6coj - Revision history

OCA at 15:08, 4 October 2023

OCA — Wed, 04 Oct 2023 15:08:36 GMT

←Older revision		Revision as of 15:08, 4 October 2023
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	==Crystal structure of Rhodococcus jostii RHA1 IpdAB E105A COCHEA-COA complex==		==Crystal structure of Rhodococcus jostii RHA1 IpdAB E105A COCHEA-COA complex==
-	<StructureSection load='6coj' size='340' side='right' caption='[[6coj]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='6coj' size='340' side='right'caption='[[6coj]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6coj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhojr Rhojr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6COJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6coj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_jostii_RHA1 Rhodococcus jostii RHA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6COJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F8G:S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl}+(5R,10R)-7-hydroxy-10-methyl-2-oxo-1-oxaspiro[4.5]dec-6-ene-6-carbothioate+(non-preferred+name)'>F8G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.4Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RHA1_ro04651 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR]), RHA1_ro04650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F8G:S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl}+(5R,10R)-7-hydroxy-10-methyl-2-oxo-1-oxaspiro[4.5]dec-6-ene-6-carbothioate+(non-preferred+name)'>F8G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6coj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6coj OCA], [~~http~~://pdbe.org/6coj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6coj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6coj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6coj 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=6coj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6coj OCA], [https://pdbe.org/6coj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6coj RCSB], [https://www.ebi.ac.uk/pdbsum/6coj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6coj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IPDA_RHOJR IPDA_RHOJR] Involved in the final steps of cholesterol and steroid degradation (PubMed:28377529, PubMed:29581275). Opens the last steroid ring of cholesterol by catalyzing the hydrolysis of (3E)-2-(2-carboxylatoethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA) to 6-methyl-3,7-dioxodecanedioyl-CoA (MeDODA-CoA) (Probable) (PubMed:29581275).<ref>PMID:28377529</ref> <ref>PMID:29581275</ref> <ref>PMID:28377529</ref>
	<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: ~~Rhojr~~]]	+	[[Category: Large Structures]]
-	[[Category: Crowe~~, A M~~]]	+	[[Category: Rhodococcus jostii RHA1]]
-	[[Category: Eltis~~, L D~~]]	+	[[Category: Crowe AM]]
-	[[Category: Strynadka~~, N C.J~~]]	+	[[Category: Eltis LD]]
-	[[Category: Watanabe, N]]	+	[[Category: Strynadka NCJ]]
-	[[Category: Workman~~, S D~~]]	+	[[Category: Watanabe N]]
-	[[Category: Worrall~~, L J]]~~	+	[[Category: Workman SD]]
-	~~[[Category: Cholesterol]]~~	+	[[Category: Worrall LJ]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ring cleaving]]~~	+
-	~~[[Category: Virulence factor~~]]	+

OCA at 08:10, 14 June 2018

OCA — Thu, 14 Jun 2018 08:10:29 GMT

←Older revision		Revision as of 08:10, 14 June 2018
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Rhojr]]		[[Category: Rhojr]]
-	[[Category: ~~Crow~~, A M]]	+	[[Category: Crowe, A M]]
	[[Category: Eltis, L D]]		[[Category: Eltis, L D]]
	[[Category: Strynadka, N C.J]]		[[Category: Strynadka, N C.J]]

OCA at 14:21, 11 April 2018

OCA — Wed, 11 Apr 2018 14:21:29 GMT

←Older revision		Revision as of 14:21, 11 April 2018
Line 3:		Line 3:
	<StructureSection load='6coj' size='340' side='right' caption='[[6coj]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6coj' size='340' side='right' caption='[[6coj]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6coj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6COJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6coj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhojr Rhojr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6COJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F8G:S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl}+(5R,10R)-7-hydroxy-10-methyl-2-oxo-1-oxaspiro[4.5]dec-6-ene-6-carbothioate+(non-preferred+name)'>F8G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F8G:S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl}+(5R,10R)-7-hydroxy-10-methyl-2-oxo-1-oxaspiro[4.5]dec-6-ene-6-carbothioate+(non-preferred+name)'>F8G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RHA1_ro04651 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR]), RHA1_ro04650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR])</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=6coj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6coj OCA], [http://pdbe.org/6coj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6coj RCSB], [http://www.ebi.ac.uk/pdbsum/6coj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6coj 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=6coj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6coj OCA], [http://pdbe.org/6coj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6coj RCSB], [http://www.ebi.ac.uk/pdbsum/6coj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6coj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycobacterium tuberculosis (Mtb) grows on host-derived cholesterol during infection. IpdAB, found in all steroid-degrading bacteria and a determinant of pathogenicity, has been implicated in the hydrolysis of the last steroid ring. Phylogenetic analyses revealed that IpdAB orthologs form a clade of CoA transferases (CoTs). In a coupled assay with a thiolase, IpdAB transformed the cholesterol catabolite (R)-2-(2-carboxyethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA) and CoASH to 4-methyl-5-oxo-octanedioyl-CoA (MOODA-CoA) and acetyl-CoA with high specificity (kcat/Km = 5.8 +/- 0.8 x 10(4) M(-1)s(-1)). The structure of MOODA-CoA was consistent with IpdAB hydrolyzing COCHEA-CoA to a beta-keto-thioester, a thiolase substrate. Contrary to characterized CoTs, IpdAB exhibited no activity toward small CoA thioesters. Further, IpdAB lacks the catalytic glutamate residue that is conserved in the beta-subunit of characterized CoTs and a glutamyl-CoA intermediate was not trapped during turnover. By contrast, Glu105(A), conserved in the alpha-subunit of IpdAB, was essential for catalysis. A crystal structure of the IpdAB.COCHEA-CoA complex, solved to 1.4 A, revealed that Glu105(A) is positioned to act as a catalytic base. Upon titration with COCHEA-CoA, the E105A(A) variant accumulated a yellow-colored species (lambdamax = 310 nm; Kd = 0.4 +/- 0.2 muM) typical of beta-keto enolates. In the presence of D2O, IpdAB catalyzed the deuteration of COCHEA-CoA adjacent to the hydroxylation site at rates consistent with kcat Based on these data and additional IpdAB variants, we propose a retro-Claisen condensation-like mechanism for the IpdAB-mediated hydrolysis of COCHEA-CoA. This study expands the range of known reactions catalyzed by the CoT superfamily and provides mechanistic insight into an important determinant of Mtb pathogenesis.
		+
		+	IpdAB, a virulence factor in Mycobacterium tuberculosis, is a cholesterol ring-cleaving hydrolase.,Crowe AM, Workman SD, Watanabe N, Worrall LJ, Strynadka NCJ, Eltis LD Proc Natl Acad Sci U S A. 2018 Mar 26. pii: 1717015115. doi:, 10.1073/pnas.1717015115. PMID:29581275<ref>PMID:29581275</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6coj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Rhojr]]
	[[Category: Crow, A M]]		[[Category: Crow, A M]]
	[[Category: Eltis, L D]]		[[Category: Eltis, L D]]

OCA at 06:41, 28 March 2018

OCA — Wed, 28 Mar 2018 06:41:15 GMT

←Older revision		Revision as of 06:41, 28 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6coj ~~is ON HOLD~~	+	==Crystal structure of Rhodococcus jostii RHA1 IpdAB E105A COCHEA-COA complex==
-		+	<StructureSection load='6coj' size='340' side='right' caption='[[6coj]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors~~: ~~Crow, A~~.M.~~, Workman, S~~.D., ~~Watanabe~~, N., ~~Worrall~~, L.J., ~~Strynadka~~, N.C.J., ~~Eltis~~, L.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6coj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6COJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6COJ FirstGlance]. <br>
-	~~Description: Crystal structure of Rhodococcus jostii RHA1 IpdAB E105A COCHEA-COA complex~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F8G:S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl}+(5R,10R)-7-hydroxy-10-methyl-2-oxo-1-oxaspiro[4.5]dec-6-ene-6-carbothioate+(non-preferred+name)'>F8G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6coj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6coj OCA], [http://pdbe.org/6coj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6coj RCSB], [http://www.ebi.ac.uk/pdbsum/6coj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6coj ProSAT]</span></td></tr>
-	[[Category: ~~Worrall~~, L.J]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Crow, A M]]
		+	[[Category: Eltis, L D]]
		+	[[Category: Strynadka, N C.J]]
	[[Category: Watanabe, N]]		[[Category: Watanabe, N]]
-	[[Category: ~~Crow~~, ~~A.M~~]]	+	[[Category: Workman, S D]]
-	[[Category: ~~Workman~~, ~~S.D~~]]	+	[[Category: Worrall, L J]]
-	[[Category: ~~Strynadka, N.C.J~~]]	+	[[Category: Cholesterol]]
-	[[Category: ~~Eltis, L.D~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Ring cleaving]]
		+	[[Category: Virulence factor]]

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

OCA — Wed, 21 Mar 2018 06:10:39 GMT

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

←Older revision

Revision as of 06:10, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 6coj is ON HOLD Authors: Crow, A.M., Workman, S.D., Watanabe, N., Worrall, L.J., Strynadka, N.C.J., Eltis, L.D. Description: Crystal structure of R...

OCA — Wed, 21 Mar 2018 06:10:38 GMT

New page: '''Unreleased structure''' The entry 6coj is ON HOLD Authors: Crow, A.M., Workman, S.D., Watanabe, N., Worrall, L.J., Strynadka, N.C.J., Eltis, L.D. Description: Crystal structure of R...

New page

'''Unreleased structure'''

The entry 6coj is ON HOLD

Authors: Crow, A.M., Workman, S.D., Watanabe, N., Worrall, L.J., Strynadka, N.C.J., Eltis, L.D.

Description: Crystal structure of Rhodococcus jostii RHA1 IpdAB E105A COCHEA-COA complex
[[Category: Unreleased Structures]]
[[Category: Worrall, L.J]]
[[Category: Watanabe, N]]
[[Category: Crow, A.M]]
[[Category: Workman, S.D]]
[[Category: Strynadka, N.C.J]]
[[Category: Eltis, L.D]]