6ra2 - Revision history

OCA at 12:18, 24 January 2024

OCA — Wed, 24 Jan 2024 12:18:00 GMT

←Older revision		Revision as of 12:18, 24 January 2024
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	<StructureSection load='6ra2' size='340' side='right'caption='[[6ra2]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6ra2' size='340' side='right'caption='[[6ra2]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ra2]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"mycobacterium_abcessus"_moore_and_frerichs_1953 "mycobacterium abcessus" moore and frerichs 1953~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RA2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6RA2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ra2]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus Mycobacteroides abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RA2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RA2 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MAB_0303 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~36809~~ "~~Mycobacterium abcessus~~" ~~Moore and Frerichs 1953~~])</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]] 2.3Å</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=6ra2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ra2 OCA], [~~http~~://pdbe.org/6ra2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ra2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ra2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ra2 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=6ra2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ra2 OCA], [https://pdbe.org/6ra2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ra2 RCSB], [https://www.ebi.ac.uk/pdbsum/6ra2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ra2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AQDC_MYCA9 AQDC_MYCA9] Ring-cleaving dioxygenase involved in the degradation pathway of the Pseudomonas aeruginosa quorum sensing signal molecules HHQ (2-heptyl-4-quinolone) and PQS (2-heptyl-3-hydroxy-4(1H)-quinolone) to anthranilate. Catalyzes the cleavage of PQS to form N-octanoylanthranilate and carbon monoxide. Thus, leads to the inactivation of PQS that plays a central role in the regulation of virulence factor production by P.aeruginosa, thereby quenching the production of antimicrobials, which may contribute to the competitiveness of M.abscessus in presence of P.aeruginosa (PubMed:31228546, PubMed:28303132). In vitro, can also use other 2-alkyl-3-hydroxy-4(1H)-quinolone (AHQ) substrates with shorter alkyl substituents at C2, but with lower efficiency (PubMed:31228546).<ref>PMID:28303132</ref> <ref>PMID:31228546</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: Mycobacterium abcessus moore and frerichs 1953]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Fetzner, S~~]]	+	[[Category: Mycobacteroides abscessus]]
-	[[Category: ~~Kobus,~~ S]]	+	[[Category: Fetzner S]]
-	[[Category: ~~Smits,~~ S H]]	+	[[Category: Kobus S]]
-	[[Category: ~~Wullich, S~~]]	+	[[Category: Smits SH]]
-	[[Category: ~~Alpha/beta hydrolase fold]]~~	+	[[Category: Wullich S]]
-	~~[[Category: Catalytic triad]]~~	+
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pseudomonas aeruginosa]]~~	+
-	~~[[Category: Pseudomonas quinolone signal]]~~	+
-	~~[[Category: Quorum sensing~~]]	+

OCA at 07:02, 25 June 2020

OCA — Thu, 25 Jun 2020 07:02:09 GMT

←Older revision		Revision as of 07:02, 25 June 2020
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	<StructureSection load='6ra2' size='340' side='right'caption='[[6ra2]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6ra2' size='340' side='right'caption='[[6ra2]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ra2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RA2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RA2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ra2]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_abcessus"_moore_and_frerichs_1953 "mycobacterium abcessus" moore and frerichs 1953]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RA2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RA2 FirstGlance]. <br>
-	</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=6ra2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ra2 OCA], [http://pdbe.org/6ra2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ra2 RCSB], [http://www.ebi.ac.uk/pdbsum/6ra2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ra2 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAB_0303 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36809 "Mycobacterium abcessus" Moore and Frerichs 1953])</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=6ra2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ra2 OCA], [http://pdbe.org/6ra2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ra2 RCSB], [http://www.ebi.ac.uk/pdbsum/6ra2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ra2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Mycobacterium abcessus moore and frerichs 1953]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fetzner, S]]		[[Category: Fetzner, S]]

OCA at 06:04, 3 July 2019

OCA — Wed, 03 Jul 2019 06:04:00 GMT

←Older revision		Revision as of 06:04, 3 July 2019
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-	'''Unreleased structure'''

-	The entry ~~6ra2~~ is ~~ON HOLD until Apr 05 2021~~	+	==Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqDC==
		+	<StructureSection load='6ra2' size='340' side='right'caption='[[6ra2]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ra2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RA2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RA2 FirstGlance]. <br>
		+	</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=6ra2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ra2 OCA], [http://pdbe.org/6ra2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ra2 RCSB], [http://www.ebi.ac.uk/pdbsum/6ra2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ra2 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cofactor-less dioxygenase AqdC of Mycobacteroides abscessus catalyzes the cleavage and thus inactivation of the Pseudomonas quinolone signal (PQS, 2-heptyl-3-hydroxy-4(1H)-quinolone), which plays a central role in the regulation of virulence factor production by Pseudomonas aeruginosa. We present here the crystal structures of AqdC in its native state and in complex with the PQS cleavage product N-octanoylanthranilic acid, and of mutant AqdC proteins in complex with PQS. AqdC possesses an alpha/beta-hydrolase fold core domain with additional helices forming a cap domain. The protein is traversed by a bipartite tunnel, with a funnel-like entry section leading to an elliptical substrate cavity where PQS positioning is mediated by a combination of hydrophobic interactions and hydrogen bonds, with the substrate's C4 carbonyl and C3 hydroxyl groups tethered by His97 and the catalytic His246, respectively. The side chain of the AqdC-bound product extends deeper into the "alkyl tail section" of the tunnel than PQS, tentatively suggesting product exit via this part of the tunnel. AqdC prefers PQS over congeners with shorter alkyl substituents at C2. Kinetic data confirmed the strict requirement of the active-site base His246 for catalysis, and suggested that evolution of the canonical nucleophile/His/Asp catalytic triad of the hydrolases to an Ala/His/Asp triad is favorable for catalyzing dioxygenolytic PQS ring cleavage.

-	~~Authors: Wullich~~, S., ~~Kobus~~, S., Smits, S.H., ~~Fetzner, S~~.	+	Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqdC, a mycobacterial dioxygenase of the alpha/beta-hydrolase fold family.,Wullich SC, Kobus S, Wienhold M, Hennecke U, Smits SHJ, Fetzner S J Struct Biol. 2019 Jun 19. pii: S1047-8477(19)30135-2. doi:, 10.1016/j.jsb.2019.06.006. PMID:31228546<ref>PMID:31228546</ref>

-	~~Description: Structural basis for recognition and ring-cleavage~~ of the ~~Pseudomonas quinolone signal (PQS) by AqDC~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Kobus, S~~]]	+	<div class="pdbe-citations 6ra2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fetzner, S]]		[[Category: Fetzner, S]]
-	[[Category: Smits, S.H]]	+	[[Category: Kobus, S]]
		+	[[Category: Smits, S H]]
	[[Category: Wullich, S]]		[[Category: Wullich, S]]
		+	[[Category: Alpha/beta hydrolase fold]]
		+	[[Category: Catalytic triad]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Pseudomonas quinolone signal]]
		+	[[Category: Quorum sensing]]

OCA: Protected "6ra2" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2019 04:20:38 GMT

Protected "6ra2" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:20, 17 April 2019

OCA: New page: '''Unreleased structure''' The entry 6ra2 is ON HOLD until Apr 05 2021 Authors: Wullich, S., Kobus, S., Smits, S.H., Fetzner, S. Description: Structural basis for recognition and ring-...

OCA — Wed, 17 Apr 2019 04:20:36 GMT

New page: '''Unreleased structure''' The entry 6ra2 is ON HOLD until Apr 05 2021 Authors: Wullich, S., Kobus, S., Smits, S.H., Fetzner, S. Description: Structural basis for recognition and ring-...

New page

'''Unreleased structure'''

The entry 6ra2 is ON HOLD until Apr 05 2021

Authors: Wullich, S., Kobus, S., Smits, S.H., Fetzner, S.

Description: Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqDC
[[Category: Unreleased Structures]]
[[Category: Kobus, S]]
[[Category: Fetzner, S]]
[[Category: Smits, S.H]]
[[Category: Wullich, S]]