5CED | pdb_00005ced

Penicillin G Acylated Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PNMClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus.

Lambert, C.Cadby, I.T.Till, R.Bui, N.K.Lerner, T.R.Hughes, W.S.Lee, D.J.Alderwick, L.J.Vollmer, W.Sockett, E.R.Lovering, A.L.

(2015) Nat Commun 6: 8884-8884

  • DOI: https://doi.org/10.1038/ncomms9884
  • Primary Citation of Related Structures:  
    5CEA, 5CEB, 5CEC, 5CED, 5CER

  • PubMed Abstract: 

    Predatory Bdellovibrio bacteriovorus are natural antimicrobial organisms, killing other bacteria by whole-cell invasion. Self-protection against prey-metabolizing enzymes is important for the evolution of predation. Initial prey entry involves the predator's peptidoglycan DD-endopeptidases, which decrosslink cell walls and prevent wasteful entry by a second predator. Here we identify and characterize a self-protection protein from B. bacteriovorus, Bd3460, which displays an ankyrin-based fold common to intracellular pathogens of eukaryotes. Co-crystal structures reveal Bd3460 complexation of dual targets, binding a conserved epitope of each of the Bd3459 and Bd0816 endopeptidases. Complexation inhibits endopeptidase activity and cell wall decrosslinking in vitro. Self-protection is vital - ΔBd3460 Bdellovibrio deleteriously decrosslink self-peptidoglycan upon invasion, adopt a round morphology, and lose predatory capacity and cellular integrity. Our analysis provides the first mechanistic examination of self-protection in Bdellovibrio, documents protection-multiplicity for products of two different genomic loci, and reveals an important evolutionary adaptation to an invasive predatory bacterial lifestyle.


  • Organizational Affiliation

    Centre for Genetics and Genomics, School of Biology, Nottingham University, 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
Bd3459446Bdellovibrio bacteriovorus HD100Mutation(s): 1 
Gene Names: Bd3459
EC: 3.4.16.4
UniProt
Find proteins for Q6MHT0 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MHT0 
Go to UniProtKB:  Q6MHT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MHT0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bd3460230Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: Bd3460
UniProt
Find proteins for Q6MHS9 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MHS9 
Go to UniProtKB:  Q6MHS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MHS9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNM
Query on PNM

Download Ideal Coordinates CCD File 
C [auth A]OPEN FORM - PENICILLIN G
C16 H20 N2 O4 S
OGFZUTGOGYUTKZ-KWCYVHTRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.54α = 90
b = 59.16β = 90
c = 192.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PNMClick on this verticalbar to view details

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: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary