6c1w: Difference between revisions
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==A tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in lactate racemase== | |||
<StructureSection load='6c1w' size='340' side='right'caption='[[6c1w]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6c1w]] is a 3 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=6C1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C1W 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]] 2.398Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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:(4~{S})-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-5-methanethioyl-4-sulfo-4~{H}-pyridine-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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6c1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c1w OCA], [https://pdbe.org/6c1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c1w RCSB], [https://www.ebi.ac.uk/pdbsum/6c1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c1w ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/LARA_LACPL 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).<ref>PMID:16166538</ref> <ref>PMID:24710389</ref> <ref>PMID:26138974</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:29489337</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6c1w" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Lactiplantibacillus plantarum WCFS1]] | |||
[[Category: Large Structures]] | |||
[[Category: Desguin B]] | |||
[[Category: Fellner M]] | |||
[[Category: Hausinger RP]] | |||
[[Category: Hu J]] | |||