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TitleStructures of two LarA-like nickel-pincer nucleotide cofactor-utilizing enzymes with a single catalytic histidine residue.
Journal, issue, pagesbioRxiv, Year 2025
Publish dateAug 21, 2025
AuthorsSanthosh Gatreddi / Sundharraman Subramanian / Dexin Sui / Tianqi Wang / Julian Urdiain-Arraiza / Benoit Desguin / Robert P Hausinger / Kristin N Parent / Jian Hu /
PubMed AbstractThe nickel pincer nucleotide (NPN) cofactor catalyzes the racemization/epimerization of α-hydroxy acids in enzymes of the LarA family. The established proton-coupled hydride transfer mechanism ...The nickel pincer nucleotide (NPN) cofactor catalyzes the racemization/epimerization of α-hydroxy acids in enzymes of the LarA family. The established proton-coupled hydride transfer mechanism requires two catalytic histidine residues that alternately act as general acids and general bases. Notably, however, a fraction of LarA homologs (LarAHs) lack one of the active site histidine residues, replacing it with an asparaginyl side chain that cannot participate in acid/base catalysis. Here, we investigated two such LarAHs and solved their cryo-electron microscopic structures with and without loaded NPN cofactor, respectively. The structures revealed a consistent octameric assembly that is unprecedented in the LarA family and unveiled a new set of active site residues that likely recognize and process substrates differently from those of the well-studied LarAHs. Genomic context analysis suggested their potential involvement in carbohydrate metabolism. Together, these findings lay the groundwork for expanding the breadth of reactions and the range of mechanisms of LarA enzymes.
External linksbioRxiv / PubMed:40894700 / PubMed Central
MethodsEM (single particle)
Resolution2.2 - 3.15 Å
Structure data

72199

9q3j

EMDB-72199, PDB-9q3j:
Structures of LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme with a single catalytic histidine residue from Blautia wexlerae
Method: EM (single particle) / Resolution: 3.15 Å

72200

9q3k

EMDB-72200, PDB-9q3k:
Structure of LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme with a single catalytic histidine residue from Streptococcus plurextorum
Method: EM (single particle) / Resolution: 2.2 Å

Chemicals

ChemComp-NI:
NICKEL (II) ION

ChemComp-4EY:
1-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-5-methanethioyl-pyridine-3-carbothioic S-acid

Source
  • blautia wexlerae (bacteria)
  • streptococcus plurextorum (bacteria)
KeywordsISOMERASE / Racemase and epimerase activity / acting on hydroxy acids and derivatives / metal ion binding / catalytic activity

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