3PBI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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:  
    3PBC, 3PBI, 3S0Q

  • 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) has been linked to the putative PG hydrolases RipA and RipB ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INVASION PROTEINA214Mycobacterium tuberculosisMutation(s): 0 
Gene Names: MT1525Rv1478
EC: 3.4
UniProt
Find proteins for P9WHU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHU5 
Go to UniProtKB:  P9WHU5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.98α = 90
b = 92.98β = 90
c = 53.192γ = 120
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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