5uds - Revision history

OCA at 13:25, 4 October 2023

2023-10-04T13:25:59Z

←Older revision		Revision as of 13:25, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5uds' size='340' side='right'caption='[[5uds]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='5uds' size='340' side='right'caption='[[5uds]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uds]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lacpl Lacpl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UDS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uds]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactiplantibacillus_plantarum_WCFS1 Lactiplantibacillus plantarum WCFS1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UDS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ATP:ADENOSINE~~-~~5-TRIPHOSPHATE'>ATP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.37Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5udq\|5udq]], [[5udr\|5udr]], [[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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">larE, lp_0109 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220668 LACPL])~~</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=5uds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uds OCA], [https://pdbe.org/5uds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uds RCSB], [https://www.ebi.ac.uk/pdbsum/5uds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uds 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=5uds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uds OCA], [~~http~~://pdbe.org/5uds PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uds RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uds PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uds ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lacpl~~]]	+	[[Category: Lactiplantibacillus plantarum WCFS1]]
	[[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]]~~	+
-	~~[[Category: Atp pyrophophatase domain]]~~	+
-	~~[[Category: Hexamer]]~~	+
-	~~[[Category: Lactate]]~~	+
-	~~[[Category: Lactate racemase]]~~	+
-	~~[[Category: Lactate racemization]]~~	+
-	~~[[Category: Lar]]~~	+
-	~~[[Category: Lare]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Pp-loop]]~~	+
-	~~[[Category: Sulfur transferase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 07:57, 27 November 2019

2019-11-27T07:57:46Z

←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 MgATP==		==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with MgATP==
-	<StructureSection load='5uds' size='340' side='right' caption='[[5uds]], [[Resolution\|resolution]] 2.37Å' scene=''>	+	<StructureSection load='5uds' size='340' side='right'caption='[[5uds]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5uds]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Lacpl Lacpl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5uds]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Lacpl Lacpl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDS FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Lacpl]]		[[Category: Lacpl]]
		+	[[Category: Large Structures]]
	[[Category: Desguin, B]]		[[Category: Desguin, B]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]

OCA at 21:05, 15 November 2017

2017-11-15T21:05:08Z

←Older revision		Revision as of 21:05, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5uds' size='340' side='right' caption='[[5uds]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='5uds' size='340' side='right' caption='[[5uds]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uds]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uds]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Lacpl Lacpl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5udq\|5udq]], [[5udr\|5udr]], [[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]], [[5udr\|5udr]], [[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">larE, lp_0109 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220668 LACPL])</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=5uds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uds OCA], [http://pdbe.org/5uds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uds RCSB], [http://www.ebi.ac.uk/pdbsum/5uds PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uds 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=5uds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uds OCA], [http://pdbe.org/5uds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uds RCSB], [http://www.ebi.ac.uk/pdbsum/5uds PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uds ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lacpl]]
	[[Category: Desguin, B]]		[[Category: Desguin, B]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]

OCA at 11:02, 24 August 2017

2017-08-24T11:02:04Z

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

-	~~The entry~~ 5uds is ~~ON HOLD until Paper~~ Publication	+	==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with MgATP==
		+	<StructureSection load='5uds' size='340' side='right' caption='[[5uds]], [[Resolution\|resolution]] 2.37Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uds]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5udq\|5udq]], [[5udr\|5udr]], [[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=5uds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uds OCA], [http://pdbe.org/5uds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uds RCSB], [http://www.ebi.ac.uk/pdbsum/5uds PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uds 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 5uds" 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]]
		+	[[Category: Atp pyrophophatase domain]]
		+	[[Category: Hexamer]]
		+	[[Category: Lactate]]
		+	[[Category: Lactate racemase]]
		+	[[Category: Lactate racemization]]
		+	[[Category: Lar]]
		+	[[Category: Lare]]
		+	[[Category: Magnesium]]
		+	[[Category: Pp-loop]]
		+	[[Category: Sulfur transferase]]
		+	[[Category: Transferase]]
		+	[[Category: Trimer]]

OCA at 14:44, 18 January 2017

2017-01-18T14:44:04Z

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

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

	Authors:		Authors:

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

2017-01-04T15:43:12Z

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

←Older revision

Revision as of 15:43, 4 January 2017

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

2017-01-04T15:43:11Z

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

New page

'''Unreleased structure'''

The entry 5uds is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]