6EWY

RipA Peptidoglycan hydrolase (Rv1477, Mycobacterium tuberculosis) N-terminal domain

Summary for 6EWY

• Entry DOI: 10.2210/pdb6ewy/pdb
• Descriptor: Peptidoglycan endopeptidase RipA (2 entities in total)
• Functional Keywords: periplasmic protein, structural protein
• Biological source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Total number of polymer chains: 1
• Total formula weight: 23274.57

Authors

Schnell, R.,Steiner, E.M.,Schneider, G.,Guy, J.,Bourenkov, G. (deposition date: 2017-11-07, release date: 2018-05-02, Last modification date: 2024-05-08)

Primary citation

Steiner, E.M.,Lyngso, J.,Guy, J.E.,Bourenkov, G.,Lindqvist, Y.,Schneider, T.R.,Pedersen, J.S.,Schneider, G.,Schnell, R.
The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity.
Proteins, 86:912-923, 2018

PubMed 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 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.

PubMed: 29722065
DOI: 10.1002/prot.25523

Experimental method

X-RAY DIFFRACTION (2.2 Å)