7eii - Revision history

OCA at 16:54, 29 November 2023

OCA — Wed, 29 Nov 2023 16:54:49 GMT

←Older revision		Revision as of 16:54, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7eii' size='340' side='right'caption='[[7eii]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='7eii' size='340' side='right'caption='[[7eii]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7eii]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EII FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7eii]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EII FirstGlance]. <br>
-	</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></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]] 2.4Å</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></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=7eii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eii OCA], [https://pdbe.org/7eii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eii RCSB], [https://www.ebi.ac.uk/pdbsum/7eii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eii 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=7eii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eii OCA], [https://pdbe.org/7eii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eii RCSB], [https://www.ebi.ac.uk/pdbsum/7eii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eii ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Hasebe, F]]	+	[[Category: Hasebe F]]
-	[[Category: Ito, S]]	+	[[Category: Ito S]]
-	[[Category: Nakano, S]]	+	[[Category: Nakano S]]
-	[[Category: Niwa, M]]	+	[[Category: Niwa M]]
-	[[Category: Sugiura, S]]	+	[[Category: Sugiura S]]
-	~~[[Category: L-lys oxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:36, 23 February 2022

OCA — Wed, 23 Feb 2022 08:36:37 GMT

←Older revision		Revision as of 08:36, 23 February 2022
Line 1:		Line 1:

	==Ancestral L-Lys oxidase K387A variant (L-Lys binding form)==		==Ancestral L-Lys oxidase K387A variant (L-Lys binding form)==
-	<StructureSection load='7eii' size='340' side='right'caption='[[7eii]]' scene=''>	+	<StructureSection load='7eii' size='340' side='right'caption='[[7eii]], [[Resolution\|resolution]] 2.40Å' 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=7EII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EII FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7eii]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EII FirstGlance]. <br>
-	</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=7eii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eii OCA], [https://pdbe.org/7eii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eii RCSB], [https://www.ebi.ac.uk/pdbsum/7eii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eii 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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=7eii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eii OCA], [https://pdbe.org/7eii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eii RCSB], [https://www.ebi.ac.uk/pdbsum/7eii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eii ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A large number of protein sequences are registered in public databases such as PubMed. Functionally uncharacterized enzymes are included in these databases, some of which likely have potential for industrial applications. However, assignment of the enzymes remained difficult tasks for now. In this study, we assigned a total of 28 original sequences to uncharacterized enzymes in the FAD-dependent oxidase family expressed in some species of bacteria including Chryseobacterium, Flavobacterium, and Pedobactor. Progenitor sequence of the assigned 28 sequences was generated by ancestral sequence reconstruction, and the generated sequence exhibited L-lysine oxidase activity; thus, we named the enzyme AncLLysO. Crystal structures of ligand-free and ligand-bound forms of AncLLysO were determined, indicating that the enzyme recognizes L-Lys by hydrogen bond formation with R76 and E383. The binding of L-Lys to AncLLysO induced dynamic structural change at a plug loop formed by residues 251 to 254. Biochemical assays of AncLLysO variants revealed the functional importance of these substrate recognition residues and the plug loop. R76A and E383D variants were also observed to lose their activity, and the kcat/Km value of G251P and Y253A mutations were approximately 800- to 1800-fold lower than that of AncLLysO, despite the indirect interaction of the substrates with the mutated residues. Taken together, our data demonstrate that combinational approaches to sequence classification from database and ancestral sequence reconstruction may be effective not only to find new enzymes using databases of unknown sequences but also to elucidate their functions.
		+
		+	Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining.,Sugiura S, Nakano S, Niwa M, Hasebe F, Matsui D, Ito S J Biol Chem. 2021 Sep;297(3):101043. doi: 10.1016/j.jbc.2021.101043. Epub 2021, Aug 4. PMID:34358565<ref>PMID:34358565</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7eii" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hasebe F]]	+	[[Category: Synthetic construct sequences]]
-	[[Category: Ito S]]	+	[[Category: Hasebe, F]]
-	[[Category: Nakano S]]	+	[[Category: Ito, S]]
-	[[Category: Niwa M]]	+	[[Category: Nakano, S]]
-	[[Category: Sugiura S]]	+	[[Category: Niwa, M]]
		+	[[Category: Sugiura, S]]
		+	[[Category: L-lys oxidase]]
		+	[[Category: Oxidoreductase]]

OCA at 06:06, 11 August 2021

OCA — Wed, 11 Aug 2021 06:06:25 GMT

←Older revision		Revision as of 06:06, 11 August 2021
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-	'''Unreleased structure'''

-	~~The entry 7eii is ON HOLD until Paper Publication~~	+	==Ancestral L-Lys oxidase K387A variant (L-Lys binding form)==
-		+	<StructureSection load='7eii' size='340' side='right'caption='[[7eii]]' scene=''>
-	~~Authors: Sugiura, S., Nakano, S., Niwa, M., Hasebe, F., Ito, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EII FirstGlance]. <br>
-	~~Description:~~ Ancestral L-Lys oxidase K387A variant (L-Lys binding form)	+	</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=7eii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eii OCA], [https://pdbe.org/7eii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eii RCSB], [https://www.ebi.ac.uk/pdbsum/7eii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eii ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Sugiura~~, S]]	+	__TOC__
-	[[Category: ~~Ito, S~~]]	+	</StructureSection>
-	[[Category: Hasebe, F]]	+	[[Category: Large Structures]]
-	[[Category: Nakano, S]]	+	[[Category: Hasebe F]]
-	[[Category: Niwa, M]]	+	[[Category: Ito S]]
		+	[[Category: Nakano S]]
		+	[[Category: Niwa M]]
		+	[[Category: Sugiura S]]

OCA at 05:34, 14 April 2021

OCA — Wed, 14 Apr 2021 05:34:50 GMT

←Older revision		Revision as of 05:34, 14 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Sugiura, S., Nakano, S., Niwa, M., Hasebe, F., Ito, S.		Authors: Sugiura, S., Nakano, S., Niwa, M., Hasebe, F., Ito, S.

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

OCA — Wed, 07 Apr 2021 04:32:27 GMT

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

←Older revision

Revision as of 04:32, 7 April 2021

OCA: New page: '''Unreleased structure''' The entry 7eii is ON HOLD Authors: Sugiura, S., Nakano, S., Niwa, M., Hasebe, F., Ito, S. Description: Ancestral L-Lys oxidase K387A variant (L-Lys binding f...

OCA — Wed, 07 Apr 2021 04:32:26 GMT

New page: '''Unreleased structure''' The entry 7eii is ON HOLD Authors: Sugiura, S., Nakano, S., Niwa, M., Hasebe, F., Ito, S. Description: Ancestral L-Lys oxidase K387A variant (L-Lys binding f...

New page

'''Unreleased structure'''

The entry 7eii is ON HOLD

Authors: Sugiura, S., Nakano, S., Niwa, M., Hasebe, F., Ito, S.

Description: Ancestral L-Lys oxidase K387A variant (L-Lys binding form)
[[Category: Unreleased Structures]]
[[Category: Sugiura, S]]
[[Category: Ito, S]]
[[Category: Hasebe, F]]
[[Category: Nakano, S]]
[[Category: Niwa, M]]