5JP6

Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Interrupting peptidoglycan deacetylation during Bdellovibrio predator-prey interaction prevents ultimate destruction of prey wall, liberating bacterial-ghosts.

Lambert, C.Lerner, T.R.Bui, N.K.Somers, H.Aizawa, S.Liddell, S.Clark, A.Vollmer, W.Lovering, A.L.Sockett, R.E.

(2016) Sci Rep 6: 26010-26010

  • DOI: https://doi.org/10.1038/srep26010
  • Primary Citation of Related Structures:  
    5JP6

  • PubMed Abstract: 

    The peptidoglycan wall, located in the periplasm between the inner and outer membranes of the cell envelope in Gram-negative bacteria, maintains cell shape and endows osmotic robustness. Predatory Bdellovibrio bacteria invade the periplasm of other bacterial prey cells, usually crossing the peptidoglycan layer, forming transient structures called bdelloplasts within which the predators replicate. Prey peptidoglycan remains intact for several hours, but is modified and then degraded by escaping predators. Here we show predation is altered by deleting two Bdellovibrio N-acetylglucosamine (GlcNAc) deacetylases, one of which we show to have a unique two domain structure with a novel regulatory"plug". Deleting the deacetylases limits peptidoglycan degradation and rounded prey cell "ghosts" persist after mutant-predator exit. Mutant predators can replicate unusually in the periplasmic region between the peptidoglycan wall and the outer membrane rather than between wall and inner-membrane, yet still obtain nutrients from the prey cytoplasm. Deleting two further genes encoding DacB/PBP4 family proteins, known to decrosslink and round prey peptidoglycan, results in a quadruple mutant Bdellovibrio which leaves prey-shaped ghosts upon predation. The resultant bacterial ghosts contain cytoplasmic membrane within bacteria-shaped peptidoglycan surrounded by outer membrane material which could have promise as "bacterial skeletons" for housing artificial chromosomes.


  • Organizational Affiliation

    Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative polysaccharide deacetylase383Bdellovibrio bacteriovorus HD100Mutation(s): 1 
Gene Names: Bd3279
EC: 3.5.1
UniProt
Find proteins for Q6MI90 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MI90 
Go to UniProtKB:  Q6MI90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MI90
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PXU
Query on PXU
A
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.434α = 90
b = 112.434β = 90
c = 79.859γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J015229/1

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-07-10
    Changes: Data collection
  • Version 1.4: 2019-10-16
    Changes: Data collection
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description