4h7u - Revision history

OCA at 15:01, 20 September 2023

OCA — Wed, 20 Sep 2023 15:01:19 GMT

←Older revision		Revision as of 15:01, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leucoagaricus_meleagris Leucoagaricus meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H7U FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leucoagaricus_meleagris Leucoagaricus meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H7U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+(2R,3S,4S)-2,3,4-trihydroxy-5-[(4aR)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl+dihydrogen+diphosphate+(non-preferred+name)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+(2R,3S,4S)-2,3,4-trihydroxy-5-[(4aR)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl+dihydrogen+diphosphate+(non-preferred+name)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=4h7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h7u OCA], [https://pdbe.org/4h7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h7u RCSB], [https://www.ebi.ac.uk/pdbsum/4h7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h7u 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=4h7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h7u OCA], [https://pdbe.org/4h7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h7u RCSB], [https://www.ebi.ac.uk/pdbsum/4h7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h7u ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:04, 3 November 2022

OCA — Thu, 03 Nov 2022 08:04:13 GMT

←Older revision		Revision as of 08:04, 3 November 2022
Line 1:		Line 1:

	==Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype==		==Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype==
-	<StructureSection load='4h7u' size='340' side='right' caption='[[4h7u]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4h7u' size='340' side='right'caption='[[4h7u]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Agaricus_meleagris Agaricus~~ meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4H7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leucoagaricus_meleagris Leucoagaricus meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H7U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+(2R,3S,4S)-2,3,4-trihydroxy-5-[(4aR)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl+dihydrogen+diphosphate+(non-preferred+name)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+(2R,3S,4S)-2,3,4-trihydroxy-5-[(4aR)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl+dihydrogen+diphosphate+(non-preferred+name)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pdh1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=201219 Agaricus meleagris])</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=4h7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h7u OCA], [https://pdbe.org/4h7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h7u RCSB], [https://www.ebi.ac.uk/pdbsum/4h7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h7u ProSAT]</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_dehydrogenase_(acceptor) Pyranose dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.29 1.1.99.29] </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=4h7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h7u OCA], [~~http~~://pdbe.org/4h7u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4h7u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4h7u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4h7u ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PDH1_LEUMG PDH1_LEUMG] Catalyzes the single-oxidation or sequential double oxidation reaction of carbohydrates primarily at carbon-2 and/or carbon-3 with the concomitant reduction of the flavin. The enzyme exhibits a broad sugar substrate specificity, oxidizing different aldopyranoses to the corresponding C-1, C-2, C-3 or C-1,2, C-2,3 and C-3,4 (di)dehydro sugars with substrate-specific regioselectivity. Accepts only a narrow range of electron acceptors such as substituted benzoquinones and complexed metal ions and reacts extremely slowly with O(2) as acceptor. May play a role in the natural recycling of plant matter by oxidizing all major monosaccharides in lignocellulose and by reducing quinone compounds or reactive radical species generated during lignin depolymerization.<ref>PMID:18083263</ref> <ref>PMID:18097667</ref> <ref>PMID:23326459</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Agaricus meleagris~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Divne, C~~]]	+	[[Category: Leucoagaricus meleagris]]
-	[[Category: ~~Spadiut, O]]~~	+	[[Category: Divne C]]
-	~~[[Category: Tan, T~~ C]]	+	[[Category: Spadiut O]]
-	[[Category: ~~Fad binding~~]]	+	[[Category: Tan TC]]
-	[[Category: ~~Flavin adduct]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Gmc-oxidoreductase family]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pyranose dehydrogenase]]~~	+
-	~~[[Category: Secreted~~]]	+

OCA at 08:37, 15 November 2017

OCA — Wed, 15 Nov 2017 08:37:02 GMT

←Older revision		Revision as of 08:37, 15 November 2017
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agaricus_meleagris Agaricus meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H7U FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agaricus_meleagris Agaricus meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H7U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-~~AMINO~~-9H-~~PURIN~~-9-YL)-3,4-~~DIHYDROXYTETRAHYDROFURAN~~-2-YL]~~METHYL~~+(2R,3S,4S)-2,3,4-~~TRIHYDROXY~~-5-[(~~4AR~~)-4A-~~HYDROXY~~-7,8-~~DIMETHYL~~-2,4-~~DIOXO~~-3,4,4A,5-~~TETRAHYDROBENZO~~[G]~~PTERIDIN~~-10(2H)-YL]~~PENTYL~~+~~DIHYDROGEN~~+~~DIPHOSPHATE~~+(~~NON~~-~~PREFERRED~~+~~NAME~~)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+(2R,3S,4S)-2,3,4-trihydroxy-5-[(4aR)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl+dihydrogen+diphosphate+(non-preferred+name)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pdh1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=201219 Agaricus meleagris])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pdh1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=201219 Agaricus meleagris])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_dehydrogenase_(acceptor) Pyranose dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.29 1.1.99.29] </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_dehydrogenase_(acceptor) Pyranose dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.29 1.1.99.29] </span></td></tr>

OCA at 01:40, 5 August 2016

OCA — Fri, 05 Aug 2016 01:40:06 GMT

←Older revision		Revision as of 01:40, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype==		==Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype==
	<StructureSection load='4h7u' size='340' side='right' caption='[[4h7u]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4h7u' size='340' side='right' caption='[[4h7u]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Leucoagaricus_meleagris Leucoagaricus~~ meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agaricus_meleagris Agaricus meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H7U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S)-2,3,4-TRIHYDROXY-5-[(4AR)-4A-HYDROXY-7,8-DIMETHYL-2,4-DIOXO-3,4,4A,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]PENTYL+DIHYDROGEN+DIPHOSPHATE+(NON-PREFERRED+NAME)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S)-2,3,4-TRIHYDROXY-5-[(4AR)-4A-HYDROXY-7,8-DIMETHYL-2,4-DIOXO-3,4,4A,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]PENTYL+DIHYDROGEN+DIPHOSPHATE+(NON-PREFERRED+NAME)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pdh1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=201219 ~~Leucoagaricus~~ meleagris])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pdh1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=201219 Agaricus meleagris])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_dehydrogenase_(acceptor) Pyranose dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.29 1.1.99.29] </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_dehydrogenase_(acceptor) Pyranose dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.29 1.1.99.29] </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=4h7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h7u RCSB], [http://www.ebi.ac.uk/pdbsum/4h7u 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=4h7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h7u OCA], [http://pdbe.org/4h7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h7u RCSB], [http://www.ebi.ac.uk/pdbsum/4h7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h7u ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4h7u" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Leucoagaricus~~ meleagris]]	+	[[Category: Agaricus meleagris]]
	[[Category: Divne, C]]		[[Category: Divne, C]]
	[[Category: Spadiut, O]]		[[Category: Spadiut, O]]

OCA at 11:06, 21 December 2014

OCA — Sun, 21 Dec 2014 11:06:45 GMT

←Older revision		Revision as of 11:06, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4h7u\| PDB=4h7u \| SCENE= }}~~	+	==Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype==
-	===Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype===	+	<StructureSection load='4h7u' size='340' side='right' caption='[[4h7u]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23326459}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4h7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Leucoagaricus_meleagris Leucoagaricus meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H7U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FED:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S)-2,3,4-TRIHYDROXY-5-[(4AR)-4A-HYDROXY-7,8-DIMETHYL-2,4-DIOXO-3,4,4A,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]PENTYL+DIHYDROGEN+DIPHOSPHATE+(NON-PREFERRED+NAME)'>FED</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pdh1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=201219 Leucoagaricus meleagris])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyranose_dehydrogenase_(acceptor) Pyranose dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.29 1.1.99.29] </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=4h7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h7u RCSB], [http://www.ebi.ac.uk/pdbsum/4h7u PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyranose dehydrogenases (PDHs) are extracellular flavin-dependent oxidoreductases secreted by litter-decomposing fungi with a role in natural recycling of plant matter. All major monosaccharides in lignocellulose are oxidized by PDH at comparable yields and efficiencies. Oxidation takes place as single-oxidation or sequential double-oxidation reactions of the carbohydrates, resulting in sugar derivatives oxidized primarily at C2, C3 or C2/3 with the concomitant reduction of the flavin. A suitable electron acceptor then reoxidizes the reduced flavin. Whereas oxygen is a poor electron acceptor for PDH, several alternative acceptors, e.g., quinone compounds, naturally present during lignocellulose degradation, can be used. We have determined the 1.6-A crystal structure of PDH from Agaricus meleagris. Interestingly, the flavin ring in PDH is modified by a covalent mono- or di-atomic species at the C(4a) position. Under normal conditions, PDH is not oxidized by oxygen; however, the related enzyme pyranose 2-oxidase (P2O) activates oxygen by a mechanism that proceeds via a covalent flavin C(4a)-hydroperoxide intermediate. Although the flavin C(4a) adduct is common in monooxygenases, it is unusual for flavoprotein oxidases, and it has been proposed that formation of the intermediate would be unfavorable in these oxidases. Thus, the flavin adduct in PDH not only shows that the adduct can be favorably accommodated in the active site, but also provides important details regarding the structural, spatial and physicochemical requirements for formation of this flavin intermediate in related oxidases. Extensive in silico modeling of carbohydrates in the PDH active site allowed us to rationalize the previously reported patterns of substrate specificity and regioselectivity. To evaluate the regioselectivity of D-glucose oxidation, reduction experiments were performed using fluorinated glucose. PDH was rapidly reduced by 3-fluorinated glucose, which has the C2 position accessible for oxidation, whereas 2-fluorinated glucose performed poorly (C3 accessible), indicating that the glucose C2 position is the primary site of attack.

-	~~==About this Structure==~~	+	The 1.6 A crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate.,Tan TC, Spadiut O, Wongnate T, Sucharitakul J, Krondorfer I, Sygmund C, Haltrich D, Chaiyen P, Peterbauer CK, Divne C PLoS One. 2013;8(1):e53567. doi: 10.1371/journal.pone.0053567. Epub 2013 Jan 9. PMID:23326459<ref>PMID:23326459</ref>
-	~~[[4h7u]] is a~~ 1 ~~chain~~ structure ~~with sequence~~ from ~~[http://en~~.~~wikipedia~~.~~org/wiki/Leucoagaricus_meleagris Leucoagaricus meleagris]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4H7U OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023326459</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Leucoagaricus meleagris]]		[[Category: Leucoagaricus meleagris]]
-	[[Category: Divne, C.]]	+	[[Category: Divne, C]]
-	[[Category: Spadiut, O.]]	+	[[Category: Spadiut, O]]
-	[[Category: Tan, T C.]]	+	[[Category: Tan, T C]]
	[[Category: Fad binding]]		[[Category: Fad binding]]
	[[Category: Flavin adduct]]		[[Category: Flavin adduct]]

OCA at 20:52, 7 August 2013

OCA — Wed, 07 Aug 2013 20:52:08 GMT

←Older revision		Revision as of 20:52, 7 August 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4h7u\| PDB=4h7u \| SCENE= }}
		+	===Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype===
		+	{{ABSTRACT_PUBMED_23326459}}

-	~~The entry~~ 4h7u is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4h7u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Leucoagaricus_meleagris Leucoagaricus meleagris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H7U OCA].

-	~~Authors~~: ~~Tan~~, T.C., Spadiut, O., ~~Divne,~~ C.	+	==Reference==
-		+	<ref group="xtra">PMID:023326459</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure of pyranose~~ dehydrogenase ~~from Agaricus meleagris, wildtype~~	+	[[Category: Leucoagaricus meleagris]]
		+	[[Category: Divne, C.]]
		+	[[Category: Spadiut, O.]]
		+	[[Category: Tan, T C.]]
		+	[[Category: Fad binding]]
		+	[[Category: Flavin adduct]]
		+	[[Category: Glycoprotein]]
		+	[[Category: Gmc-oxidoreductase family]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pyranose dehydrogenase]]
		+	[[Category: Secreted]]

OCA at 07:08, 24 October 2012

OCA — Wed, 24 Oct 2012 07:08:15 GMT

←Older revision		Revision as of 07:08, 24 October 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4h7u is ON HOLD	+	The entry 4h7u is ON HOLD until Paper Publication

	Authors: Tan, T.C., Spadiut, O., Divne, C.		Authors: Tan, T.C., Spadiut, O., Divne, C.

	Description: Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype		Description: Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype

OCA: Protected "4h7u" [edit=sysop:move=sysop]

OCA — Wed, 26 Sep 2012 20:15:34 GMT

Protected "4h7u" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:15, 26 September 2012

OCA: New page: '''Unreleased structure''' The entry 4h7u is ON HOLD Authors: Tan, T.C., Spadiut, O., Divne, C. Description: Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildty...

OCA — Wed, 26 Sep 2012 20:15:33 GMT

New page: '''Unreleased structure''' The entry 4h7u is ON HOLD Authors: Tan, T.C., Spadiut, O., Divne, C. Description: Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildty...

New page

'''Unreleased structure'''

The entry 4h7u is ON HOLD

Authors: Tan, T.C., Spadiut, O., Divne, C.

Description: Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype