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6c1w

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Revision as of 08:03, 21 March 2018

A tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in lactate racemase

Structural highlights

6c1w is a 3 chain structure with sequence from Lacpl. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Gene:	larA, lp_0104 (LACPL)
Activity:	Lactate racemase, with EC number 5.1.2.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[LARA_LACPL] Catalyzes the interconversion between the D- and L-isomers of lactate (PubMed:24710389, PubMed:26138974). May act as a rescue enzyme to ensure D-lactate production in physiological conditions where its production by the D-lactate dehydrogenase LdhD is not sufficient (PubMed:16166538). D-Lactate is absolutely required for growth of L.plantarum and is an essential component of the cell wall peptidoglycan in this species, where it is incorporated as the last residue of the muramoyl-pentadepsipeptide peptidoglycan precursor; its incorporation confers high level of vancomycin resistance (PubMed:16166538).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Lactate racemase (LarA) of Lactobacillus plantarum contains a novel organometallic cofactor with nickel coordinated to a covalently tethered pincer ligand, pyridinium-3-thioamide-5-thiocarboxylic acid mononucleotide, but its function in the enzyme mechanism has not been elucidated. This study presents direct evidence that the nickel-pincer cofactor facilitates a proton-coupled hydride transfer (PCHT) mechanism during LarA-catalyzed lactate racemization. No signal was detected by electron paramagnetic resonance spectroscopy for LarA in the absence or presence of substrate, consistent with a +2 metal oxidation state and inconsistent with a previously proposed proton-coupled electron transfer mechanism. Pyruvate, the predicted intermediate for a PCHT mechanism, was observed in quenched solutions of LarA. A normal substrate kinetic isotope effect ( kH/ kD of 3.11 +/- 0.17) was established using 2-alpha-(2)H-lactate, further supporting a PCHT mechanism. UV-visible spectroscopy revealed a lactate-induced perturbation of the cofactor spectrum, notably increasing the absorbance at 340 nm, and demonstrated an interaction of the cofactor with the inhibitor sulfite. A crystal structure of LarA provided greater resolution (2.4 A) than previously reported and revealed sulfite binding to the pyridinium C4 atom of the reduced pincer cofactor, mimicking hydride reduction during a PCHT catalytic cycle. Finally, computational modeling supports hydride transfer to the cofactor at the C4 position or to the nickel atom, but with formation of a nickel-hydride species requiring dissociation of the His200 metal ligand. In aggregate, these studies provide compelling evidence that the nickel-pincer cofactor acts by a PCHT mechanism.

Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism.,Rankin JA, Mauban RC, Fellner M, Desguin B, McCracken J, Hu J, Varganov SA, Hausinger RP Biochemistry. 2018 Mar 9. doi: 10.1021/acs.biochem.8b00100. PMID:29489337^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Goffin P, Deghorain M, Mainardi JL, Tytgat I, Champomier-Verges MC, Kleerebezem M, Hols P. Lactate racemization as a rescue pathway for supplying D-lactate to the cell wall biosynthesis machinery in Lactobacillus plantarum. J Bacteriol. 2005 Oct;187(19):6750-61. doi: 10.1128/JB.187.19.6750-6761.2005. PMID:16166538 doi:http://dx.doi.org/10.1128/JB.187.19.6750-6761.2005
↑ Desguin B, Goffin P, Viaene E, Kleerebezem M, Martin-Diaconescu V, Maroney MJ, Declercq JP, Soumillion P, Hols P. Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system. Nat Commun. 2014 Apr 7;5:3615. doi: 10.1038/ncomms4615. PMID:24710389 doi:http://dx.doi.org/10.1038/ncomms4615
↑ Desguin B, Zhang T, Soumillion P, Hols P, Hu J, Hausinger RP. METALLOPROTEINS. A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase. Science. 2015 Jul 3;349(6243):66-9. doi: 10.1126/science.aab2272. PMID:26138974 doi:http://dx.doi.org/10.1126/science.aab2272
↑ Rankin JA, Mauban RC, Fellner M, Desguin B, McCracken J, Hu J, Varganov SA, Hausinger RP. Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism. Biochemistry. 2018 Mar 9. doi: 10.1021/acs.biochem.8b00100. PMID:29489337 doi:http://dx.doi.org/10.1021/acs.biochem.8b00100

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6c1w"

@@ Line 3: / Line 3: @@
 <StructureSection load='6c1w' size='340' side='right' caption='[[6c1w]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6c1w]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C1W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6c1w]] is a 3 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=6C1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C1W FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4EY:1-[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]-5-METHANETHIOYL-PYRIDINE-3-CARBOTHIOIC+S-ACID'>4EY</scene>, <scene name='pdbligand=ENJ:(4S)-5-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-4-sulfo-1,4-dihydropyridine-3-carbothioic+S-acid'>ENJ</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</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">larA, lp_0104 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220668 LACPL])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lactate_racemase Lactate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.1 5.1.2.1] </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=6c1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c1w OCA], [http://pdbe.org/6c1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c1w RCSB], [http://www.ebi.ac.uk/pdbsum/6c1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c1w ProSAT]</span></td></tr>
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Lacpl]]
 [[Category: Lactate racemase]]
 [[Category: Desguin, B]]

6c1w

From Proteopedia

Revision as of 08:03, 21 March 2018

A tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in lactate racemase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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