6b2o - Revision history

OCA at 14:31, 4 October 2023

OCA — Wed, 04 Oct 2023 14:31:46 GMT

←Older revision		Revision as of 14:31, 4 October 2023
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	<StructureSection load='6b2o' size='340' side='right'caption='[[6b2o]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='6b2o' size='340' side='right'caption='[[6b2o]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b2o]] 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=6B2O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6B2O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b2o]] 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=6B2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B2O FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=PO4:PHOSPHATE+ION'>PO4</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.35Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6b2m\|6b2m]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">A8P51_04975, AVR82_02840, BIZ32_00440, IV39_GL000116, LPJSA22_00116, 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=6b2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b2o OCA], [https://pdbe.org/6b2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b2o RCSB], [https://www.ebi.ac.uk/pdbsum/6b2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b2o 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=6b2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b2o OCA], [~~http~~://pdbe.org/6b2o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6b2o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6b2o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6b2o 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lactobacillus arabinosus fred et al~~]]	+	[[Category: Lactiplantibacillus plantarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[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: Cysteine to alanine]]~~	+
-	~~[[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 08:16, 27 November 2019

OCA — Wed, 27 Nov 2019 08:16:37 GMT

←Older revision		Revision as of 08:16, 27 November 2019
Line 1:		Line 1:

	==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, C176A variant==		==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, C176A variant==
-	<StructureSection load='6b2o' size='340' side='right' caption='[[6b2o]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='6b2o' size='340' side='right'caption='[[6b2o]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6b2o]] 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=6B2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B2O FirstGlance]. <br>		<table><tr><td colspan='2'>[[6b2o]] 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=6B2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B2O FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Lactobacillus arabinosus fred et al]]		[[Category: Lactobacillus arabinosus fred et al]]
		+	[[Category: Large Structures]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]
	[[Category: Hausinger, R P]]		[[Category: Hausinger, R P]]

OCA at 07:49, 12 September 2018

OCA — Wed, 12 Sep 2018 07:49:13 GMT

←Older revision		Revision as of 07:49, 12 September 2018
Line 3:		Line 3:
	<StructureSection load='6b2o' size='340' side='right' caption='[[6b2o]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='6b2o' size='340' side='right' caption='[[6b2o]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b2o]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B2O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b2o]] 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=6B2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B2O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6b2m\|6b2m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6b2m\|6b2m]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">A8P51_04975, AVR82_02840, BIZ32_00440, IV39_GL000116, LPJSA22_00116, 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=6b2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b2o OCA], [http://pdbe.org/6b2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b2o RCSB], [http://www.ebi.ac.uk/pdbsum/6b2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b2o 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=6b2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b2o OCA], [http://pdbe.org/6b2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b2o RCSB], [http://www.ebi.ac.uk/pdbsum/6b2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b2o ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LarE from Lactobacillus plantarum is an ATP-dependent sulfur transferase that sacrifices its Cys176 sulfur atom to form a dehydroalanine (Dha) side chain during biosynthesis of the covalently linked nickel-pincer nucleotide (NPN) cofactor (pyridinium 3-thioamide-5-thiocarboxylic acid mononucleotide) of lactate racemase. Coenzyme A (CoA) stabilizes LarE and forms a CoA-Cys176 mixed disulfide with the protein. This study presents the crystal structure of the LarE/CoA complex, revealing protein interactions with CoA that mimic those for binding ATP. CoA weakly inhibits LarE activity, and the persulfide of CoA is capable of partially regenerating functional LarE from the Dha176 form of the protein. The physiological relevance of this cycling reaction is unclear. A new form of LarE was discovered, an NPN-LarE covalent adduct, explaining prior results in which activation of the lactate racemase apoprotein required only the isolated LarE. The crystal structure of the inactive C176A variant revealed a fold essentially identical to that of wild-type LarE. Additional active site variants of LarE were created and their activities characterized, with all LarE variants analyzed in terms of the structure. Finally, the L. plantarum LarE structure was compared to a homology model of Thermoanaerobacterium thermosaccharolyticum LarE, predicted to contain three cysteine residues at the active site, and to other proteins with a similar fold and multiple active site cysteine residues. These findings suggest that some LarE orthologs may not be sacrificial but instead may catalyze sulfur transfer by using a persulfide mechanism or from a labile site on a [4Fe-4S] cluster at this position.
		+
		+	Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum.,Fellner M, Rankin JA, Desguin B, Hu J, Hausinger RP Biochemistry. 2018 Sep 11. doi: 10.1021/acs.biochem.8b00601. PMID:30157639<ref>PMID:30157639</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6b2o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lactobacillus arabinosus fred et al]]
	[[Category: Fellner, M]]		[[Category: Fellner, M]]
	[[Category: Hausinger, R P]]		[[Category: Hausinger, R P]]

OCA at 10:03, 5 September 2018

OCA — Wed, 05 Sep 2018 10:03:51 GMT

←Older revision		Revision as of 10:03, 5 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6b2o is ~~ON HOLD until Paper Publication~~	+	==LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, C176A variant==
-		+	<StructureSection load='6b2o' size='340' side='right' caption='[[6b2o]], [[Resolution\|resolution]] 2.35Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6b2o]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B2O FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6b2m\|6b2m]]</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=6b2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b2o OCA], [http://pdbe.org/6b2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b2o RCSB], [http://www.ebi.ac.uk/pdbsum/6b2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b2o ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fellner, M]]
		+	[[Category: Hausinger, R P]]
		+	[[Category: Hu, J]]
		+	[[Category: Ampylation]]
		+	[[Category: Atp]]
		+	[[Category: Atp pyrophophatase domain]]
		+	[[Category: Cysteine to alanine]]
		+	[[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: Protected "6b2o" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 17:06:41 GMT

Protected "6b2o" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:06, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6b2o is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 17:06:40 GMT

New page: '''Unreleased structure''' The entry 6b2o is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6b2o is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]