Article ; Online: Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains.
The Journal of biological chemistry
2023 Volume 300, Issue 1, Page(s) 105494
Abstract: Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a ... ...
| Abstract | Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a donor stem and the third residue of an acceptor stem (4-3 cross-links). Some bacterial peptidoglycans also contain 3-3 cross-links that are formed by another class of enzymes called L,D-transpeptidases which contain a YkuD catalytic domain. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software that can identify 1-3 cross-links and report the high-resolution peptidoglycan structure of Gluconobacter oxydans (a model organism within the Acetobacteraceae family). We reveal that G. oxydans peptidoglycan contains peptide stems made of a single alanine as well as several dipeptide stems with unusual amino acids at their C-terminus. Using a bioinformatics approach, we identified a G. oxydans mutant from a transposon library with a drastic reduction in 1-3 cross-links. Through complementation experiments in G. oxydans and recombinant protein production in a heterologous host, we identify an L,D-transpeptidase enzyme with a domain distantly related to the YkuD domain responsible for these non-canonical reactions. This work revisits the enzymatic capabilities of L,D-transpeptidases, a versatile family of enzymes that play a key role in bacterial peptidoglycan remodelling. |
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| MeSH term(s) | Amino Acids/genetics ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Catalytic Domain/genetics ; Peptidoglycan/chemistry ; Peptidoglycan/genetics ; Peptidoglycan/metabolism ; Peptidyl Transferases/chemistry ; Peptidyl Transferases/genetics ; Peptidyl Transferases/metabolism ; Software ; Gluconobacter oxydans/enzymology ; Gluconobacter oxydans/genetics ; Computational Biology ; Genetic Complementation Test ; Models, Molecular ; Protein Structure, Tertiary |
| Chemical Substances | Amino Acids ; Bacterial Proteins ; Peptidoglycan ; Peptidyl Transferases (EC 2.3.2.12) |
| Language | English |
| Publishing date | 2023-11-23 |
| Publishing country | United States |
| Document type | Journal Article |
| ZDB-ID | 2997-x |
| ISSN | 1083-351X ; 0021-9258 |
| ISSN (online) | 1083-351X |
| ISSN | 0021-9258 |
| DOI | 10.1016/j.jbc.2023.105494 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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