3PBI

Structure of the peptidoglycan hydrolase RipB (Rv1478) from Mycobacterium tuberculosis at 1.6 resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Peptidoglycan Remodeling in Mycobacterium tuberculosis: Comparison of Structures and Catalytic Activities of RipA and RipB.

Both, D.Schneider, G.Schnell, R.

(2011) J.Mol.Biol. 413: 247-260

  • DOI: 10.1016/j.jmb.2011.08.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The success of Mycobacterium tuberculosis in sustaining long-term survival within the host macrophages partly relies on its unique cell envelop that also confers low susceptibility to several antibiotics. Remodeling of the septal peptidoglycan (PG) h ...

    The success of Mycobacterium tuberculosis in sustaining long-term survival within the host macrophages partly relies on its unique cell envelop that also confers low susceptibility to several antibiotics. Remodeling of the septal peptidoglycan (PG) has been linked to the putative PG hydrolases RipA and RipB. The crystal structures of RipB (Rv1478) and the homologous module of RipA (Rv1477) were determined to 1.60 Å and 1.38 Å resolution, respectively. Both proteins contain a C-terminal core domain resembling the NlpC-type PG hydrolases. However, the structure of RipB exhibits striking differences to the structures of this domain in RipA reported here and previously by others. Major structural differences were found in the N-terminal segments of 70 amino acids and in an adjacent loop, which form part of the substrate binding groove. Both RipA and RipB are able to bind PG. RipA, its C-terminal module and RipB cleave defined PG fragments between d-glutamate and meso-diaminopimelate with pH optima of 5 and 6, respectively. The peptidase module of RipA is also able to degrade Bacillus subtilis PG, which displays peptide stems and cross-links identical with those found in mycobacterial murein. RipB did not show comparable hydrolase activity with this substrate. Removal of the N-terminal segments previously suggested to have a role in auto-inhibition did not change the activity of either RipA or RipB. A comparison of the putative active-site clefts in the two enzymes provides structural insights into the basis of the differences in their substrate specificity.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INVASION PROTEIN
A
214Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ripB
EC: 3.4.-.-
Find proteins for P9WHU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHU5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 92.980α = 90.00
b = 92.980β = 90.00
c = 53.192γ = 120.00
Software Package:
Software NamePurpose
DNAdata collection
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-10-19
    Type: Database references