5udr - Revision history

OCA at 14:26, 6 March 2024

OCA — Wed, 06 Mar 2024 14:26:27 GMT

←Older revision		Revision as of 14:26, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5udr' size='340' side='right'caption='[[5udr]], [[Resolution\|resolution]] 2.62Å' scene=''>		<StructureSection load='5udr' size='340' side='right'caption='[[5udr]], [[Resolution\|resolution]] 2.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5udr]] is a 6 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=5UDR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5udr]] is a 6 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=5UDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UDR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MN:MANGANESE+(II)+ION'>MN</scene~~>, ~~<scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</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]] 2.62Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5udq\|5udq]], [[5udt\|5udt]], [[5udu\|5udu]], [[5udv\|5udv]], [[5udw\|5udw]], [[5udx\|5udx]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">A8P51_04975, IV39_GL000116, Nizo1839_0768, Nizo2891_3302, SRCM101060_01452 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 "Lactobacillus arabinosus" Fred et al.])</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=5udr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udr OCA], [https://pdbe.org/5udr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5udr RCSB], [https://www.ebi.ac.uk/pdbsum/5udr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5udr 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=5udr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udr OCA], [~~http~~://pdbe.org/5udr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5udr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5udr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5udr ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/LARE_LACPL LARE_LACPL] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Catalyzes the ATP-dependent incorporation of two sulfur atoms in pyridinium-3,5-biscarboxylic acid mononucleotide (P2CMN) to yield pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN). The source of sulfur is the enzyme itself: Cys-176 of LarE is the sulfur donor, thereby being converted into dehydroalanine, and is not regenerated in vivo. Thus, two molecules of LarE undergo sacrificial sulfur transfer to create one P2TMN (PubMed:27114550). Binds nickel (PubMed:24710389). Is required for the activation of the lactate racemase LarA (PubMed:24710389). May also be involved in the activation of other nickel-pincer cofactor-dependent enzymes (PubMed:27114550).<ref>PMID:24710389</ref> <ref>PMID:27114550</ref>
-	~~The lar operon in Lactobacillus plantarum encodes five Lar proteins (LarA~~/B/C/D/~~E) that collaboratively synthesize and incorporate~~ a ~~niacin~~-~~derived Ni-containing~~ cofactor ~~into LarA, an~~ Ni-dependent ~~lactate racemase. Previous studies have established that~~ two ~~molecules of LarE catalyze successive thiolation reactions by donating the~~ sulfur atom of their exclusive cysteine residues to the substrate. However, the catalytic mechanism of this very unusual sulfur-sacrificing reaction remains elusive. In this work, we present the crystal structures of LarE in ~~ligand~~-~~free and several ligand-bound forms~~, ~~demonstrating that LarE is a member of the N~~-~~type ATP pyrophosphatase~~ (~~PPase~~) ~~family with a conserved N~~-~~terminal ATP PPase domain and a unique C-terminal domain harboring the putative catalytic site. Structural analysis~~, ~~combined with structure~~-~~guided mutagenesis, leads us to propose a catalytic mechanism that establishes LarE as a paradigm for sulfur transfer through sacrificing its catalytic cysteine residue~~.	+
-		+
-	~~Structural insights into the catalytic mechanism~~ of ~~a sacrificial~~ sulfur ~~insertase of~~ the N-~~type ATP pyrophosphatase family,~~ LarE.,~~Fellner M~~, ~~Desguin B~~, ~~Hausinger RP, Hu J Proc Natl Acad Sci U S A~~. ~~2017 Aug 22;114~~(34):~~9074-9079~~. ~~doi~~:~~, 10~~.~~1073/pnas.1704967114. Epub 2017 Aug 7. PMID:28784764~~<ref>PMID:~~28784764~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5udr" 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: Ampylation]]~~	+
-	~~[[Category: Atp pyrophophatase domain]]~~	+
-	~~[[Category: Hexamer]]~~	+
-	~~[[Category: Lactate]]~~	+
-	~~[[Category: Lactate racemase]]~~	+
-	~~[[Category: Lactate racemization]]~~	+
-	~~[[Category: Lar]]~~	+
-	~~[[Category: Lare]]~~	+
-	~~[[Category: Pp-loop]]~~	+
-	~~[[Category: Sulfur transferase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 07:57, 27 November 2019

OCA — Wed, 27 Nov 2019 07:57:44 GMT

←Older revision		Revision as of 07:57, 27 November 2019
Line 1:		Line 1:

	==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with nicotinamide mononucleotid NMN==		==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with nicotinamide mononucleotid NMN==
-	<StructureSection load='5udr' size='340' side='right' caption='[[5udr]], [[Resolution\|resolution]] 2.62Å' scene=''>	+	<StructureSection load='5udr' size='340' side='right'caption='[[5udr]], [[Resolution\|resolution]] 2.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5udr]] is a 6 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=5UDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5udr]] is a 6 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=5UDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDR FirstGlance]. <br>
Line 23:		Line 23:
	</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 21:04, 15 November 2017

OCA — Wed, 15 Nov 2017 21:04:56 GMT

←Older revision		Revision as of 21:04, 15 November 2017
Line 1:		Line 1:

-	==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase~~, apo form~~==	+	==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with nicotinamide mononucleotid NMN==
	<StructureSection load='5udr' size='340' side='right' caption='[[5udr]], [[Resolution\|resolution]] 2.62Å' scene=''>		<StructureSection load='5udr' size='340' side='right' caption='[[5udr]], [[Resolution\|resolution]] 2.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5udr]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5udr]] is a 6 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=5UDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5udq\|5udq]], [[5udt\|5udt]], [[5udu\|5udu]], [[5udv\|5udv]], [[5udw\|5udw]], [[5udx\|5udx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5udq\|5udq]], [[5udt\|5udt]], [[5udu\|5udu]], [[5udv\|5udv]], [[5udw\|5udw]], [[5udx\|5udx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">A8P51_04975, IV39_GL000116, Nizo1839_0768, Nizo2891_3302, SRCM101060_01452 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 "Lactobacillus arabinosus" Fred et al.])</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=5udr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udr OCA], [http://pdbe.org/5udr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5udr RCSB], [http://www.ebi.ac.uk/pdbsum/5udr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5udr 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=5udr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udr OCA], [http://pdbe.org/5udr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5udr RCSB], [http://www.ebi.ac.uk/pdbsum/5udr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5udr ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lactobacillus arabinosus fred et al]]
	[[Category: Desguin, B]]		[[Category: Desguin, B]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]

OCA at 11:02, 24 August 2017

OCA — Thu, 24 Aug 2017 11:02:12 GMT

←Older revision		Revision as of 11:02, 24 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5udr is ~~ON HOLD until Paper~~ Publication	+	==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, apo form==
		+	<StructureSection load='5udr' size='340' side='right' caption='[[5udr]], [[Resolution\|resolution]] 2.62Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5udr]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5udq\|5udq]], [[5udt\|5udt]], [[5udu\|5udu]], [[5udv\|5udv]], [[5udw\|5udw]], [[5udx\|5udx]]</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=5udr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udr OCA], [http://pdbe.org/5udr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5udr RCSB], [http://www.ebi.ac.uk/pdbsum/5udr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5udr ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The lar operon in Lactobacillus plantarum encodes five Lar proteins (LarA/B/C/D/E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. Previous studies have established that two molecules of LarE catalyze successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to the substrate. However, the catalytic mechanism of this very unusual sulfur-sacrificing reaction remains elusive. In this work, we present the crystal structures of LarE in ligand-free and several ligand-bound forms, demonstrating that LarE is a member of the N-type ATP pyrophosphatase (PPase) family with a conserved N-terminal ATP PPase domain and a unique C-terminal domain harboring the putative catalytic site. Structural analysis, combined with structure-guided mutagenesis, leads us to propose a catalytic mechanism that establishes LarE as a paradigm for sulfur transfer through sacrificing its catalytic cysteine residue.

-	~~Authors~~:	+	Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.,Fellner M, Desguin B, Hausinger RP, Hu J Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):9074-9079. doi:, 10.1073/pnas.1704967114. Epub 2017 Aug 7. PMID:28784764<ref>PMID:28784764</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5udr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Desguin, B]]
		+	[[Category: Fellner, M]]
		+	[[Category: Hausinger, R P]]
		+	[[Category: Hu, J]]
		+	[[Category: Ampylation]]
		+	[[Category: Atp pyrophophatase domain]]
		+	[[Category: Hexamer]]
		+	[[Category: Lactate]]
		+	[[Category: Lactate racemase]]
		+	[[Category: Lactate racemization]]
		+	[[Category: Lar]]
		+	[[Category: Lare]]
		+	[[Category: Pp-loop]]
		+	[[Category: Sulfur transferase]]
		+	[[Category: Transferase]]
		+	[[Category: Trimer]]

OCA at 14:44, 18 January 2017

OCA — Wed, 18 Jan 2017 14:44:01 GMT

←Older revision		Revision as of 14:44, 18 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5udr is ON HOLD	+	The entry 5udr is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5udr" [edit=sysop:move=sysop]

OCA — Wed, 04 Jan 2017 15:43:09 GMT

Protected "5udr" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:43, 4 January 2017

OCA: New page: '''Unreleased structure''' The entry 5udr is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Jan 2017 15:43:07 GMT

New page: '''Unreleased structure''' The entry 5udr is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5udr is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]