5hxw - Revision history

OCA at 10:59, 16 August 2023

OCA — Wed, 16 Aug 2023 10:59:11 GMT

←Older revision		Revision as of 10:59, 16 August 2023
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	<StructureSection load='5hxw' size='340' side='right'caption='[[5hxw]], [[Resolution\|resolution]] 2.63Å' scene=''>		<StructureSection load='5hxw' size='340' side='right'caption='[[5hxw]], [[Resolution\|resolution]] 2.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hxw]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_29905 Atcc 29905~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HXW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hxw]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HXW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=16A:CETYL~~-~~TRIMETHYL-AMMONIUM'>16A</scene>~~, ~~<scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 2.63Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>LAD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~585 ATCC 29905])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=16A:CETYL-TRIMETHYL-AMMONIUM'>16A</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/L-amino-acid_oxidase L-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.2 1.4.3.2]~~ </~~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=5hxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxw OCA], [https://pdbe.org/5hxw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hxw RCSB], [https://www.ebi.ac.uk/pdbsum/5hxw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxw ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5hxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxw OCA], [~~http~~://pdbe.org/5hxw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hxw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hxw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxw ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9LCB2_PROVU Q9LCB2_PROVU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 29905]]
-	[[Category: L-amino-acid oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ju, Y]]	+	[[Category: Proteus vulgaris]]
-	[[Category: Niu, L]]	+	[[Category: Ju Y]]
-	[[Category: Teng, M]]	+	[[Category: Niu L]]
-	[[Category: Zhou, H]]	+	[[Category: Teng M]]
-	~~[[Category: L-amino acid oxidase]]~~	+	[[Category: Zhou H]]
-	~~[[Category: Laad]]~~	+
-	~~[[Category: Laao]]~~	+
-	~~[[Category: Lad]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:36, 27 May 2020

OCA — Wed, 27 May 2020 08:36:15 GMT

←Older revision		Revision as of 08:36, 27 May 2020
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	==L-amino acid deaminase from Proteus vulgaris==		==L-amino acid deaminase from Proteus vulgaris==
-	<StructureSection load='5hxw' size='340' side='right' caption='[[5hxw]], [[Resolution\|resolution]] 2.63Å' scene=''>	+	<StructureSection load='5hxw' size='340' side='right'caption='[[5hxw]], [[Resolution\|resolution]] 2.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hxw]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HXW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hxw]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29905 Atcc 29905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HXW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=16A:CETYL-TRIMETHYL-AMMONIUM'>16A</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=16A:CETYL-TRIMETHYL-AMMONIUM'>16A</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LAD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-amino-acid_oxidase L-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.2 1.4.3.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-amino-acid_oxidase L-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.2 1.4.3.2] </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=5hxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxw OCA], [http://pdbe.org/5hxw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hxw RCSB], [http://www.ebi.ac.uk/pdbsum/5hxw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxw ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5hxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxw OCA], [http://pdbe.org/5hxw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hxw RCSB], [http://www.ebi.ac.uk/pdbsum/5hxw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxw ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5hxw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5hxw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 29905]]
	[[Category: L-amino-acid oxidase]]		[[Category: L-amino-acid oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Ju, Y]]		[[Category: Ju, Y]]
	[[Category: Niu, L]]		[[Category: Niu, L]]

OCA at 04:00, 4 August 2016

OCA — Thu, 04 Aug 2016 04:00:47 GMT

←Older revision		Revision as of 04:00, 4 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hxw is ~~ON HOLD until Paper~~ Publication	+	==L-amino acid deaminase from Proteus vulgaris==
		+	<StructureSection load='5hxw' size='340' side='right' caption='[[5hxw]], [[Resolution\|resolution]] 2.63Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hxw]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HXW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=16A:CETYL-TRIMETHYL-AMMONIUM'>16A</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-amino-acid_oxidase L-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.2 1.4.3.2] </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=5hxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hxw OCA], [http://pdbe.org/5hxw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hxw RCSB], [http://www.ebi.ac.uk/pdbsum/5hxw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hxw ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	l-amino acid oxidases/deaminases (LAAOs/LAADs) are a class of oxidoreductases catalyzing the oxidative deamination of l-amino acids to alpha-keto acids. They are widely distributed in eukaryotic and prokaryotic organisms, and exhibit diverse substrate specificity, post-translational modifications and cellular localization. While LAAOs isolated from snake venom have been extensively characterized, the structures and functions of LAAOs from other species are largely unknown. Here, we reported crystal structure of a bacterial membrane-bound LAAD from Proteus vulgaris (pvLAAD) in complex with flavin adenine dinucleotide (FAD). We found that the overall fold of pvLAAD does not resemble typical LAAOs. Instead it, is similar to d-amino acid oxidases (DAAOs) with an additional hydrophobic insertion module on protein surface. Structural analysis and liposome-binding assays suggested that the hydrophobic module serves as an extra membrane-binding site for LAADs. Bacteria from genera Proteus and Providencia were found to encode two classes of membrane-bound LAADs. Based on our structure, the key roles of residues Q278 and L317 in substrate selectivity were proposed and biochemically analyzed. While LAADs on the membrane were proposed to transfer electrons to respiratory chain for FAD re-oxidization, we observed that the purified pvLAAD could generate a significant amount of hydrogen peroxide in vitro, suggesting it could use dioxygen to directly re-oxidize FADH2 as what typical LAAOs usually do. These findings provide a novel insights for a better understanding this class of enzymes and will help developing biocatalysts for industrial applications.

-	~~Authors: Zhou, H~~., Ju, Y., ~~Niu~~, L., Teng, M.	+	Crystal structure of a membrane-bound l-amino acid deaminase from Proteus vulgaris.,Ju Y, Tong S, Gao Y, Zhao W, Liu Q, Gu Q, Xu J, Niu L, Teng M, Zhou H J Struct Biol. 2016 Jul 13. pii: S1047-8477(16)30149-6. doi:, 10.1016/j.jsb.2016.07.008. PMID:27422658<ref>PMID:27422658</ref>

-	~~Description: L~~-~~amino acid deaminase from Proteus vulgaris~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Zhou~~, H]]	+	<div class="pdbe-citations 5hxw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: L-amino-acid oxidase]]
		+	[[Category: Ju, Y]]
	[[Category: Niu, L]]		[[Category: Niu, L]]
	[[Category: Teng, M]]		[[Category: Teng, M]]
-	[[Category: Ju, Y]]	+	[[Category: Zhou, H]]
		+	[[Category: L-amino acid oxidase]]
		+	[[Category: Laad]]
		+	[[Category: Laao]]
		+	[[Category: Lad]]
		+	[[Category: Membrane protein]]
		+	[[Category: Oxidoreductase]]

OCA at 01:18, 21 February 2016

OCA — Sun, 21 Feb 2016 01:18:09 GMT

←Older revision		Revision as of 01:18, 21 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hxw is ON HOLD	+	The entry 5hxw is ON HOLD until Paper Publication

	Authors: Zhou, H., Ju, Y., Niu, L., Teng, M.		Authors: Zhou, H., Ju, Y., Niu, L., Teng, M.

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

OCA — Wed, 10 Feb 2016 15:52:21 GMT

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

←Older revision

Revision as of 15:52, 10 February 2016

OCA: New page: '''Unreleased structure''' The entry 5hxw is ON HOLD Authors: Zhou, H., Ju, Y., Niu, L., Teng, M. Description: L-amino acid deaminase from Proteus vulgaris [[Category: Unreleased Struc...

OCA — Wed, 10 Feb 2016 15:52:19 GMT

New page: '''Unreleased structure''' The entry 5hxw is ON HOLD Authors: Zhou, H., Ju, Y., Niu, L., Teng, M. Description: L-amino acid deaminase from Proteus vulgaris [[Category: Unreleased Struc...

New page

'''Unreleased structure'''

The entry 5hxw is ON HOLD

Authors: Zhou, H., Ju, Y., Niu, L., Teng, M.

Description: L-amino acid deaminase from Proteus vulgaris
[[Category: Unreleased Structures]]
[[Category: Zhou, H]]
[[Category: Niu, L]]
[[Category: Teng, M]]
[[Category: Ju, Y]]