5fay - Revision history

OCA at 06:44, 19 July 2023

OCA — Wed, 19 Jul 2023 06:44:38 GMT

←Older revision		Revision as of 06:44, 19 July 2023
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	<StructureSection load='5fay' size='340' side='right'caption='[[5fay]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5fay' size='340' side='right'caption='[[5fay]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fay]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Desag Desag~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FAY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FAY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fay]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oleidesulfovibrio_alaskensis_G20 Oleidesulfovibrio alaskensis G20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FAY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.901Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fau\|5fau]]~~, [[~~5fav~~\|~~5fav]], [[5faw\|5faw~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Dde_3282 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=207559 DESAG])</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=5fay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fay OCA], [https://pdbe.org/5fay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fay RCSB], [https://www.ebi.ac.uk/pdbsum/5fay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fay ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Choline_trimethylamine-lyase Choline trimethylamine-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.99.4 4.3.99.4]~~ </~~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=5fay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fay OCA], [~~http~~://pdbe.org/5fay PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fay RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fay PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fay ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~CUTC_DESAG CUTC_DESAG]~~] Glycine radical enzyme that catalyzes the cleavage of a C-N bond in choline, producing trimethylamine (TMA) and acetaldehyde (PubMed:23151509, PubMed:24854437). Is involved in the anaerobic choline utilization pathway that allows D.alaskensis to grow on choline as a source of carbon and energy (PubMed:23151509). Is strictly specific for choline as substrate (PubMed:24854437).<ref>PMID:23151509</ref> <ref>PMID:24854437</ref>	+	[https://www.uniprot.org/uniprot/CUTC_OLEA2 CUTC_OLEA2] Glycine radical enzyme that catalyzes the cleavage of a C-N bond in choline, producing trimethylamine (TMA) and acetaldehyde (PubMed:23151509, PubMed:24854437). Is involved in the anaerobic choline utilization pathway that allows D.alaskensis to grow on choline as a source of carbon and energy (PubMed:23151509). Is strictly specific for choline as substrate (PubMed:24854437).<ref>PMID:23151509</ref> <ref>PMID:24854437</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Choline trimethylamine-lyase]]
-	[[Category: Desag]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Drennan, C L~~]]	+	[[Category: Oleidesulfovibrio alaskensis G20]]
-	[[Category: ~~Funk, M A~~]]	+	[[Category: Drennan CL]]
-	[[Category: ~~Lyase]]~~	+	[[Category: Funk MA]]
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Radical~~]]	+

OCA at 07:35, 27 November 2019

OCA — Wed, 27 Nov 2019 07:35:05 GMT

←Older revision		Revision as of 07:35, 27 November 2019
Line 1:		Line 1:

	==Y208F mutant of choline TMA-lyase==		==Y208F mutant of choline TMA-lyase==
-	<StructureSection load='5fay' size='340' side='right' caption='[[5fay]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5fay' size='340' side='right'caption='[[5fay]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5fay]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desag Desag]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FAY FirstGlance]. <br>		<table><tr><td colspan='2'>[[5fay]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desag Desag]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FAY FirstGlance]. <br>
Line 27:		Line 27:
	[[Category: Choline trimethylamine-lyase]]		[[Category: Choline trimethylamine-lyase]]
	[[Category: Desag]]		[[Category: Desag]]
		+	[[Category: Large Structures]]
	[[Category: Drennan, C L]]		[[Category: Drennan, C L]]
	[[Category: Funk, M A]]		[[Category: Funk, M A]]

OCA at 09:15, 1 November 2017

OCA — Wed, 01 Nov 2017 09:15:15 GMT

←Older revision		Revision as of 09:15, 1 November 2017
Line 3:		Line 3:
	<StructureSection load='5fay' size='340' side='right' caption='[[5fay]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5fay' size='340' side='right' caption='[[5fay]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fay]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FAY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fay]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desag Desag]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FAY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fau\|5fau]], [[5fav\|5fav]], [[5faw\|5faw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fau\|5fau]], [[5fav\|5fav]], [[5faw\|5faw]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dde_3282 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207559 DESAG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Choline_trimethylamine-lyase Choline trimethylamine-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.99.4 4.3.99.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Choline_trimethylamine-lyase Choline trimethylamine-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.99.4 4.3.99.4] </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=5fay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fay OCA], [http://pdbe.org/5fay PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fay RCSB], [http://www.ebi.ac.uk/pdbsum/5fay PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fay 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=5fay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fay OCA], [http://pdbe.org/5fay PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fay RCSB], [http://www.ebi.ac.uk/pdbsum/5fay PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fay ProSAT]</span></td></tr>
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Choline trimethylamine-lyase]]		[[Category: Choline trimethylamine-lyase]]
		+	[[Category: Desag]]
	[[Category: Drennan, C L]]		[[Category: Drennan, C L]]
	[[Category: Funk, M A]]		[[Category: Funk, M A]]

OCA at 16:43, 3 October 2016

OCA — Mon, 03 Oct 2016 16:43:21 GMT

←Older revision		Revision as of 16:43, 3 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fay is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Y208F mutant of choline TMA-lyase==
		+	<StructureSection load='5fay' size='340' side='right' caption='[[5fay]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fay]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FAY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CHT:CHOLINE+ION'>CHT</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fau\|5fau]], [[5fav\|5fav]], [[5faw\|5faw]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Choline_trimethylamine-lyase Choline trimethylamine-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.99.4 4.3.99.4] </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=5fay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fay OCA], [http://pdbe.org/5fay PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fay RCSB], [http://www.ebi.ac.uk/pdbsum/5fay PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fay ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CUTC_DESAG CUTC_DESAG]] Glycine radical enzyme that catalyzes the cleavage of a C-N bond in choline, producing trimethylamine (TMA) and acetaldehyde (PubMed:23151509, PubMed:24854437). Is involved in the anaerobic choline utilization pathway that allows D.alaskensis to grow on choline as a source of carbon and energy (PubMed:23151509). Is strictly specific for choline as substrate (PubMed:24854437).<ref>PMID:23151509</ref> <ref>PMID:24854437</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. This work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.

-	~~Authors:~~ Funk, M.A., ~~Drennan, C~~.L.	+	Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase.,Bodea S, Funk MA, Balskus EP, Drennan CL Cell Chem Biol. 2016 Sep 23. pii: S2451-9456(16)30287-2. doi:, 10.1016/j.chembiol.2016.07.020. PMID:27642068<ref>PMID:27642068</ref>

-	~~Description: Y208F mutant~~ of ~~choline TMA~~-lyase	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Funk, M.A]]	+	<div class="pdbe-citations 5fay" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Drennan, C.L~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Choline trimethylamine-lyase]]
		+	[[Category: Drennan, C L]]
		+	[[Category: Funk, M A]]
		+	[[Category: Lyase]]
		+	[[Category: Mutant]]
		+	[[Category: Radical]]

OCA at 10:51, 7 January 2016

OCA — Thu, 07 Jan 2016 10:51:27 GMT

←Older revision		Revision as of 10:51, 7 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Funk, M.A., Drennan, C.L.		Authors: Funk, M.A., Drennan, C.L.

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

OCA — Wed, 23 Dec 2015 11:23:17 GMT

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

←Older revision

Revision as of 11:23, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fay is ON HOLD Authors: Funk, M.A., Drennan, C.L. Description: Y208F mutant of choline TMA-lyase Category: Unreleased Structures [[Category: F...

OCA — Wed, 23 Dec 2015 11:23:15 GMT

New page: '''Unreleased structure''' The entry 5fay is ON HOLD Authors: Funk, M.A., Drennan, C.L. Description: Y208F mutant of choline TMA-lyase Category: Unreleased Structures [[Category: F...

New page

'''Unreleased structure'''

The entry 5fay is ON HOLD

Authors: Funk, M.A., Drennan, C.L.

Description: Y208F mutant of choline TMA-lyase
[[Category: Unreleased Structures]]
[[Category: Funk, M.A]]
[[Category: Drennan, C.L]]