4JXB

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

Summary for 4JXB

• Entry DOI: 10.2210/pdb4jxb/pdb
• Descriptor: Invasion-associated protein, ACETATE ION (3 entities in total)
• Functional Keywords: cell wall, envelope biogenesis, nlpc/p60, cell invasion
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 2
• Total formula weight: 28605.43

Authors

Both, D.,Steiner, E.M.,Schnell, R.,Schneider, G. (deposition date: 2013-03-28, release date: 2013-10-30, Last modification date: 2024-02-28)

Primary citation

Both, D.,Steiner, E.M.,Izumi, A.,Schneider, G.,Schnell, R.
RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.
Biochem.J., 457:33-41, 2014

PubMed Abstract: 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.

PubMed: 24107184
DOI: 10.1042/BJ20131227

Experimental method

X-RAY DIFFRACTION (1.56 Å)