A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria

Akbar Espaillat, Laura Alvarez, Gabriel Torrens, Josy ter Beek, Vega Miguel-Ruano, Oihane Irazoki, Federico Gago, Juan A. Hermoso, Ronnie P-A. Berntsson and Felipe Cava ()
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Akbar Espaillat: Umeå University
Laura Alvarez: Umeå University
Gabriel Torrens: Umeå University
Josy ter Beek: Umeå University
Vega Miguel-Ruano: Institute of Physical Chemistry “Blas Cabrera”, CSIC
Oihane Irazoki: Umeå University
Federico Gago: University of Alcalá
Juan A. Hermoso: Institute of Physical Chemistry “Blas Cabrera”, CSIC
Ronnie P-A. Berntsson: Umeå University
Felipe Cava: Umeå University

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract The bacterial cell-wall peptidoglycan is made of glycan strands crosslinked by short peptide stems. Crosslinks are catalyzed by DD-transpeptidases (4,3-crosslinks) and LD-transpeptidases (3,3-crosslinks). However, recent research on non-model species has revealed novel crosslink types, suggesting the existence of uncharacterized enzymes. Here, we identify an LD-transpeptidase, LDTGo, that generates 1,3-crosslinks in the acetic-acid bacterium Gluconobacter oxydans. LDTGo-like proteins are found in Alpha- and Betaproteobacteria lacking LD3,3-transpeptidases. In contrast with the strict specificity of typical LD- and DD-transpeptidases, LDTGo can use non-terminal amino acid moieties for crosslinking. A high-resolution crystal structure of LDTGo reveals unique features when compared to LD3,3-transpeptidases, including a proline-rich region that appears to limit substrate access, and a cavity accommodating both glycan chain and peptide stem from donor muropeptides. Finally, we show that DD-crosslink turnover is involved in supplying the necessary substrate for LD1,3-transpeptidation. This phenomenon underscores the interplay between distinct crosslinking mechanisms in maintaining cell wall integrity in G. oxydans.

Date: 2024
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DOI: 10.1038/s41467-024-45620-5

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