6EWY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Steiner, E.M.Lyngso, J.Guy, J.E.Bourenkov, G.Lindqvist, Y.Schneider, T.R.Pedersen, J.S.Schneider, G.Schnell, R.

(2018) Proteins 86: 912-923

  • DOI: 10.1002/prot.25523

  • 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 pot ...

    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.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, S-17 177, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan endopeptidase RipA
A
219Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ripA
EC: 3.4.-.-
Find proteins for O53168 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  O53168
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 44.916α = 90.00
b = 93.960β = 90.00
c = 138.672γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXDEphasing
AutoPROCdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RAC-VRSweden--

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Database references