8ezh
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase R98A/R100A variant modeled with sulfite-NPN adduct== | |
| + | <StructureSection load='8ezh' size='340' side='right'caption='[[8ezh]], [[Resolution|resolution]] 1.99Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[8ezh]] is a 1 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=8EZH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8EZH 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]] 1.99Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=8ezh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ezh OCA], [https://pdbe.org/8ezh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ezh RCSB], [https://www.ebi.ac.uk/pdbsum/8ezh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ezh 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 == | ||
| + | The nickel-pincer nucleotide (NPN) cofactor discovered in lactate racemase from Lactiplantibacillus plantarum (LarA(Lp)) is essential for the activities of racemases/epimerases in the highly diverse LarA superfamily. Prior mechanistic studies have established a proton-coupled hydride-transfer mechanism for LarA(Lp), but direct evidence showing that hydride attacks the C4 atom in the pyridinium ring of NPN has been lacking. Here, we show that sodium borohydride (NaBH(4)) irreversibly inactivates LarA(Lp) accompanied by a rapid color change of the enzyme. The altered ultraviolet-visible spectra during NaBH(4) titration supported hydride transfer to C4 of NPN, and the concomitant Ni loss unraveled by mass spectrometry experiments accounted for the irreversible inactivation. High resolution structures of LarA(Lp) revealed a substantially weakened C-Ni bond in the metastable sulfite-NPN adduct where the NPN cofactor is in the reduced state. These findings allowed us to propose a mechanism of LarA(Lp) inactivation by NaBH(4) that provides key insights into the enzyme-catalyzed reaction and sheds light on the reactivity of small molecule NPN mimetics. | ||
| - | + | Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor.,Gatreddi S, Sui D, Hausinger RP, Hu J ACS Catal. 2023 Jan 20;13(2):1441-1448. doi: 10.1021/acscatal.2c05461. Epub 2023 , Jan 10. PMID:37886035<ref>PMID:37886035</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 8ezh" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Lactiplantibacillus plantarum WCFS1]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Gatreddi S]] | ||
| + | [[Category: Hausinger RP]] | ||
| + | [[Category: Hu J]] | ||
Current revision
A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase R98A/R100A variant modeled with sulfite-NPN adduct
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