5yb6 - Revision history

OCA at 08:25, 22 November 2023

OCA — Wed, 22 Nov 2023 08:25:40 GMT

←Older revision		Revision as of 08:25, 22 November 2023
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	==L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-lysine complex==		==L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-lysine complex==
-	<StructureSection load='5yb6' size='340' side='right' caption='[[5yb6]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5yb6' size='340' side='right'caption='[[5yb6]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yb6]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pseudomonas_sp.~~_aiu_813~~ Pseudomonas sp. ~~aiu~~ 813]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YB6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YB6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yb6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._AIU_813 Pseudomonas sp. AIU 813]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YB6 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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</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]] 2.1Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">laao, mog ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1355242 Pseudomonas sp. AIU 813])</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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene></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=5yb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yb6 OCA], [~~http~~://pdbe.org/5yb6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yb6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yb6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yb6 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=5yb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yb6 OCA], [https://pdbe.org/5yb6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yb6 RCSB], [https://www.ebi.ac.uk/pdbsum/5yb6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yb6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/W6JQJ6_9PSED W6JQJ6_9PSED]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:

	==See Also==		==See Also==
-	*[[Amino acid oxidase\|Amino acid oxidase]]	+	*[[Amino acid oxidase 3D structures\|Amino acid oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pseudomonas sp. ~~aiu~~ 813]]	+	[[Category: Large Structures]]
-	[[Category: Arakawa, T]]	+	[[Category: Pseudomonas sp. AIU 813]]
-	[[Category: Asano, Y]]	+	[[Category: Arakawa T]]
-	[[Category: Fushinobu, S]]	+	[[Category: Asano Y]]
-	[[Category: Im, D]]	+	[[Category: Fushinobu S]]
-	[[Category: Isobe, K]]	+	[[Category: Im D]]
-	[[Category: Matsui, D]]	+	[[Category: Isobe K]]
-	~~[[Category: Flavin monooxygenase]]~~	+	[[Category: Matsui D]]
-	~~[[Category: Flavin-containing monoamine oxidase family]]~~	+
-	~~[[Category: L-amino acid oxidase/monooxygenase]]~~	+
-	~~[[Category: L-lysine]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:59, 21 March 2018

OCA — Wed, 21 Mar 2018 07:59:57 GMT

←Older revision		Revision as of 07:59, 21 March 2018
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	<StructureSection load='5yb6' size='340' side='right' caption='[[5yb6]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5yb6' size='340' side='right' caption='[[5yb6]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yb6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YB6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yb6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp._aiu_813 Pseudomonas sp. aiu 813]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YB6 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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">laao, mog ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1355242 Pseudomonas sp. AIU 813])</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=5yb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yb6 OCA], [http://pdbe.org/5yb6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yb6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yb6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yb6 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=5yb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yb6 OCA], [http://pdbe.org/5yb6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yb6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yb6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yb6 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	l-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the alpha-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition. Asp238 is located at the ceiling of a long hydrophobic pocket and forms a strong interaction with the terminal, positively charged group of the substrates. A mutational analysis on the D238A mutant indicated that the interaction is critical for substrate binding but not for catalytic control between the oxidase/monooxygenase activities. The catalytic activities of the D238E mutant unexpectedly increased, while the D238F mutant exhibited altered substrate specificity to long hydrophobic substrates. In the ligand-free structure, there are two channels connecting the active site and solvent, and a short region located at the dimer interface is disordered. In the l-Lys complex structure, a loop region is displaced to plug the channels. Moreover, the disordered region in the ligand-free structure forms a short helix in the substrate complex structures and creates the second binding site for the substrate. It is assumed that the amino acid substrate enters the active site of l-AAO/MOG through this route. Database: The atomic coordinates and structure factors (codes 5YB6, 5YB7, and 5YB8) have been deposited in the Protein Data Bank (http://wwpdb.org/). EC numbers: 1.4.3.2 (l-amino acid oxidase), 1.13.12.2 (lysine 2-monooxygenase).
		+
		+	Ligand complex structures of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change.,Im D, Matsui D, Arakawa T, Isobe K, Asano Y, Fushinobu S FEBS Open Bio. 2018 Feb 8;8(3):314-324. doi: 10.1002/2211-5463.12387. eCollection, 2018 Mar. PMID:29511608<ref>PMID:29511608</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yb6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Amino acid oxidase\|Amino acid oxidase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pseudomonas sp. aiu 813]]
	[[Category: Arakawa, T]]		[[Category: Arakawa, T]]
	[[Category: Asano, Y]]		[[Category: Asano, Y]]

OCA at 06:16, 7 February 2018

OCA — Wed, 07 Feb 2018 06:16:17 GMT

←Older revision		Revision as of 06:16, 7 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yb6 is ~~ON HOLD until Sep 03 2019~~	+	==L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-lysine complex==
-		+	<StructureSection load='5yb6' size='340' side='right' caption='[[5yb6]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yb6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YB6 FirstGlance]. <br>
-	~~Description~~:	+	</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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5yb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yb6 OCA], [http://pdbe.org/5yb6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yb6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yb6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yb6 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arakawa, T]]
		+	[[Category: Asano, Y]]
		+	[[Category: Fushinobu, S]]
		+	[[Category: Im, D]]
		+	[[Category: Isobe, K]]
		+	[[Category: Matsui, D]]
		+	[[Category: Flavin monooxygenase]]
		+	[[Category: Flavin-containing monoamine oxidase family]]
		+	[[Category: L-amino acid oxidase/monooxygenase]]
		+	[[Category: L-lysine]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5yb6" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:21:46 GMT

Protected "5yb6" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:21, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yb6 is ON HOLD until Sep 03 2019 Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:21:45 GMT

New page: '''Unreleased structure''' The entry 5yb6 is ON HOLD until Sep 03 2019 Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yb6 is ON HOLD until Sep 03 2019

Authors:

Description:
[[Category: Unreleased Structures]]