 1.90&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'>[[1gyc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trametes_versicolor Trametes versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GYC 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]] 1.9&#8491;</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=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_1gyc|  PDB=1gyc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyc OCA], [https://pdbe.org/1gyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gyc RCSB], [https://www.ebi.ac.uk/pdbsum/1gyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LAC2_TRAVE LAC2_TRAVE] Lignin degradation and detoxification of lignin-derived products (Probable).
+== 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/gy/1gyc_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=1gyc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Laccase is a polyphenol oxidase, which belongs to the family of blue multicopper oxidases. These enzymes catalyze the one-electron oxidation of four reducing-substrate molecules concomitant with the four-electron reduction of molecular oxygen to water. Laccases oxidize a broad range of substrates, preferably phenolic compounds. In the presence of mediators, fungal laccases exhibit an enlarged substrate range and are then able to oxidize compounds with a redox potential exceeding their own. Until now, only one crystal structure of a laccase in an inactive, type-2 copper-depleted form has been reported. We present here the first crystal structure of an active laccase containing a full complement of coppers, the complete polypeptide chain together with seven carbohydrate moieties. Despite the presence of all coppers in the new structure, the folds of the two laccases are quite similar. The coordination of the type-3 coppers, however, is distinctly different. The geometry of the trinuclear copper cluster in the Trametes versicolor laccase is similar to that found in the ascorbate oxidase and that of mammalian ceruloplasmin structures, suggesting a common reaction mechanism for the copper oxidation and the O(2) reduction. In contrast to most blue copper proteins, the type-1 copper in the T. versicolor laccase has no axial ligand and is only 3-fold coordinated. Previously, a modest elevation of the redox potential was attributed to the lack of an axial ligand. Based on the present structural data and sequence comparisons, a mechanism is presented to explain how laccases could tune their redox potential by as much as 200 mV.
-===CRYSTAL STRUCTURE DETERMINATION AT ROOM TEMPERATURE OF A LACCASE FROM TRAMETES VERSICOLOR IN ITS OXIDISED FORM CONTAINING A FULL COMPLEMENT OF COPPER IONS===
+Crystal structure of a laccase from the fungus Trametes versicolor at 1.90-A resolution containing a full complement of coppers.,Piontek K, Antorini M, Choinowski T J Biol Chem. 2002 Oct 4;277(40):37663-9. Epub 2002 Aug 5. PMID:12163489<ref>PMID:12163489</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1gyc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12163489}}, adds the Publication Abstract to the page
+*[[Laccase 3D structures|Laccase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12163489 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12163489}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[1gyc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trametes_versicolor Trametes versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GYC OCA].
-==Reference==
-<ref group="xtra">PMID:012163489</ref><ref group="xtra">PMID:011825613</ref><ref group="xtra">PMID:012051905</ref><references group="xtra"/>
-[[Category: Laccase]]
 [[Category: Trametes versicolor]]
-[[Category: Antorini, M.]]
+[[Category: Antorini M]]
-[[Category: Choinowski, T.]]
+[[Category: Choinowski T]]
-[[Category: Piontek, K.]]
+[[Category: Piontek K]]
-[[Category: Diphenol oxidase]]
-[[Category: Laccase]]
-[[Category: Lignin degradation]]
-[[Category: Oxidoreductase]]