5xao - Revision history

OCA at 07:58, 22 November 2023

OCA — Wed, 22 Nov 2023 07:58:20 GMT

←Older revision		Revision as of 07:58, 22 November 2023
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	==Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala in complexes with sodium and chloride ions==		==Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala in complexes with sodium and chloride ions==
-	<StructureSection load='5xao' size='340' side='right' caption='[[5xao]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5xao' size='340' side='right'caption='[[5xao]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xao]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Glume_blotch_fungus Glume blotch fungus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XAO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XAO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xao]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Parastagonospora_nodorum_SN15 Parastagonospora nodorum SN15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XAO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XAO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t1f\|5t1f]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNOG_08398 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=321614 Glume blotch fungus])</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=5xao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xao OCA], [https://pdbe.org/5xao PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xao RCSB], [https://www.ebi.ac.uk/pdbsum/5xao PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xao ProSAT]</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=5xao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xao OCA], [~~http~~://pdbe.org/5xao PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xao RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xao PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xao ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q0UIL6_PHANO Q0UIL6_PHANO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Glume blotch fungus~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kamitori, S~~]]	+	[[Category: Parastagonospora nodorum SN15]]
-	[[Category: ~~Sode, K~~]]	+	[[Category: Kamitori S]]
-	[[Category: ~~Yoshida, H~~]]	+	[[Category: Sode K]]
-	[[Category: ~~Fad]]~~	+	[[Category: Yoshida H]]
-	~~[[Category: Fructosyl peptide oxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:28, 6 November 2017

OCA — Mon, 06 Nov 2017 11:28:45 GMT

←Older revision		Revision as of 11:28, 6 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xao is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala in complexes with sodium and chloride ions==
		+	<StructureSection load='5xao' size='340' side='right' caption='[[5xao]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xao]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Glume_blotch_fungus Glume blotch fungus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XAO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5t1f\|5t1f]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNOG_08398 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=321614 Glume blotch fungus])</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=5xao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xao OCA], [http://pdbe.org/5xao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xao RCSB], [http://www.ebi.ac.uk/pdbsum/5xao PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xao ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Current enzymatic systems for quantifying glycated hemoglobin are based on the FAD-containing enzyme fructosyl peptide oxidase (FPOX). FPOX has substrate specificity for fructosyl-alpha N-valyl-histidine derived from proteolytic digestion of the N-terminus of the HbA1c beta-chain. This study reports the X-ray structures of the wild-type and Asn56Ala (N56A) mutant of Phaeosphaeria nodorum fructosyl peptide oxidase (PnFPOX) to elucidate the residues responsible for the oxidative half-reaction. N56A showed decreased oxidase activity compared to the wild -type, while its dye-mediated dehydrogenase activity was higher than that of wild type. In wild-type PnFPOX, Asn56 forms a hydrogen bond with Lys274, thereby preventing it from forming a salt bridge with Asp54. By contrast, Lys274 of PnFPOX N56A moves toward Asp54, and they approach each other to form a salt bridge at a distance of 2.92-3.35 A. Site-directed mutagenesis studies and protein channel analysis suggest that Asp54 assists in accepting oxygen properly at the position of the bound water molecule in the main oxygen channel. These results reveal that Asn56 in PnFPOX is essential for maintaining an effective oxygen accession path, and support the role of Asp54 as a gate keeper that cooperates with Lys274 to enable oxygen to reach the active site properly.

-	~~Authors~~:	+	X-ray structures of fructosyl peptide oxidases revealing residues responsible for gating oxygen access in the oxidative half reaction.,Shimasaki T, Yoshida H, Kamitori S, Sode K Sci Rep. 2017 Jun 5;7(1):2790. doi: 10.1038/s41598-017-02657-5. PMID:28584265<ref>PMID:28584265</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xao" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glume blotch fungus]]
		+	[[Category: Kamitori, S]]
		+	[[Category: Sode, K]]
		+	[[Category: Yoshida, H]]
		+	[[Category: Fad]]
		+	[[Category: Fructosyl peptide oxidase]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5xao" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 12:25:29 GMT

Protected "5xao" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:25, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xao is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Apr 2017 12:25:28 GMT

New page: '''Unreleased structure''' The entry 5xao is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xao is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]