6nd3 - Revision history

OCA at 06:49, 11 October 2023

OCA — Wed, 11 Oct 2023 06:49:48 GMT

←Older revision		Revision as of 06:49, 11 October 2023
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	<StructureSection load='6nd3' size='340' side='right'caption='[[6nd3]], [[Resolution\|resolution]] 2.36Å' scene=''>		<StructureSection load='6nd3' size='340' side='right'caption='[[6nd3]], [[Resolution\|resolution]] 2.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nd3]] is a 8 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=6ND3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ND3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nd3]] is a 8 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=6ND3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ND3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=BTL:BETAINE+ALDEHYDE'>BTL</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]] 2.364Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">cutC, Dde_3282 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=207559 DESAG])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTL:BETAINE+ALDEHYDE'>BTL</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nd3 OCA], [https://pdbe.org/6nd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nd3 RCSB], [https://www.ebi.ac.uk/pdbsum/6nd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nd3 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=6nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nd3 OCA], [~~http~~://pdbe.org/6nd3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nd3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nd3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nd3 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 ==
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	__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: ~~Barrel]]~~	+	[[Category: Funk MA]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Radical~~]]	+

OCA at 09:21, 1 May 2019

OCA — Wed, 01 May 2019 09:21:13 GMT

←Older revision		Revision as of 09:21, 1 May 2019
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	==wild-type choline TMA lyase in complex with betaine aldehyde==		==wild-type choline TMA lyase in complex with betaine aldehyde==
-	<StructureSection load='6nd3' size='340' side='right' caption='[[6nd3]], [[Resolution\|resolution]] 2.36Å' scene=''>	+	<StructureSection load='6nd3' size='340' side='right'caption='[[6nd3]], [[Resolution\|resolution]] 2.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nd3]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ND3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nd3]] is a 8 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=6ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ND3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTL:BETAINE+ALDEHYDE'>BTL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTL:BETAINE+ALDEHYDE'>BTL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cutC, 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=6nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nd3 OCA], [http://pdbe.org/6nd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/6nd3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nd3 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=6nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nd3 OCA], [http://pdbe.org/6nd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/6nd3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nd3 ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Choline trimethylamine-lyase]]		[[Category: Choline trimethylamine-lyase]]
		+	[[Category: Desag]]
		+	[[Category: Large Structures]]
	[[Category: Drennan, C L]]		[[Category: Drennan, C L]]
	[[Category: Funk, M A]]		[[Category: Funk, M A]]

OCA at 12:16, 16 January 2019

OCA — Wed, 16 Jan 2019 12:16:08 GMT

←Older revision		Revision as of 12:16, 16 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nd3 is ~~ON HOLD~~	+	==wild-type choline TMA lyase in complex with betaine aldehyde==
		+	<StructureSection load='6nd3' size='340' side='right' caption='[[6nd3]], [[Resolution\|resolution]] 2.36Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6nd3]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ND3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ND3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTL:BETAINE+ALDEHYDE'>BTL</scene></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=6nd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nd3 OCA], [http://pdbe.org/6nd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nd3 RCSB], [http://www.ebi.ac.uk/pdbsum/6nd3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nd3 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 ==
		+	The anaerobic gut microbial pathway that converts choline into trimethylamine (TMA) is broadly linked to human disease. Here, we describe the discovery that betaine aldehyde inhibits TMA production from choline by human gut bacterial isolates and a complex gut community. In vitro assays and a crystal structure suggest betaine aldehyde targets the gut microbial enzyme choline TMA-lyase (CutC). In our system, we do not observe activity for the previously reported CutC inhibitor 3,3-dimethylbutanol (DMB). The workflow we establish for identifying and characterizing betaine aldehyde provides a framework for developing additional inhibitors of gut microbial choline metabolism, including therapeutic candidates.

-	~~Authors:~~ Funk, M~~.A.~~, Drennan, C.L.	+	Structure-Guided Identification of a Small Molecule That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria.,Orman M, Bodea S, Funk MA, Campo AM, Bollenbach M, Drennan CL, Balskus EP J Am Chem Soc. 2018 Dec 17. doi: 10.1021/jacs.8b04883. PMID:30557011<ref>PMID:30557011</ref>

-	~~Description~~: ~~wild~~-~~type choline TMA~~ lyase ~~in complex with betaine aldehyde~~	+	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 6nd3" 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: Barrel]]
		+	[[Category: Lyase]]
		+	[[Category: Radical]]

OCA: Protected "6nd3" [edit=sysop:move=sysop]

OCA — Wed, 19 Dec 2018 06:39:24 GMT

Protected "6nd3" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:39, 19 December 2018

OCA: New page: '''Unreleased structure''' The entry 6nd3 is ON HOLD Authors: Funk, M.A., Drennan, C.L. Description: wild-type choline TMA lyase in complex with betaine aldehyde [[Category: Unreleased...

OCA — Wed, 19 Dec 2018 06:39:22 GMT

New page: '''Unreleased structure''' The entry 6nd3 is ON HOLD Authors: Funk, M.A., Drennan, C.L. Description: wild-type choline TMA lyase in complex with betaine aldehyde [[Category: Unreleased...

New page

'''Unreleased structure'''

The entry 6nd3 is ON HOLD

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

Description: wild-type choline TMA lyase in complex with betaine aldehyde
[[Category: Unreleased Structures]]
[[Category: Funk, M.A]]
[[Category: Drennan, C.L]]