2ign - Revision history

OCA at 09:02, 21 February 2024

2024-02-21T09:02:59Z

← Older revision		Revision as of 09:02, 21 February 2024
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	<StructureSection load='2ign' size='340' side='right'caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2ign' size='340' side='right'caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Coriolus_zonatus Coriolus zonatus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IGN FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.65Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>p2o ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~230624 Coriolus zonatus])</td~~><~~/tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10]~~ </~~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=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [https://pdbe.org/2ign PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [https://www.ebi.ac.uk/pdbsum/2ign PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ign ProSAT]</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=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [https://pdbe.org/2ign PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [https://www.ebi.ac.uk/pdbsum/2ign PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ign ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q7ZA32_TRAOC Q7ZA32_TRAOC]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=2ign ConSurf].		</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=2ign ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Pyranose 2-oxidase (P2Ox) participates in fungal lignin degradation by producing the H2O2 needed for lignin-degrading peroxidases. The enzyme oxidizes cellulose- and hemicellulose-derived aldopyranoses at C2 preferentially, but also on C3, to the corresponding ketoaldoses. To investigate the structural determinants of catalysis, covalent flavinylation, substrate binding, and regioselectivity, wild-type and mutant P2Ox enzymes were produced and characterized biochemically and structurally. Removal of the histidyl-FAD linkage resulted in a catalytically competent enzyme containing tightly, but noncovalently bound FAD. This mutant (H167A) is characterized by a 5-fold lower kcat, and a 35-mV lower redox potential, although no significant structural changes were seen in its crystal structure. In previous structures of P2Ox, the substrate loop (residues 452-457) covering the active site has been either disordered or in a conformation incompatible with carbohydrate binding. We present here the crystal structure of H167A in complex with a slow substrate, 2-fluoro-2-deoxy-D-glucose. Based on the details of 2-fluoro-2-deoxy-D-glucose binding in position for oxidation at C3, we also outline a probable binding mode for D-glucose positioned for regioselective oxidation at C2. The tentative determinant for discriminating between the two binding modes is the position of the O6 hydroxyl group, which in the C2-oxidation mode can make favorable interactions with Asp452 in the substrate loop and, possibly, a nearby arginine residue (Arg472). We also substantiate our hypothesis with steady-state kinetics data for the alanine replacements of Asp452 and Arg472 as well as the double alanine 452/472 mutant.

	Structural basis for substrate binding and regioselective oxidation of monosaccharides at C3 by pyranose 2-oxidase.,Kujawa M, Ebner H, Leitner C, Hallberg BM, Prongjit M, Sucharitakul J, Ludwig R, Rudsander U, Peterbauer C, Chaiyen P, Haltrich D, Divne C J Biol Chem. 2006 Nov 17;281(46):35104-15. Epub 2006 Sep 19. PMID:16984920<ref>PMID:16984920</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2ign" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Pyranose oxidase\|Pyranose oxidase]]		*[[Pyranose oxidase\|Pyranose oxidase]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Coriolus zonatus]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Pyranose oxidase~~]]		[[Category: Trametes ochracea]]
	[[Category: Divne, C]]		[[Category: Divne C]]
	~~[[Category: Gmc oxidoreductase]]~~
	~~[[Category: H167a mutant]]~~
	~~[[Category: Homotetramer]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Phbh fold]]~~
	~~[[Category: Rossmann fold~~]]

OCA at 11:15, 31 March 2021

2021-03-31T11:15:45Z

← Older revision		Revision as of 11:15, 31 March 2021
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	==Crystal structure of recombinant pyranose 2-oxidase H167A mutant==		==Crystal structure of recombinant pyranose 2-oxidase H167A mutant==
	<StructureSection load='2ign' size='340' side='right' caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2ign' size='340' side='right'caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Coriolus_zonatus Coriolus zonatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2IGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Coriolus_zonatus Coriolus zonatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IGN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [~~http~~://pdbe.org/2ign PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ign PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ign ProSAT]</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=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [https://pdbe.org/2ign PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [https://www.ebi.ac.uk/pdbsum/2ign PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ign ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/2ign_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/2ign_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</StructureSection>		</StructureSection>
	[[Category: Coriolus zonatus]]		[[Category: Coriolus zonatus]]
			[[Category: Large Structures]]
	[[Category: Pyranose oxidase]]		[[Category: Pyranose oxidase]]
	[[Category: Divne, C]]		[[Category: Divne, C]]

OCA at 08:30, 18 October 2017

2017-10-18T08:30:00Z

← Older revision		Revision as of 08:30, 18 October 2017
Line 1:		Line 1:

	==Crystal structure of recombinant pyranose 2-oxidase H167A mutant==		==Crystal structure of recombinant pyranose 2-oxidase H167A mutant==
	<StructureSection load='2ign' size='340' side='right' caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2ign' size='340' side='right' caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://pdbe.org/2ign PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://pdbe.org/2ign PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ign ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</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=2ign ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:15, 11 September 2015

2015-09-11T09:15:58Z

← Older revision		Revision as of 09:15, 11 September 2015
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://pdbe.org/2ign PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2ign" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Pyranose oxidase\|Pyranose oxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:27, 25 January 2015

2015-01-25T10:27:42Z

← Older revision		Revision as of 10:27, 25 January 2015
Line 2:		Line 2:
	<StructureSection load='2ign' size='340' side='right' caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2ign' size='340' side='right' caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Coriolus_zonatus Coriolus zonatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IGN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Coriolus zonatus])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>
Line 30:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Coriolus zonatus]]
	[[Category: Pyranose oxidase]]		[[Category: Pyranose oxidase]]
	[[Category: Divne, C]]		[[Category: Divne, C]]

OCA at 07:18, 12 November 2014

2014-11-12T07:18:02Z

← Older revision		Revision as of 07:18, 12 November 2014
Line 2:		Line 2:
	<StructureSection load='2ign' size='340' side='right' caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2ign' size='340' side='right' caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IGN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Trametes ochracea])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>
Line 32:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Pyranose oxidase]]		[[Category: Pyranose oxidase]]
	~~[[Category: Trametes ochracea]]~~		[[Category: Divne, C]]
	[[Category: Divne, C.]]
	[[Category: Gmc oxidoreductase]]		[[Category: Gmc oxidoreductase]]
	[[Category: H167a mutant]]		[[Category: H167a mutant]]

OCA at 14:26, 3 November 2014

2014-11-03T14:26:18Z

← Older revision		Revision as of 14:26, 3 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IGN FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Trametes ochracea])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Trametes ochracea])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 39:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Phbh fold]]		[[Category: Phbh fold]]
	[[Category: ~~Rossman~~ fold]]		[[Category: Rossmann fold]]

OCA at 09:31, 30 September 2014

2014-09-30T09:31:42Z

← Older revision		Revision as of 09:31, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2ign~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of recombinant pyranose 2-oxidase H167A mutant==
			<StructureSection load='2ign' size='340' side='right' caption='[[2ign]], [[Resolution\|resolution]] 1.65Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2ign]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IGN FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tt0\|1tt0]], [[2igk\|2igk]], [[2igm\|2igm]], [[2igo\|2igo]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2o ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=230624 Trametes ochracea])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_oxidase Pyranose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.10 1.1.3.10] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ign FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ign OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ign RCSB], [http://www.ebi.ac.uk/pdbsum/2ign PDBsum]</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/ig/2ign_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/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Pyranose 2-oxidase (P2Ox) participates in fungal lignin degradation by producing the H2O2 needed for lignin-degrading peroxidases. The enzyme oxidizes cellulose- and hemicellulose-derived aldopyranoses at C2 preferentially, but also on C3, to the corresponding ketoaldoses. To investigate the structural determinants of catalysis, covalent flavinylation, substrate binding, and regioselectivity, wild-type and mutant P2Ox enzymes were produced and characterized biochemically and structurally. Removal of the histidyl-FAD linkage resulted in a catalytically competent enzyme containing tightly, but noncovalently bound FAD. This mutant (H167A) is characterized by a 5-fold lower kcat, and a 35-mV lower redox potential, although no significant structural changes were seen in its crystal structure. In previous structures of P2Ox, the substrate loop (residues 452-457) covering the active site has been either disordered or in a conformation incompatible with carbohydrate binding. We present here the crystal structure of H167A in complex with a slow substrate, 2-fluoro-2-deoxy-D-glucose. Based on the details of 2-fluoro-2-deoxy-D-glucose binding in position for oxidation at C3, we also outline a probable binding mode for D-glucose positioned for regioselective oxidation at C2. The tentative determinant for discriminating between the two binding modes is the position of the O6 hydroxyl group, which in the C2-oxidation mode can make favorable interactions with Asp452 in the substrate loop and, possibly, a nearby arginine residue (Arg472). We also substantiate our hypothesis with steady-state kinetics data for the alanine replacements of Asp452 and Arg472 as well as the double alanine 452/472 mutant.

	~~{{STRUCTURE_2ign\| PDB=2ign \| SCENE= }}~~		Structural basis for substrate binding and regioselective oxidation of monosaccharides at C3 by pyranose 2-oxidase.,Kujawa M, Ebner H, Leitner C, Hallberg BM, Prongjit M, Sucharitakul J, Ludwig R, Rudsander U, Peterbauer C, Chaiyen P, Haltrich D, Divne C J Biol Chem. 2006 Nov 17;281(46):35104-15. Epub 2006 Sep 19. PMID:16984920<ref>PMID:16984920</ref>

	~~===Crystal structure~~ of ~~recombinant pyranose 2-oxidase H167A mutant===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16984920}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2ign]] is a 8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Trametes_ochracea Trametes ochracea]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016984920<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Pyranose oxidase]]		[[Category: Pyranose oxidase]]
	[[Category: Trametes ochracea]]		[[Category: Trametes ochracea]]

OCA: Protected "2ign" [edit=sysop:move=sysop]

2013-01-07T14:25:41Z

Protected "2ign" [edit=sysop:move=sysop]

← Older revision	Revision as of 14:25, 7 January 2013
(No difference)

OCA at 14:25, 7 January 2013

2013-01-07T14:25:38Z

← Older revision		Revision as of 14:25, 7 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2ign.png\|left\|200px]]		[[Image:2ign.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2ign", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2ign\| PDB=2ign \| SCENE= }}		{{STRUCTURE_2ign\| PDB=2ign \| SCENE= }}

	===Crystal structure of recombinant pyranose 2-oxidase H167A mutant===		===Crystal structure of recombinant pyranose 2-oxidase H167A mutant===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16984920}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16984920 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16984920}}		{{ABSTRACT_PUBMED_16984920}}

	==About this Structure==		==About this Structure==
	~~2IGN~~ is a 8 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA].		[[2ign]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Trametes_ochracea Trametes ochracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IGN OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16984920~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016984920</ref><references group="xtra"/>
	[[Category: Pyranose oxidase]]		[[Category: Pyranose oxidase]]
	[[Category: Trametes ochracea]]		[[Category: Trametes ochracea]]
Line 33:		Line 21:
	[[Category: Phbh fold]]		[[Category: Phbh fold]]
	[[Category: Rossman fold]]		[[Category: Rossman fold]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:35:14 2009''~~