8std - Revision history

OCA at 23:15, 27 December 2023

2023-12-27T23:15:51Z

← Older revision		Revision as of 23:15, 27 December 2023
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	~~'''Unreleased structure'''~~

	~~The entry~~ 8std is ~~ON HOLD until Paper~~ Publication		==S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2==
			<StructureSection load='8std' size='340' side='right'caption='[[8std]], [[Resolution\|resolution]] 2.65Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[8std]] 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=8STD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8STD FirstGlance]. <br>
			</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.65Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DND:NICOTINIC+ACID+ADENINE+DINUCLEOTIDE'>DND</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=8std FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8std OCA], [https://pdbe.org/8std PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8std RCSB], [https://www.ebi.ac.uk/pdbsum/8std PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8std ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/LARB_LACPL LARB_LACPL] Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Carboxylates the pyridinium ring of nicotinic acid adenine dinucleotide (NaAD) and cleaves the phosphoanhydride bond to release AMP and generate pyridinium-3,5-biscarboxylic acid mononucleotide (P2CMN) (PubMed:27114550). LarB can hydrolyze NaAD directly or it first forms an adduct with NaAD that releases AMP and reacts with bicarbonate/CO2 to generate P2CMN (PubMed:27114550). 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;">
			== Publication Abstract from PubMed ==
			LarB catalyzes the first step of biosynthesis for the nickel-pincer nucleotide cofactor by converting nicotinic acid adenine dinucleotide (NaAD) to AMP and pyridinium-3,5-biscarboxylic acid mononucleotide (P2CMN). Prior studies had shown that LarB uses CO(2) for substrate carboxylation and reported the structure of a Lactiplantibacillus plantarum LarB.NAD(+) complex, revealing a covalent linkage between Cys221 and C4 of the pyridine ring. This interaction was proposed to promote C5 carboxylation, with C5-carboxylated-NaAD suggested to activate magnesium-bound water, leading to phosphoanhydride hydrolysis. Here, we extended the analysis of wild-type LarB by using ultraviolet-visible spectroscopy to obtain additional evidence for cysteinyl side chain attachment to the ring of NAD(+), thus demonstrating that this linkage is not a crystallization artifact. Using the S127A variant of L. plantarum LarB, a form of the enzyme with a reduced rate of NaAD hydrolysis, we examined its interaction with the authentic substrate. The intermediate arising from C5 carboxylation of NaAD, dinicotinic acid adenine dinucleotide (DaAD), was identified by using mass spectrometry. S127A LarB exhibited spectroscopic evidence of a Cys221-NAD(+) adduct, but a covalent enzyme-NaAD linkage was not detectable. We determined the S127A LarB.NaAD structure, providing new insights into the enzyme mechanism, and tentatively identified the position and mode of CO(2) binding. The crystal structure revealed the location of the side chain for Glu180, which was previously disordered, but showed that it is not well positioned to abstract the C5 proton in the adduct species to restore aromaticity as Cys221 is expelled. Based on these combined results, we propose a revised catalytic mechanism of LarB..

	~~Authors:~~ Chatterjee, S., Rankin, J.A.~~, Hu, J~~., ~~Hausinger, R.P~~.		Structure of the LarB-Substrate Complex and Identification of a Reaction Intermediate during Nickel-Pincer Nucleotide Cofactor Biosynthesis.,Chatterjee S, Nevarez JL, Rankin JA, Hu J, Hausinger RP Biochemistry. 2023 Nov 7;62(21):3096-3104. doi: 10.1021/acs.biochem.3c00242. Epub , 2023 Oct 13. PMID:37831946<ref>PMID:37831946</ref>

	~~Description: S127A variant of LarB~~, a ~~carboxylase/hydrolase involved in synthesis~~ of the ~~cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: ~~Hausinger, R.P~~]]		<div class="pdbe-citations 8std" style="background-color:#fffaf0;"></div>
	[[Category: ~~Hu, J~~]]		== References ==
	[[Category: ~~Chatterjee, S~~]]		<references/>
	[[Category: Rankin~~, J.A~~]]		__TOC__
			</StructureSection>
			[[Category: Lactiplantibacillus plantarum WCFS1]]
			[[Category: Large Structures]]
			[[Category: Chatterjee S]]
			[[Category: Hausinger RP]]
			[[Category: Hu J]]
			[[Category: Rankin JA]]

OCA at 04:45, 23 August 2023

2023-08-23T04:45:53Z

← Older revision		Revision as of 04:45, 23 August 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8std is ON HOLD		The entry 8std is ON HOLD until Paper Publication

	Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.		Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.

OCA at 06:52, 16 August 2023

2023-08-16T06:52:57Z

← Older revision		Revision as of 06:52, 16 August 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8std is ON HOLD ~~until Paper Publication~~		The entry 8std is ON HOLD

	Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.		Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.
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	Description: S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2		Description: S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	~~[[Category: Chatterjee, S]]~~
	[[Category: Hausinger, R.P]]		[[Category: Hausinger, R.P]]
	[[Category: Hu, J]]		[[Category: Hu, J]]
			[[Category: Chatterjee, S]]
	[[Category: Rankin, J.A]]		[[Category: Rankin, J.A]]

OCA at 02:47, 25 May 2023

2023-05-25T02:47:54Z

← Older revision		Revision as of 02:47, 25 May 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8std is ON HOLD		The entry 8std is ON HOLD until Paper Publication

	Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.		Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.
Line 7:		Line 7:
	Description: S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2		Description: S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Chatterjee, S]]
	[[Category: Hausinger, R.P]]		[[Category: Hausinger, R.P]]
	[[Category: Hu, J]]		[[Category: Hu, J]]
	~~[[Category: Chatterjee, S]]~~
	[[Category: Rankin, J.A]]		[[Category: Rankin, J.A]]

OCA: Protected "8std" [edit=sysop:move=sysop]

2023-05-18T06:00:55Z

Protected "8std" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:00, 18 May 2023
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8std is ON HOLD Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P. Description: S127A variant of LarB, a carboxylase/hydrolase involved...

2023-05-18T06:00:54Z

New page: '''Unreleased structure''' The entry 8std is ON HOLD Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P. Description: S127A variant of LarB, a carboxylase/hydrolase involved...

New page

'''Unreleased structure'''

The entry 8std is ON HOLD

Authors: Chatterjee, S., Rankin, J.A., Hu, J., Hausinger, R.P.

Description: S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2
[[Category: Unreleased Structures]]
[[Category: Hausinger, R.P]]
[[Category: Hu, J]]
[[Category: Chatterjee, S]]
[[Category: Rankin, J.A]]