4JXB

RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein, adaptation to peptidoglycan-binding function


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.

Both, D.Steiner, E.M.Izumi, A.Schneider, G.Schnell, R.

(2014) Biochem J 457: 33-41

  • DOI: https://doi.org/10.1042/BJ20131227
  • Primary Citation of Related Structures:  
    4JXB, 4LJ1

  • PubMed Abstract: 

    Enzymes carrying NlpC/p60 domains, for instance RipA and RipB from Mycobacterium tuberculosis, are bacterial peptidoglycan hydrolases that cleave the peptide stems and contribute to cell wall remodelling during cell division. A member of this protein family, RipD (Rv1566c) from M. tuberculosis described in the present study, displays sequence alterations in the NlpC/p60 catalytic triad and carries a pentapeptide repeat at its C-terminus. Bioinformatics analysis revealed RipD-like proteins in eleven mycobacterial genomes, whereas similar pentapeptide repeats occur in cell-wall-localized bacterial proteins and in a mycobacteriophage. In contrast with previously known members of the NlpC/p60 family, RipD does not show peptidoglycan hydrolase activity, which is consistent with the sequence alterations at the catalytic site. A strong interaction of the catalytically inactive core domain with peptidoglycan is however retained, presenting the first example of the NlpC/p60 domains that evolved to a non-catalytic peptidoglycan-binding function. Full-length RipD carrying the C-terminal repeat shows, however, a decrease in binding affinity to peptidoglycan, suggesting that the C-terminal tail modulates the interaction with bacterial cell wall components. The pentapeptide repeat at the C-terminus does not adopt a defined secondary structure in solution which is in accordance with results from the 1.17 Å (1 Å=0.1 nm) crystal structure of the protein carrying two repeat units.


  • Organizational Affiliation

    *Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Invasion-associated protein
A, B
134Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1566cRVBD_1566c
UniProt
Find proteins for O06624 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06624 
Go to UniProtKB:  O06624
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06624
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.822α = 90
b = 56.114β = 109.02
c = 57.157γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations