6jqm - Revision history

OCA at 10:39, 27 March 2024

OCA — Wed, 27 Mar 2024 10:39:15 GMT

←Older revision		Revision as of 10:39, 27 March 2024
Line 3:		Line 3:
	<SX load='6jqm' size='340' side='right' viewer='molstar' caption='[[6jqm]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6jqm' size='340' side='right' viewer='molstar' caption='[[6jqm]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jqm]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6JQM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jqm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JQM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>paaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=83333 ECOLI])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Oxepin~~-~~CoA_hydrolase Oxepin~~-~~CoA hydrolase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.3.2.12 3.3.2.12]~~ </~~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=6jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqm OCA], [https://pdbe.org/6jqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jqm RCSB], [https://www.ebi.ac.uk/pdbsum/6jqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqm 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=6jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqm OCA], [~~http~~://pdbe.org/6jqm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jqm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jqm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PAAZ_ECOLI PAAZ_ECOLI]] Catalyzes the hydrolytic ring cleavage of 2-oxepin-2(3H)-ylideneacetyl-CoA (oxepin-CoA) via the open-chain aldehyde intermediate to yield 3-oxo-5,6-dehydrosuberyl-CoA. The enzyme consists of a C-terminal (R)-specific enoyl-CoA hydratase domain (formerly MaoC) that cleaves the ring and produces the highly reactive 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde and an N-terminal NADP-dependent aldehyde dehydrogenase domain that oxidizes the aldehyde to 3-oxo-5,6-dehydrosuberyl-CoA. Can also use crotonyl-CoA as substrate.<ref>PMID:20660314</ref> <ref>PMID:21296885</ref> <ref>PMID:9748275</ref>	+	[https://www.uniprot.org/uniprot/PAAZ_ECOLI PAAZ_ECOLI] Catalyzes the hydrolytic ring cleavage of 2-oxepin-2(3H)-ylideneacetyl-CoA (oxepin-CoA) via the open-chain aldehyde intermediate to yield 3-oxo-5,6-dehydrosuberyl-CoA. The enzyme consists of a C-terminal (R)-specific enoyl-CoA hydratase domain (formerly MaoC) that cleaves the ring and produces the highly reactive 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde and an N-terminal NADP-dependent aldehyde dehydrogenase domain that oxidizes the aldehyde to 3-oxo-5,6-dehydrosuberyl-CoA. Can also use crotonyl-CoA as substrate.<ref>PMID:20660314</ref> <ref>PMID:21296885</ref> <ref>PMID:9748275</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.	+
-		+
-	Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.,Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR Nat Commun. 2019 Sep 11;10(1):4127. doi: 10.1038/s41467-019-11931-1. PMID:31511507<ref>PMID:31511507</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6jqm" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Oxepin-CoA hydrolase]]~~	+	[[Category: Cannone G]]
-	[[Category: Cannone, G]]	+	[[Category: Gakher L]]
-	[[Category: Gakher, L]]	+	[[Category: Katagihallimath N]]
-	[[Category: Katagihallimath, N]]	+	[[Category: Sathyanarayanan N]]
-	[[Category: Sathyanarayanan, N]]	+	[[Category: Sowdhamini R]]
-	[[Category: Sowdhamini, R]]	+	[[Category: Vinothkumar KR]]
-	[[Category: Vinothkumar~~, K R]]~~	+
-	~~[[Category: Bi-functional enzyme]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Substrate channeling~~]]	+

OCA at 02:14, 11 April 2020

OCA — Sat, 11 Apr 2020 02:14:32 GMT

←Older revision		Revision as of 02:14, 11 April 2020
Line 3:		Line 3:
	<SX load='6jqm' size='340' side='right' viewer='molstar' caption='[[6jqm]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6jqm' size='340' side='right' viewer='molstar' caption='[[6jqm]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jqm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JQM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jqm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JQM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">paaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">paaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxepin-CoA_hydrolase Oxepin-CoA hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.2.12 3.3.2.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxepin-CoA_hydrolase Oxepin-CoA hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.2.12 3.3.2.12] </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=6jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqm OCA], [http://pdbe.org/6jqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jqm RCSB], [http://www.ebi.ac.uk/pdbsum/6jqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqm 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=6jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqm OCA], [http://pdbe.org/6jqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jqm RCSB], [http://www.ebi.ac.uk/pdbsum/6jqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 22:19, 6 March 2020

OCA — Fri, 06 Mar 2020 22:19:45 GMT

←Older revision		Revision as of 22:19, 6 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jqm is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of PaaZ with NADPH==
		+	<SX load='6jqm' size='340' side='right' viewer='molstar' caption='[[6jqm]], [[Resolution\|resolution]] 3.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jqm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JQM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">paaZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxepin-CoA_hydrolase Oxepin-CoA hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.2.12 3.3.2.12] </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=6jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqm OCA], [http://pdbe.org/6jqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jqm RCSB], [http://www.ebi.ac.uk/pdbsum/6jqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqm ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAAZ_ECOLI PAAZ_ECOLI]] Catalyzes the hydrolytic ring cleavage of 2-oxepin-2(3H)-ylideneacetyl-CoA (oxepin-CoA) via the open-chain aldehyde intermediate to yield 3-oxo-5,6-dehydrosuberyl-CoA. The enzyme consists of a C-terminal (R)-specific enoyl-CoA hydratase domain (formerly MaoC) that cleaves the ring and produces the highly reactive 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde and an N-terminal NADP-dependent aldehyde dehydrogenase domain that oxidizes the aldehyde to 3-oxo-5,6-dehydrosuberyl-CoA. Can also use crotonyl-CoA as substrate.<ref>PMID:20660314</ref> <ref>PMID:21296885</ref> <ref>PMID:9748275</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.

-	~~Authors: Sathyanarayanan~~, N., Cannone, G~~., Gakher~~, L., Katagihallimath, N., Sowdhamini, R., Ramaswamy, S., Vinothkumar~~, K~~.R.	+	Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.,Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR Nat Commun. 2019 Sep 11;10(1):4127. doi: 10.1038/s41467-019-11931-1. PMID:31511507<ref>PMID:31511507</ref>

-	~~Description: Structure~~ of ~~PaaZ with NADPH~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Ramaswamy, S~~]]	+	<div class="pdbe-citations 6jqm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</SX>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
		+	[[Category: Oxepin-CoA hydrolase]]
	[[Category: Cannone, G]]		[[Category: Cannone, G]]
		+	[[Category: Gakher, L]]
	[[Category: Katagihallimath, N]]		[[Category: Katagihallimath, N]]
-	[[Category: Vinothkumar, K.R]]
	[[Category: Sathyanarayanan, N]]		[[Category: Sathyanarayanan, N]]
	[[Category: Sowdhamini, R]]		[[Category: Sowdhamini, R]]
-	[[Category: ~~Gakher~~, L]]	+	[[Category: Vinothkumar, K R]]
		+	[[Category: Bi-functional enzyme]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Substrate channeling]]

OCA at 20:55, 5 June 2019

OCA — Wed, 05 Jun 2019 20:55:42 GMT

←Older revision		Revision as of 20:55, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jqm is ON HOLD	+	The entry 6jqm is ON HOLD until Paper Publication

	Authors: Sathyanarayanan, N., Cannone, G., Gakher, L., Katagihallimath, N., Sowdhamini, R., Ramaswamy, S., Vinothkumar, K.R.		Authors: Sathyanarayanan, N., Cannone, G., Gakher, L., Katagihallimath, N., Sowdhamini, R., Ramaswamy, S., Vinothkumar, K.R.

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

OCA — Wed, 10 Apr 2019 05:22:50 GMT

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

←Older revision

Revision as of 05:22, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6jqm is ON HOLD Authors: Sathyanarayanan, N., Cannone, G., Gakher, L., Katagihallimath, N., Sowdhamini, R., Ramaswamy, S., Vinothkumar, K.R. Descri...

OCA — Wed, 10 Apr 2019 05:22:49 GMT

New page: '''Unreleased structure''' The entry 6jqm is ON HOLD Authors: Sathyanarayanan, N., Cannone, G., Gakher, L., Katagihallimath, N., Sowdhamini, R., Ramaswamy, S., Vinothkumar, K.R. Descri...

New page

'''Unreleased structure'''

The entry 6jqm is ON HOLD

Authors: Sathyanarayanan, N., Cannone, G., Gakher, L., Katagihallimath, N., Sowdhamini, R., Ramaswamy, S., Vinothkumar, K.R.

Description: Structure of PaaZ with NADPH
[[Category: Unreleased Structures]]
[[Category: Ramaswamy, S]]
[[Category: Cannone, G]]
[[Category: Katagihallimath, N]]
[[Category: Vinothkumar, K.R]]
[[Category: Sathyanarayanan, N]]
[[Category: Sowdhamini, R]]
[[Category: Gakher, L]]