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

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.150 

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This is version 1.5 of the entry. See complete history


Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.

Desguin, B.Fellner, M.Riant, O.Hu, J.Hausinger, R.P.Hols, P.Soumillion, P.

(2018) J Biol Chem 293: 12303-12317

  • DOI: https://doi.org/10.1074/jbc.RA118.003741
  • Primary Citation of Related Structures:  
    6BWO, 6BWQ, 6BWR

  • 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 Lactobacillus plantarum 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 2+ -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 in vitro synthesis and purification of the NPN cofactor, opening new opportunities for the study of this intriguing cofactor and of NPN-utilizing enzymes.

  • Organizational Affiliation

    From the Institute of Life Sciences and benoit.desguin@uclouvain.be.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
A, B
149Lactiplantibacillus plantarumMutation(s): 0 
Find proteins for F9UST1 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Explore F9UST1 
Go to UniProtKB:  F9UST1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF9UST1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CTP

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
C9 H16 N3 O14 P3
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.150 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.215α = 90
b = 97.215β = 90
c = 97.215γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1516126

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description