7xkg - Revision history

OCA at 19:46, 29 May 2024

OCA — Wed, 29 May 2024 19:46:04 GMT

←Older revision		Revision as of 19:46, 29 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7xkg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseiflexus_castenholzii_DSM_13941 Roseiflexus castenholzii DSM 13941]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKG FirstGlance]. <br>		<table><tr><td colspan='2'>[[7xkg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseiflexus_castenholzii_DSM_13941 Roseiflexus castenholzii DSM 13941]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKG FirstGlance]. <br>
-	</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=7xkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkg OCA], [https://pdbe.org/7xkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkg RCSB], [https://www.ebi.ac.uk/pdbsum/7xkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkg ProSAT]</span></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]] 2.5Å</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=7xkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkg OCA], [https://pdbe.org/7xkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkg RCSB], [https://www.ebi.ac.uk/pdbsum/7xkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A7NHS9_ROSCS A7NHS9_ROSCS]]	+	[https://www.uniprot.org/uniprot/A7NHS9_ROSCS A7NHS9_ROSCS]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Coenzyme A (CoA) transferases catalyze reversible transfer of CoA groups from CoA-thioesters to free acids, playing important roles in the metabolism of carboxylic acids in all organisms. An intramolecular CoA transferase, Mesaconyl-CoA C1-C4 CoA transferase (MCT) was identified in the autotrophic CO(2) fixation pathway, 3-hydroxypropionic acid cycle of filamentous anoxygenic phototrophs (FAPs). Different from the well-known CoA transferases that catalyze CoA transfer between two distinct substrates, MCT specifically catalyzes the reversible transformation of mesaconyl-C1-CoA to mesaconyl-C4-CoA, a key reaction intermediate for carbon fixation. However, the molecular mechanism of MCT in employing one substrate is enigmatic. Here we determined the crystal structure of MCT from a chlorosome-less FAP Roseiflexus castenholzii at 2.5 A resolution, and characterized the catalytic mechanisms through structural analyses and molecular dynamic simulations. The structure of R. castenholzii MCT consists of a Rossmann fold larger domain and a small domain that are connected by two linkers. Two MCT subunits are cross interlocked at the linker regions to form a functional dimer in solution, in which the substrate binding pockets are located at the interface of the Rossmann fold larger domain from one subunit and the small domain from the other subunit. In the simulated binding structures, both the substrate mesaconyl-C1-CoA and product mesaconyl-C4-CoA form extensive electrostatic and hydrogen bonding interactions with MCT. But some differences exist in the binding mode of these two CoA analogs, Arg314' from the second subunit of the dimer presenting dramatic conformational changes in binding with mesaconyl-C4-CoA. Together with Arg47 and one water molecule, a strictly conserved residue Asp165 are essential for catalyzing the reversible intramolecular CoA transfer reaction, through the electrostatic and hydrogen bonding interactions with the mesaconic tail of both the substrate and product. This study revealed a previously unrecognized mechanism for the uncommon intramolecular CoA transfer reaction, which will not only broaden the knowledge on the catalytic mechanisms of CoA transferases, but also contribute to enzyme engineering or biosynthetic applications of the 3-HP cycle for synthesis of fine chemicals and important metabolites.
		+
		+	Crystal Structure of an Intramolecular Mesaconyl-Coenzyme A Transferase From the 3-Hydroxypropionic Acid Cycle of Roseiflexus castenholzii.,Min Z, Zhang X, Wu W, Xin Y, Liu M, Wang K, Zhang X, He Y, Fan C, Wang Z, Xu X Front Microbiol. 2022 May 26;13:923367. doi: 10.3389/fmicb.2022.923367. , eCollection 2022. PMID:35711761<ref>PMID:35711761</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7xkg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:25, 8 September 2022

OCA — Thu, 08 Sep 2022 07:25:54 GMT

←Older revision		Revision as of 07:25, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7xkg' size='340' side='right'caption='[[7xkg]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='7xkg' size='340' side='right'caption='[[7xkg]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7xkg]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7xkg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Roseiflexus_castenholzii_DSM_13941 Roseiflexus castenholzii DSM 13941]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKG FirstGlance]. <br>
	</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=7xkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkg OCA], [https://pdbe.org/7xkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkg RCSB], [https://www.ebi.ac.uk/pdbsum/7xkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkg ProSAT]</span></td></tr>		</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=7xkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkg OCA], [https://pdbe.org/7xkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkg RCSB], [https://www.ebi.ac.uk/pdbsum/7xkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkg ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/A7NHS9_ROSCS A7NHS9_ROSCS]]
-	Coenzyme A (CoA) transferases catalyze reversible transfer of CoA groups from CoA-thioesters to free acids, playing important roles in the metabolism of carboxylic acids in all organisms. An intramolecular CoA transferase, Mesaconyl-CoA C1-C4 CoA transferase (MCT) was identified in the autotrophic CO2 fixation pathway, 3-hydroxypropionic acid cycle of filamentous anoxygenic phototrophs (FAPs). Different from the well-known CoA transferases that catalyze CoA transfer between two distinct substrates, MCT specifically catalyzes the reversible transformation of mesaconyl-C1-CoA to mesaconyl-C4-CoA, a key reaction intermediate for carbon fixation. However, the molecular mechanism of MCT in employing one substrate is enigmatic. Here we determined the crystal structure of MCT from a chlorosome-less FAP Roseiflexus castenholzii at 2.5 A resolution, and characterized the catalytic mechanisms through structural analyses and molecular dynamic simulations. The structure of R. castenholzii MCT consists of a Rossmann fold larger domain and a small domain that are connected by two linkers. Two MCT subunits are cross interlocked at the linker regions to form a functional dimer in solution, in which the substrate binding pockets are located at the interface of the Rossmann fold larger domain from one subunit and the small domain from the other subunit. In the simulated binding structures, both the substrate mesaconyl-C1-CoA and product mesaconyl-C4-CoA form extensive electrostatic and hydrogen bonding interactions with MCT. But some differences exist in the binding mode of these two CoA analogs, Arg314' from the second subunit of the dimer presenting dramatic conformational changes in binding with mesaconyl-C4-CoA. Together with Arg47 and one water molecule, a strictly conserved residue Asp165 are essential for catalyzing the reversible intramolecular CoA transfer reaction, through the electrostatic and hydrogen bonding interactions with the mesaconic tail of both the substrate and product. This study revealed a previously unrecognized mechanism for the uncommon intramolecular CoA transfer reaction, which will not only broaden the knowledge on the catalytic mechanisms of CoA transferases, but also contribute to enzyme engineering or biosynthetic applications of the 3-HP cycle for synthesis of fine chemicals and important metabolites.	+
-		+
-	Crystal Structure of an Intramolecular Mesaconyl-Coenzyme A Transferase From the 3-Hydroxypropionic Acid Cycle of Roseiflexus castenholzii.,Min Z, Zhang X, Wu W, Xin Y, Liu M, Wang K, Zhang X, He Y, Fan C, Wang Z, Xu X Front Microbiol. 2022 May 26;13:~~923367. doi: 10.3389~~/~~fmicb.2022.923367., eCollection 2022. PMID:35711761<ref>PMID:35711761<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 7xkg" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fan~~, C P~~]]	+	[[Category: Roseiflexus castenholzii DSM 13941]]
-	[[Category: Liu~~, M H~~]]	+	[[Category: Fan CP]]
-	[[Category: Min~~, Z Z~~]]	+	[[Category: Liu MH]]
-	[[Category: Wang~~, Z G~~]]	+	[[Category: Min ZZ]]
-	[[Category: Wu~~, W P~~]]	+	[[Category: Wang ZG]]
-	[[Category: Xin~~, Y Y~~]]	+	[[Category: Wu WP]]
-	[[Category: Xu~~, X L~~]]	+	[[Category: Xin YY]]
-	[[Category: Zhang, X]]	+	[[Category: Xu XL]]
-	~~[[Category: Transferase~~]]	+	[[Category: Zhang X]]

OCA at 16:27, 6 July 2022

OCA — Wed, 06 Jul 2022 16:27:27 GMT

←Older revision		Revision as of 16:27, 6 July 2022
Line 1:		Line 1:

	==Crystal structure of an intramolecular mesacyl-CoA transferase from the 3-hydroxypropionic acid cycle of Roseiflexus castenholzii==		==Crystal structure of an intramolecular mesacyl-CoA transferase from the 3-hydroxypropionic acid cycle of Roseiflexus castenholzii==
-	<StructureSection load='7xkg' size='340' side='right'caption='[[7xkg]]' scene=''>	+	<StructureSection load='7xkg' size='340' side='right'caption='[[7xkg]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7xkg]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKG FirstGlance]. <br>
	</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=7xkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkg OCA], [https://pdbe.org/7xkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkg RCSB], [https://www.ebi.ac.uk/pdbsum/7xkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkg ProSAT]</span></td></tr>		</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=7xkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkg OCA], [https://pdbe.org/7xkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkg RCSB], [https://www.ebi.ac.uk/pdbsum/7xkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Coenzyme A (CoA) transferases catalyze reversible transfer of CoA groups from CoA-thioesters to free acids, playing important roles in the metabolism of carboxylic acids in all organisms. An intramolecular CoA transferase, Mesaconyl-CoA C1-C4 CoA transferase (MCT) was identified in the autotrophic CO2 fixation pathway, 3-hydroxypropionic acid cycle of filamentous anoxygenic phototrophs (FAPs). Different from the well-known CoA transferases that catalyze CoA transfer between two distinct substrates, MCT specifically catalyzes the reversible transformation of mesaconyl-C1-CoA to mesaconyl-C4-CoA, a key reaction intermediate for carbon fixation. However, the molecular mechanism of MCT in employing one substrate is enigmatic. Here we determined the crystal structure of MCT from a chlorosome-less FAP Roseiflexus castenholzii at 2.5 A resolution, and characterized the catalytic mechanisms through structural analyses and molecular dynamic simulations. The structure of R. castenholzii MCT consists of a Rossmann fold larger domain and a small domain that are connected by two linkers. Two MCT subunits are cross interlocked at the linker regions to form a functional dimer in solution, in which the substrate binding pockets are located at the interface of the Rossmann fold larger domain from one subunit and the small domain from the other subunit. In the simulated binding structures, both the substrate mesaconyl-C1-CoA and product mesaconyl-C4-CoA form extensive electrostatic and hydrogen bonding interactions with MCT. But some differences exist in the binding mode of these two CoA analogs, Arg314' from the second subunit of the dimer presenting dramatic conformational changes in binding with mesaconyl-C4-CoA. Together with Arg47 and one water molecule, a strictly conserved residue Asp165 are essential for catalyzing the reversible intramolecular CoA transfer reaction, through the electrostatic and hydrogen bonding interactions with the mesaconic tail of both the substrate and product. This study revealed a previously unrecognized mechanism for the uncommon intramolecular CoA transfer reaction, which will not only broaden the knowledge on the catalytic mechanisms of CoA transferases, but also contribute to enzyme engineering or biosynthetic applications of the 3-HP cycle for synthesis of fine chemicals and important metabolites.
		+
		+	Crystal Structure of an Intramolecular Mesaconyl-Coenzyme A Transferase From the 3-Hydroxypropionic Acid Cycle of Roseiflexus castenholzii.,Min Z, Zhang X, Wu W, Xin Y, Liu M, Wang K, Zhang X, He Y, Fan C, Wang Z, Xu X Front Microbiol. 2022 May 26;13:923367. doi: 10.3389/fmicb.2022.923367., eCollection 2022. PMID:35711761<ref>PMID:35711761</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7xkg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fan CP]]	+	[[Category: Fan, C P]]
-	[[Category: Liu MH]]	+	[[Category: Liu, M H]]
-	[[Category: Min ZZ]]	+	[[Category: Min, Z Z]]
-	[[Category: Wang ZG]]	+	[[Category: Wang, Z G]]
-	[[Category: Wu WP]]	+	[[Category: Wu, W P]]
-	[[Category: Xin YY]]	+	[[Category: Xin, Y Y]]
-	[[Category: Xu XL]]	+	[[Category: Xu, X L]]
-	[[Category: Zhang X]]	+	[[Category: Zhang, X]]
		+	[[Category: Transferase]]

OCA at 05:12, 15 June 2022

OCA — Wed, 15 Jun 2022 05:12:44 GMT

←Older revision		Revision as of 05:12, 15 June 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7xkg is ~~ON HOLD~~	+	==Crystal structure of an intramolecular mesacyl-CoA transferase from the 3-hydroxypropionic acid cycle of Roseiflexus castenholzii==
-		+	<StructureSection load='7xkg' size='340' side='right'caption='[[7xkg]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKG FirstGlance]. <br>
-	~~Description~~:	+	</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=7xkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkg OCA], [https://pdbe.org/7xkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkg RCSB], [https://www.ebi.ac.uk/pdbsum/7xkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkg ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Fan CP]]
		+	[[Category: Liu MH]]
		+	[[Category: Min ZZ]]
		+	[[Category: Wang ZG]]
		+	[[Category: Wu WP]]
		+	[[Category: Xin YY]]
		+	[[Category: Xu XL]]
		+	[[Category: Zhang X]]

OCA: Protected "7xkg" [edit=sysop:move=sysop]

OCA — Wed, 27 Apr 2022 10:34:55 GMT

Protected "7xkg" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:34, 27 April 2022

OCA: New page: '''Unreleased structure''' The entry 7xkg is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Apr 2022 10:34:54 GMT

New page: '''Unreleased structure''' The entry 7xkg is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7xkg is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]