8QZG

1,3 L,D-transpeptidase from Gluconobacter oxydans

Summary for 8QZG

• Entry DOI: 10.2210/pdb8qzg/pdb
• Descriptor: YkuD domain-containing protein, CHLORIDE ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: transpeptidase, peptidoglycan, gluconobacter oxydans, cell wall, antibiotics resistance, lipoprotein, transferase
• Biological source: Gluconobacter oxydans
• Total number of polymer chains: 1
• Total formula weight: 36116.64

Authors

ter Beek, J.,Berntsson, R.P. (deposition date: 2023-10-27, release date: 2023-11-08, Last modification date: 2024-03-06)

Primary citation

Espaillat, A.,Alvarez, L.,Torrens, G.,Ter Beek, J.,Miguel-Ruano, V.,Irazoki, O.,Gago, F.,Hermoso, J.A.,Berntsson, R.P.,Cava, F.
A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria.
Nat Commun, 15:1343-1343, 2024

PubMed 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, LDT, that generates 1,3-crosslinks in the acetic-acid bacterium Gluconobacter oxydans. LDT-like proteins are found in Alpha- and Betaproteobacteria lacking LD3,3-transpeptidases. In contrast with the strict specificity of typical LD- and DD-transpeptidases, LDT can use non-terminal amino acid moieties for crosslinking. A high-resolution crystal structure of LDT 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.

PubMed: 38351082
DOI: 10.1038/s41467-024-45620-5

Experimental method

X-RAY DIFFRACTION (1.73 Å)