5yss - Revision history

OCA at 08:36, 22 November 2023

OCA — Wed, 22 Nov 2023 08:36:57 GMT

←Older revision		Revision as of 08:36, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of aminocaproic acid cyclase in complex with NAD (+)==		==Crystal structure of aminocaproic acid cyclase in complex with NAD (+)==
-	<StructureSection load='5yss' size='340' side='right' caption='[[5yss]], [[Resolution\|resolution]] 2.28Å' scene=''>	+	<StructureSection load='5yss' size='340' side='right'caption='[[5yss]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yss]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacterium_freundii"_braak_1928 "bacterium~~ freundii~~" braak 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YSS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YSS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yss]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YSS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</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]] 2.276Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>AZ002_004124, BED45_07125, CES93_13130, HMPREF3212_01462, TO64_00155 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~546~~ "~~Bacterium freundii~~" ~~Braak 1928])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=5yss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yss OCA], [~~http~~://pdbe.org/5yss PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yss RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yss PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yss 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=5yss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yss OCA], [https://pdbe.org/5yss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yss RCSB], [https://www.ebi.ac.uk/pdbsum/5yss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yss ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0D7LY80_CITFR A0A0D7LY80_CITFR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ freundii ~~braak 1928~~]]	+	[[Category: Citrobacter freundii]]
-	[[Category: ~~Fu, Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lee, S G~~]]	+	[[Category: Fu Y]]
-	[[Category: ~~Yeom, S J~~]]	+	[[Category: Lee SG]]
-	[[Category: ~~Complex]]~~	+	[[Category: Yeom SJ]]
-	~~[[Category: Cyclase]]~~	+
-	~~[[Category: Nad binding protein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:06, 12 December 2018

OCA — Wed, 12 Dec 2018 07:06:08 GMT

←Older revision		Revision as of 07:06, 12 December 2018
Line 3:		Line 3:
	<StructureSection load='5yss' size='340' side='right' caption='[[5yss]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='5yss' size='340' side='right' caption='[[5yss]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yss]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YSS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yss]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YSS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AZ002_004124, BED45_07125, CES93_13130, HMPREF3212_01462, TO64_00155 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=546 "Bacterium freundii" Braak 1928])</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=5yss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yss OCA], [http://pdbe.org/5yss PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yss RCSB], [http://www.ebi.ac.uk/pdbsum/5yss PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yss 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=5yss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yss OCA], [http://pdbe.org/5yss PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yss RCSB], [http://www.ebi.ac.uk/pdbsum/5yss PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yss ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biocatalytic cyclization is highly desirable for efficient synthesis of biologically derived chemical substances, such as the commodity chemicals epsilon-caprolactam and delta-valerolactam. To identify biocatalysts in lactam biosynthesis, we develop a caprolactam-detecting genetic enzyme screening system (CL-GESS). The Alcaligenes faecalis regulatory protein NitR is adopted for the highly specific detection of lactam compounds against lactam biosynthetic intermediates. We further systematically optimize the genetic components of the CL-GESS to enhance sensitivity, achieving 10-fold improvement. Using this highly sensitive GESS, we screen marine metagenomes and find an enzyme that cyclizes omega-amino fatty acids to lactam. Moreover, we determine the X-ray crystal structure and catalytic residues based on mutational analysis of the cyclase. The cyclase is also used as a helper enzyme to sense intracellular omega-amino fatty acids. We expect this simple and accurate biosensor to have wide-ranging applications in rapid screening of new lactam-synthesizing enzymes and metabolic engineering for lactam bio-production.
		+
		+	A synthetic microbial biosensor for high-throughput screening of lactam biocatalysts.,Yeom SJ, Kim M, Kwon KK, Fu Y, Rha E, Park SH, Lee H, Kim H, Lee DH, Kim DM, Lee SG Nat Commun. 2018 Nov 29;9(1):5053. doi: 10.1038/s41467-018-07488-0. PMID:30498220<ref>PMID:30498220</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yss" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium freundii braak 1928]]
	[[Category: Fu, Y]]		[[Category: Fu, Y]]
	[[Category: Lee, S G]]		[[Category: Lee, S G]]

OCA at 06:44, 31 October 2018

OCA — Wed, 31 Oct 2018 06:44:33 GMT

←Older revision		Revision as of 06:44, 31 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5yss is ON HOLD until Paper Publication~~	+	==Crystal structure of aminocaproic acid cyclase in complex with NAD (+)==
-		+	<StructureSection load='5yss' size='340' side='right' caption='[[5yss]], [[Resolution\|resolution]] 2.28Å' scene=''>
-	~~Authors: Fu, Y., Yeom, S.J., Lee, S.G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yss]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YSS FirstGlance]. <br>
-	~~Description:~~ Crystal structure of aminocaproic acid cyclase in complex with NAD (+)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=5yss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yss OCA], [http://pdbe.org/5yss PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yss RCSB], [http://www.ebi.ac.uk/pdbsum/5yss PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yss ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Yeom~~, S.J]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fu, Y]]		[[Category: Fu, Y]]
-	[[Category: Lee, S.G]]	+	[[Category: Lee, S G]]
		+	[[Category: Yeom, S J]]
		+	[[Category: Complex]]
		+	[[Category: Cyclase]]
		+	[[Category: Nad binding protein]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 22 Nov 2017 06:28:23 GMT

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

←Older revision

Revision as of 06:28, 22 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yss is ON HOLD until Paper Publication Authors: Fu, Y., Yeom, S.J., Lee, S.G. Description: Crystal structure of aminocaproic acid cyclase in compl...

OCA — Wed, 22 Nov 2017 06:28:22 GMT

New page: '''Unreleased structure''' The entry 5yss is ON HOLD until Paper Publication Authors: Fu, Y., Yeom, S.J., Lee, S.G. Description: Crystal structure of aminocaproic acid cyclase in compl...

New page

'''Unreleased structure'''

The entry 5yss is ON HOLD until Paper Publication

Authors: Fu, Y., Yeom, S.J., Lee, S.G.

Description: Crystal structure of aminocaproic acid cyclase in complex with NAD (+)
[[Category: Unreleased Structures]]
[[Category: Yeom, S.J]]
[[Category: Fu, Y]]
[[Category: Lee, S.G]]