6BWR

LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, in complex with nickel

Summary for 6BWR

• Entry DOI: 10.2210/pdb6bwr/pdb
• Descriptor: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein, NICKEL (II) ION (3 entities in total)
• Functional Keywords: lar, nickel transferase, larc, hexamer, trimer, ctp, nickel, lactate, lactate racemization, lactate racemase, metal binding protein
• Biological source: Lactobacillus plantarum
• Total number of polymer chains: 2
• Total formula weight: 33873.06

Authors

Fellner, M.,Hausinger, R.P.,Hu, J. (deposition date: 2017-12-15, release date: 2018-06-20, Last modification date: 2023-10-04)

Primary citation

Desguin, B.,Fellner, M.,Riant, O.,Hu, J.,Hausinger, R.P.,Hols, P.,Soumillion, P.
Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.
J. Biol. Chem., 293:12303-12317, 2018

PubMed Abstract: Bacterial lactate racemase is a nickel-dependent enzyme that contains a cofactor, nickel pyridinium-3,5-bisthiocarboxylic acid mononucleotide, hereafter named nickel-pincer nucleotide (NPN). The LarC enzyme from the bacterium participates in NPN biosynthesis by inserting nickel ion into pyridinium-3,5-bisthiocarboxylic acid mononucleotide. This reaction, known in organometallic chemistry as a cyclometalation, is characterized by the formation of new metal-carbon and metal-sulfur σ bonds. LarC is therefore the first cyclometallase identified in nature, but the molecular mechanism of LarC-catalyzed cyclometalation is unknown. Here, we show that LarC activity requires Mn-dependent CTP hydrolysis. The crystal structure of the C-terminal domain of LarC at 1.85 Å resolution revealed a hexameric ferredoxin-like fold and an unprecedented CTP-binding pocket. The loss-of-function of LarC variants with alanine variants of acidic residues leads us to propose a carboxylate-assisted mechanism for nickel insertion. This work also demonstrates the synthesis and purification of the NPN cofactor, opening new opportunities for the study of this intriguing cofactor and of NPN-utilizing enzymes.

PubMed: 29887527
DOI: 10.1074/jbc.RA118.003741

Experimental method

X-RAY DIFFRACTION (1.81 Å)