7mj0 - Revision history

OCA at 16:12, 18 October 2023

OCA — Wed, 18 Oct 2023 16:12:51 GMT

←Older revision		Revision as of 16:12, 18 October 2023
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	==LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with adenosine monophosphate AMP==		==LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with adenosine monophosphate AMP==
-	<StructureSection load='7mj0' size='340' side='right'caption='[[7mj0]]' scene=''>	+	<StructureSection load='7mj0' size='340' side='right'caption='[[7mj0]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MJ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MJ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7mj0]] 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=7MJ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MJ0 FirstGlance]. <br>
-	</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=7mj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mj0 OCA], [https://pdbe.org/7mj0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mj0 RCSB], [https://www.ebi.ac.uk/pdbsum/7mj0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mj0 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]] 3.01Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=7mj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mj0 OCA], [https://pdbe.org/7mj0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mj0 RCSB], [https://www.ebi.ac.uk/pdbsum/7mj0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mj0 ProSAT]</span></td></tr>
	</table>		</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 ==
		+	Enzymes possessing the nickel-pincer nucleotide (NPN) cofactor catalyze C2 racemization or epimerization reactions of alpha-hydroxyacid substrates. LarB initiates synthesis of the NPN cofactor from nicotinic acid adenine dinucleotide (NaAD) by performing dual reactions: pyridinium ring C5 carboxylation and phosphoanhydride hydrolysis. Here, we show that LarB uses carbon dioxide, not bicarbonate, as the substrate for carboxylation and activates water for hydrolytic attack on the AMP-associated phosphate of C5-carboxylated-NaAD. Structural investigations show that LarB has an N-terminal domain of unique fold and a C-terminal domain homologous to aminoimidazole ribonucleotide carboxylase/mutase (PurE). Like PurE, LarB is octameric with four active sites located at subunit interfaces. The complex of LarB with NAD(+), an analog of NaAD, reveals the formation of a covalent adduct between the active site Cys221 and C4 of NAD(+), resulting in a boat-shaped dearomatized pyridine ring. The formation of such an intermediate with NaAD would enhance the reactivity of C5 to facilitate carboxylation. Glu180 is well positioned to abstract the C5 proton, restoring aromaticity as Cys221 is expelled. The structure of as-isolated LarB and its complexes with NAD(+) and the product AMP identify additional residues potentially important for substrate binding and catalysis. In combination with these findings, the results from structure-guided mutagenesis studies lead us to propose enzymatic mechanisms for both the carboxylation and hydrolysis reactions of LarB that are distinct from that of PurE.
		+
		+	The LarB carboxylase/hydrolase forms a transient cysteinyl-pyridine intermediate during nickel-pincer nucleotide cofactor biosynthesis.,Rankin JA, Chatterjee S, Tariq Z, Lagishetty S, Desguin B, Hu J, Hausinger RP Proc Natl Acad Sci U S A. 2021 Sep 28;118(39). pii: 2106202118. doi:, 10.1073/pnas.2106202118. PMID:34548397<ref>PMID:34548397</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7mj0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lactiplantibacillus plantarum WCFS1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chatterjee S]]		[[Category: Chatterjee S]]

OCA at 08:50, 29 September 2021

OCA — Wed, 29 Sep 2021 08:50:26 GMT

←Older revision		Revision as of 08:50, 29 September 2021
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-	'''Unreleased structure'''

-	~~The entry 7mj0 is ON HOLD until Paper Publication~~	+	==LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with adenosine monophosphate AMP==
-		+	<StructureSection load='7mj0' size='340' side='right'caption='[[7mj0]]' scene=''>
-	~~Authors: Chatterjee, S., Rankin, J.A., Lagishetty, S., Hu, J., Hausinger, R.P.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MJ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MJ0 FirstGlance]. <br>
-	~~Description:~~ LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with adenosine monophosphate AMP	+	</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=7mj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mj0 OCA], [https://pdbe.org/7mj0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mj0 RCSB], [https://www.ebi.ac.uk/pdbsum/7mj0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mj0 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Lagishetty~~, S]]	+	__TOC__
-	[[Category: ~~Hausinger, R.P~~]]	+	</StructureSection>
-	[[Category: Chatterjee, S]]	+	[[Category: Large Structures]]
-	[[Category: Hu, J]]	+	[[Category: Chatterjee S]]
-	[[Category: Rankin~~, J.A~~]]	+	[[Category: Hausinger RP]]
		+	[[Category: Hu J]]
		+	[[Category: Lagishetty S]]
		+	[[Category: Rankin JA]]

OCA at 04:57, 18 August 2021

OCA — Wed, 18 Aug 2021 04:57:16 GMT

←Older revision		Revision as of 04:57, 18 August 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7mj0 is ON HOLD	+	The entry 7mj0 is ON HOLD until Paper Publication

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

OCA: Protected "7mj0" [edit=sysop:move=sysop]

OCA — Wed, 28 Apr 2021 04:19:48 GMT

Protected "7mj0" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:19, 28 April 2021

OCA: New page: '''Unreleased structure''' The entry 7mj0 is ON HOLD Authors: Chatterjee, S., Rankin, J.A., Lagishetty, S., Hu, J., Hausinger, R.P. Description: LarB, a carboxylase/hydrolase involved ...

OCA — Wed, 28 Apr 2021 04:19:47 GMT

New page: '''Unreleased structure''' The entry 7mj0 is ON HOLD Authors: Chatterjee, S., Rankin, J.A., Lagishetty, S., Hu, J., Hausinger, R.P. Description: LarB, a carboxylase/hydrolase involved ...

New page

'''Unreleased structure'''

The entry 7mj0 is ON HOLD

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

Description: LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with adenosine monophosphate AMP
[[Category: Unreleased Structures]]
[[Category: Lagishetty, S]]
[[Category: Hausinger, R.P]]
[[Category: Chatterjee, S]]
[[Category: Hu, J]]
[[Category: Rankin, J.A]]