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

Böth, Dominic ; Steiner, Eva Maria LU orcid ; Izumi, Atsushi ; Schneider, Gunter and Schnell, Robert (2014) In Biochemical Journal 457(1). p.33-41
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 cellwall remodelling during cell division.Amember 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... (More)

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 cellwall remodelling during cell division.Amember 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.

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author
; ; ; and
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Catalytic site, Cell wall, Mycobacterium tuberculosis, NlpC/p60, Peptidoglycan binding, Proline-rich, Protein repeat, Protein structure
in
Biochemical Journal
volume
457
issue
1
pages
33 - 41
publisher
Portland Press
external identifiers
  • pmid:24107184
  • scopus:84890039458
ISSN
0264-6021
DOI
10.1042/BJ20131227
language
English
LU publication?
no
id
f19b27c8-e815-449d-bc18-688352fb5c10
date added to LUP
2024-12-11 10:45:14
date last changed
2025-04-04 15:21:48
@article{f19b27c8-e815-449d-bc18-688352fb5c10,
  abstract     = {{<p>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 cellwall remodelling during cell division.Amember 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.</p>}},
  author       = {{Böth, Dominic and Steiner, Eva Maria and Izumi, Atsushi and Schneider, Gunter and Schnell, Robert}},
  issn         = {{0264-6021}},
  keywords     = {{Catalytic site; Cell wall; Mycobacterium tuberculosis; NlpC/p60; Peptidoglycan binding; Proline-rich; Protein repeat; Protein structure}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{1}},
  pages        = {{33--41}},
  publisher    = {{Portland Press}},
  series       = {{Biochemical Journal}},
  title        = {{RipD (Rv1566c) from mycobacterium tuberculosis : Adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function}},
  url          = {{http://dx.doi.org/10.1042/BJ20131227}},
  doi          = {{10.1042/BJ20131227}},
  volume       = {{457}},
  year         = {{2014}},
}