RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.

Böth D, Steiner EM, Izumi A, Schneider G, Schnell R

Biochem. J. 457 (1) 33-41 [2014-01-01; online 2013-10-11]

Enzymes carrying NlpC/p60 domains, for instance RipA and RipB from Mycobacterium tuberculosis, are bacterial peptidoglycan hydrolases that cleave the peptide stems and contribute to cell wall remodelling during cell division. A member of this protein family, RipD (Rv1566c) from M. tuberculosis described in the present study, displays sequence alterations in the NlpC/p60 catalytic triad and carries a pentapeptide repeat at its C-terminus. Bioinformatics analysis revealed RipD-like proteins in eleven mycobacterial genomes, whereas similar pentapeptide repeats occur in cell-wall-localized bacterial proteins and in a mycobacteriophage. In contrast with previously known members of the NlpC/p60 family, RipD does not show peptidoglycan hydrolase activity, which is consistent with the sequence alterations at the catalytic site. A strong interaction of the catalytically inactive core domain with peptidoglycan is however retained, presenting the first example of the NlpC/p60 domains that evolved to a non-catalytic peptidoglycan-binding function. Full-length RipD carrying the C-terminal repeat shows, however, a decrease in binding affinity to peptidoglycan, suggesting that the C-terminal tail modulates the interaction with bacterial cell wall components. The pentapeptide repeat at the C-terminus does not adopt a defined secondary structure in solution which is in accordance with results from the 1.17 Å (1 Å=0.1 nm) crystal structure of the protein carrying two repeat units.

Protein Science Facility (PSF)

PubMed 24107184

DOI 10.1042/BJ20131227

Crossref 10.1042/BJ20131227

pii: BJ20131227