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The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity

Steiner, Eva Maria LU orcid ; Lyngsø, Jeppe ; Guy, Jodie E. ; Bourenkov, Gleb ; Lindqvist, Ylva ; Schneider, Thomas R. ; Pedersen, Jan Skov ; Schneider, Gunter and Schnell, Robert (2018) In Proteins: Structure, Function and Bioinformatics 86(9). p.912-923
Abstract

RipA plays a vital role during cell division of Mycobacterium tuberculosis by degrading the cell wall peptidoglycan at the septum, allowing daughter cell separation. The peptidoglycan degrading activity relies on the NlpC/P60 domain, and as it is potentially harmful when deregulated, spatial and temporal control is necessary in this process. The N-terminal domain of RipA has been proposed to play an inhibitory role blocking the C-terminal NlpC/P60 domain. Accessibility of the active site cysteine residue is however not limited by the presence of the N-terminal domain, but by the lid-module of the inter-domain linker, which is situated in the peptide binding groove of the crystal structures of the catalytic domain. The 2.2 Å resolution... (More)

RipA plays a vital role during cell division of Mycobacterium tuberculosis by degrading the cell wall peptidoglycan at the septum, allowing daughter cell separation. The peptidoglycan degrading activity relies on the NlpC/P60 domain, and as it is potentially harmful when deregulated, spatial and temporal control is necessary in this process. The N-terminal domain of RipA has been proposed to play an inhibitory role blocking the C-terminal NlpC/P60 domain. Accessibility of the active site cysteine residue is however not limited by the presence of the N-terminal domain, but by the lid-module of the inter-domain linker, which is situated in the peptide binding groove of the crystal structures of the catalytic domain. The 2.2 Å resolution structure of the N-terminal domain, determined by Se-SAD phasing, reveals an all-α-fold with 2 long α-helices, and shows similarity to bacterial periplasmic protein domains with scaffold-building role. Size exclusion chromatography and SAXS experiments are consistent with dimer formation of this domain in solution. The SAXS data from the periplasmic two-domain RipA construct suggest a rigid baton-like structure of the N-terminal module, with the catalytic domain connected by a 24 residue long flexible linker. This flexible linker allows for a catalytic zone, which is part of the spatiotemporal control of peptidoglycan degradation.

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author
; ; ; ; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
cell wall remodeling, NlpC/P60, peptidoglycan cleavage, protein structure, SAXS, X-ray crystallography
in
Proteins: Structure, Function and Bioinformatics
volume
86
issue
9
pages
912 - 923
publisher
Wiley-Liss Inc.
external identifiers
  • scopus:85047815945
  • pmid:29722065
ISSN
0887-3585
DOI
10.1002/prot.25523
language
English
LU publication?
no
additional info
Publisher Copyright: © 2018 Wiley Periodicals, Inc.
id
643e4c13-9215-4214-8fc0-04bc5d9adb62
date added to LUP
2024-06-24 11:30:12
date last changed
2025-10-29 08:16:31
@article{643e4c13-9215-4214-8fc0-04bc5d9adb62,
  abstract     = {{<p>RipA plays a vital role during cell division of Mycobacterium tuberculosis by degrading the cell wall peptidoglycan at the septum, allowing daughter cell separation. The peptidoglycan degrading activity relies on the NlpC/P60 domain, and as it is potentially harmful when deregulated, spatial and temporal control is necessary in this process. The N-terminal domain of RipA has been proposed to play an inhibitory role blocking the C-terminal NlpC/P60 domain. Accessibility of the active site cysteine residue is however not limited by the presence of the N-terminal domain, but by the lid-module of the inter-domain linker, which is situated in the peptide binding groove of the crystal structures of the catalytic domain. The 2.2 Å resolution structure of the N-terminal domain, determined by Se-SAD phasing, reveals an all-α-fold with 2 long α-helices, and shows similarity to bacterial periplasmic protein domains with scaffold-building role. Size exclusion chromatography and SAXS experiments are consistent with dimer formation of this domain in solution. The SAXS data from the periplasmic two-domain RipA construct suggest a rigid baton-like structure of the N-terminal module, with the catalytic domain connected by a 24 residue long flexible linker. This flexible linker allows for a catalytic zone, which is part of the spatiotemporal control of peptidoglycan degradation.</p>}},
  author       = {{Steiner, Eva Maria and Lyngsø, Jeppe and Guy, Jodie E. and Bourenkov, Gleb and Lindqvist, Ylva and Schneider, Thomas R. and Pedersen, Jan Skov and Schneider, Gunter and Schnell, Robert}},
  issn         = {{0887-3585}},
  keywords     = {{cell wall remodeling; NlpC/P60; peptidoglycan cleavage; protein structure; SAXS; X-ray crystallography}},
  language     = {{eng}},
  number       = {{9}},
  pages        = {{912--923}},
  publisher    = {{Wiley-Liss Inc.}},
  series       = {{Proteins: Structure, Function and Bioinformatics}},
  title        = {{The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity}},
  url          = {{http://dx.doi.org/10.1002/prot.25523}},
  doi          = {{10.1002/prot.25523}},
  volume       = {{86}},
  year         = {{2018}},
}