5JP6

Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/srep26010

  • 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 b ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative polysaccharide deacetylase
A
383Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)Mutation(s): 1 
EC: 3.5.1.-
Find proteins for Q6MI90 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100))
Go to UniProtKB:  Q6MI90
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PXU
Query on PXU
A
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.145 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 112.434α = 90.00
b = 112.434β = 90.00
c = 79.859γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-05-03 
  • Released Date: 2016-06-01 
  • Deposition Author(s): Lovering, A.L.

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

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence
  • Version 1.2: 2019-02-20
    Type: Advisory, Data collection, Derived calculations