7c3i - Revision history

OCA at 15:54, 29 November 2023

OCA — Wed, 29 Nov 2023 15:54:01 GMT

←Older revision		Revision as of 15:54, 29 November 2023
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	<StructureSection load='7c3i' size='340' side='right'caption='[[7c3i]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='7c3i' size='340' side='right'caption='[[7c3i]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7c3i]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~C.p.k._1997 C.p.k. 1997~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C3I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7C3I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7c3i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_viride Trichoderma viride]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C3I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C3I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3x0v\|3x0v]], [[7c3h\|7c3h]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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-lysine_oxidase L-lysine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.14 1.4.3.14] </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=7c3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c3i OCA], [https://pdbe.org/7c3i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c3i RCSB], [https://www.ebi.ac.uk/pdbsum/7c3i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c3i 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=7c3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c3i OCA], [~~http~~://pdbe.org/7c3i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7c3i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7c3i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7c3i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0G4DCU0_HYPRU A0A0G4DCU0_HYPRU]
	<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: C p.k. 1997]]
-	[[Category: L-lysine oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Imada, K]]	+	[[Category: Trichoderma viride]]
-	[[Category: Inagaki, K]]	+	[[Category: Imada K]]
-	[[Category: Kitagawa, M]]	+	[[Category: Inagaki K]]
-	[[Category: Matsumoto, Y]]	+	[[Category: Kitagawa M]]
-	~~[[Category: L-amino acid oxidase]]~~	+	[[Category: Matsumoto Y]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:40, 4 November 2020

OCA — Wed, 04 Nov 2020 07:40:30 GMT

←Older revision		Revision as of 07:40, 4 November 2020
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	==Structure of L-lysine oxidase D212A/D315A==		==Structure of L-lysine oxidase D212A/D315A==
-	<StructureSection load='7c3i' size='340' side='right'caption='[[7c3i]]' scene=''>	+	<StructureSection load='7c3i' size='340' side='right'caption='[[7c3i]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C3I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7C3I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7c3i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/C.p.k._1997 C.p.k. 1997]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C3I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7C3I FirstGlance]. <br>
-	</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=7c3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c3i OCA], [http://pdbe.org/7c3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7c3i RCSB], [http://www.ebi.ac.uk/pdbsum/7c3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7c3i ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3x0v\|3x0v]], [[7c3h\|7c3h]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lysine_oxidase L-lysine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.14 1.4.3.14] </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=7c3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c3i OCA], [http://pdbe.org/7c3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7c3i RCSB], [http://www.ebi.ac.uk/pdbsum/7c3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7c3i ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	l-Lysine oxidase (LysOX) is a FAD-dependent homodimeric enzyme that catalyzes the oxidative deamination of l-lysine to produce alpha-keto-epsilon-aminocaproate with ammonia and hydrogen peroxide. LysOX shows strict substrate specificity for l-lysine, whereas most l-amino acid oxidases (LAAOs) exhibit broad substrate specificity for l-amino acids. Previous studies of LysOX showed that overall structural similarity to the well-studied snake venom LAAOs. However, the molecular mechanism of strict specificity for l-lysine was still unclear. We here determined the structure of LysOX in complex with l-lysine at 1.7 A resolution. The structure revealed that the hydrogen bonding network formed by D212, D315, and A440 with two water molecules is responsible for the recognition of the side chain amino group. In addition, a narrow hole formed by five hydrophobic residues in the active site contributes to strict substrate specificity. Mutation studies demonstrated that D212 and D315 are essential for l-lysine recognition, and the D212A/D315A double mutant LysOX showed different substrate specificity from LysOX. Moreover, the structural basis of the substrate specificity change has also been revealed by the structural analysis of the mutant variant and its substrate complexes. These results clearly explain the molecular mechanism of the strict specificity of LysOX and suggest that LysOX is a potential candidate for a template to design LAAOs specific to other l-amino acids.
		+
		+	Structural basis of strict substrate recognition of l-lysine alpha-oxidase from Trichoderma viride.,Kondo H, Kitagawa M, Matsumoto Y, Saito M, Amano M, Sugiyama S, Tamura T, Kusakabe H, Inagaki K, Imada K Protein Sci. 2020 Sep 7. doi: 10.1002/pro.3946. PMID:32894626<ref>PMID:32894626</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7c3i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: C p.k. 1997]]
		+	[[Category: L-lysine oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Imada K]]	+	[[Category: Imada, K]]
-	[[Category: Inagaki K]]	+	[[Category: Inagaki, K]]
-	[[Category: Kitagawa M]]	+	[[Category: Kitagawa, M]]
-	[[Category: Matsumoto Y]]	+	[[Category: Matsumoto, Y]]
		+	[[Category: L-amino acid oxidase]]
		+	[[Category: Oxidoreductase]]

OCA at 11:15, 23 September 2020

OCA — Wed, 23 Sep 2020 11:15:48 GMT

←Older revision		Revision as of 11:15, 23 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7c3i is ~~ON HOLD until Paper Publication~~	+	==Structure of L-lysine oxidase D212A/D315A==
-		+	<StructureSection load='7c3i' size='340' side='right'caption='[[7c3i]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C3I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7C3I FirstGlance]. <br>
-	~~Description~~:	+	</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=7c3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c3i OCA], [http://pdbe.org/7c3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7c3i RCSB], [http://www.ebi.ac.uk/pdbsum/7c3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7c3i ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Imada K]]
		+	[[Category: Inagaki K]]
		+	[[Category: Kitagawa M]]
		+	[[Category: Matsumoto Y]]

OCA at 05:15, 10 June 2020

OCA — Wed, 10 Jun 2020 05:15:24 GMT

←Older revision		Revision as of 05:15, 10 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7c3i is ON HOLD	+	The entry 7c3i is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7c3i" [edit=sysop:move=sysop]

OCA — Wed, 20 May 2020 04:39:12 GMT

Protected "7c3i" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:39, 20 May 2020

OCA: New page: '''Unreleased structure''' The entry 7c3i is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 May 2020 04:39:10 GMT

New page: '''Unreleased structure''' The entry 7c3i is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7c3i is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]