6bwo - Revision history

OCA at 14:24, 13 March 2024

2024-03-13T14:24:43Z

←Older revision		Revision as of 14:24, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6bwo' size='340' side='right'caption='[[6bwo]], [[Resolution\|resolution]] 2.03Å' scene=''>		<StructureSection load='6bwo' size='340' side='right'caption='[[6bwo]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bwo]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BWO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BWO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bwo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum Lactiplantibacillus plantarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BWO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BWO 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=6bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bwo OCA], [~~http~~://pdbe.org/6bwo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bwo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bwo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bwo 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]] 2.03Å</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=6bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bwo OCA], [https://pdbe.org/6bwo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bwo RCSB], [https://www.ebi.ac.uk/pdbsum/6bwo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bwo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LARC_LACPL LARC_LACPL]] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes.<ref>PMID:24710389</ref> <ref>PMID:27114550</ref>	+	[https://www.uniprot.org/uniprot/LARC_LACPL LARC_LACPL] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes.<ref>PMID:24710389</ref> <ref>PMID:27114550</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Bacterial lactate racemase is a nickel-dependent enzyme that contains a cofactor, nickel pyridinium-3,5-bisthiocarboxylic acid mononucleotide, hereafter named nickel-pincer nucleotide (NPN). The LarC enzyme from the bacterium Lactobacillus plantarum participates in NPN biosynthesis by inserting nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide,. This reaction, known in organometallic chemistry as a cyclometalation, is characterized by the formation of new metal-carbon and metal-sulfur sigma bonds. LarC is therefore the first cyclometallase identified in nature, but the molecular mechanism of LarC-catalyzed cylometalation is unknown. Here, we show that LarC activity requires Mn(2+)-dependent CTP hydrolysis. The crystal structure of the C-terminal domain of LarC at 1.85 A resolution revealed a hexameric ferredoxin-like fold and an unprecedented CTP binding pocket. The loss of function of LarC variants with alanine variants of acidic residues lead us to propose a carboxylate-assisted mechanism for nickel insertion. This works also demonstrates the in vitro synthesis and purification of the NPN cofactor, opening new opportunities for the study of this intriguing cofactor and of NPN-utilizing enzymes.	+
-		+
-	Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.,Desguin B, Fellner M, Riant O, Hu J, Hausinger R, Hols P, Soumillion P J Biol Chem. 2018 Jun 10. pii: RA118.003741. doi: 10.1074/jbc.RA118.003741. PMID:29887527<ref>PMID:29887527</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6bwo" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lactobacillus arabinosus fred et al~~]]	+	[[Category: Lactiplantibacillus plantarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Desguin, B]]	+	[[Category: Desguin B]]
-	[[Category: Fellner, M]]	+	[[Category: Fellner M]]
-	[[Category: Hausinger~~, R P~~]]	+	[[Category: Hausinger RP]]
-	[[Category: Hu, J]]	+	[[Category: Hu J]]
-	~~[[Category: Ctp]]~~	+
-	~~[[Category: Hexamer]]~~	+
-	~~[[Category: Lactate]]~~	+
-	~~[[Category: Lactate racemase]]~~	+
-	~~[[Category: Lactate racemization]]~~	+
-	~~[[Category: Lar]]~~	+
-	~~[[Category: Larc]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Nickel]]~~	+
-	~~[[Category: Nickel transferase]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 08:21, 27 November 2019

2019-11-27T08:21:28Z

←Older revision		Revision as of 08:21, 27 November 2019
Line 1:		Line 1:

	==LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, apo form==		==LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, apo form==
-	<StructureSection load='6bwo' size='340' side='right' caption='[[6bwo]], [[Resolution\|resolution]] 2.03Å' scene=''>	+	<StructureSection load='6bwo' size='340' side='right'caption='[[6bwo]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bwo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BWO FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bwo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BWO FirstGlance]. <br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Lactobacillus arabinosus fred et al]]		[[Category: Lactobacillus arabinosus fred et al]]
		+	[[Category: Large Structures]]
	[[Category: Desguin, B]]		[[Category: Desguin, B]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]

OCA at 05:53, 27 June 2018

2018-06-27T05:53:20Z

←Older revision		Revision as of 05:53, 27 June 2018
Line 3:		Line 3:
	<StructureSection load='6bwo' size='340' side='right' caption='[[6bwo]], [[Resolution\|resolution]] 2.03Å' scene=''>		<StructureSection load='6bwo' size='340' side='right' caption='[[6bwo]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bwo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BWO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bwo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BWO 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=6bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bwo OCA], [http://pdbe.org/6bwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bwo RCSB], [http://www.ebi.ac.uk/pdbsum/6bwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bwo ProSAT]</span></td></tr>		</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=6bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bwo OCA], [http://pdbe.org/6bwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bwo RCSB], [http://www.ebi.ac.uk/pdbsum/6bwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bwo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/LARC_LACPL LARC_LACPL]] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes.<ref>PMID:24710389</ref> <ref>PMID:27114550</ref>		[[http://www.uniprot.org/uniprot/LARC_LACPL LARC_LACPL]] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes.<ref>PMID:24710389</ref> <ref>PMID:27114550</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial lactate racemase is a nickel-dependent enzyme that contains a cofactor, nickel pyridinium-3,5-bisthiocarboxylic acid mononucleotide, hereafter named nickel-pincer nucleotide (NPN). The LarC enzyme from the bacterium Lactobacillus plantarum participates in NPN biosynthesis by inserting nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide,. This reaction, known in organometallic chemistry as a cyclometalation, is characterized by the formation of new metal-carbon and metal-sulfur sigma bonds. LarC is therefore the first cyclometallase identified in nature, but the molecular mechanism of LarC-catalyzed cylometalation is unknown. Here, we show that LarC activity requires Mn(2+)-dependent CTP hydrolysis. The crystal structure of the C-terminal domain of LarC at 1.85 A resolution revealed a hexameric ferredoxin-like fold and an unprecedented CTP binding pocket. The loss of function of LarC variants with alanine variants of acidic residues lead us to propose a carboxylate-assisted mechanism for nickel insertion. This works also demonstrates the in vitro synthesis and purification of the NPN cofactor, opening new opportunities for the study of this intriguing cofactor and of NPN-utilizing enzymes.
		+
		+	Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.,Desguin B, Fellner M, Riant O, Hu J, Hausinger R, Hols P, Soumillion P J Biol Chem. 2018 Jun 10. pii: RA118.003741. doi: 10.1074/jbc.RA118.003741. PMID:29887527<ref>PMID:29887527</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6bwo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lactobacillus arabinosus fred et al]]
	[[Category: Desguin, B]]		[[Category: Desguin, B]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]

OCA at 05:49, 20 June 2018

2018-06-20T05:49:08Z

←Older revision		Revision as of 05:49, 20 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bwo is ~~ON HOLD~~ ~~until Paper Publication~~	+	==LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, apo form==
-		+	<StructureSection load='6bwo' size='340' side='right' caption='[[6bwo]], [[Resolution\|resolution]] 2.03Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6bwo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BWO FirstGlance]. <br>
-	~~Description~~:	+	</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=6bwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bwo OCA], [http://pdbe.org/6bwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bwo RCSB], [http://www.ebi.ac.uk/pdbsum/6bwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bwo ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LARC_LACPL LARC_LACPL]] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2+), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is required for the activation of the lactate racemase LarA. May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes.<ref>PMID:24710389</ref> <ref>PMID:27114550</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Desguin, B]]
		+	[[Category: Fellner, M]]
		+	[[Category: Hausinger, R P]]
		+	[[Category: Hu, J]]
		+	[[Category: Ctp]]
		+	[[Category: Hexamer]]
		+	[[Category: Lactate]]
		+	[[Category: Lactate racemase]]
		+	[[Category: Lactate racemization]]
		+	[[Category: Lar]]
		+	[[Category: Larc]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Nickel]]
		+	[[Category: Nickel transferase]]
		+	[[Category: Trimer]]

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

2017-12-27T07:19:12Z

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

←Older revision

Revision as of 07:19, 27 December 2017

OCA: New page: '''Unreleased structure''' The entry 6bwo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-12-27T07:19:11Z

New page: '''Unreleased structure''' The entry 6bwo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6bwo is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]