7O21

Structure of Bdellovibrio bacteriovorus Bd1075


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Asymmetric peptidoglycan editing generates cell curvature in Bdellovibrio predatory bacteria.

Banks, E.J.Valdivia-Delgado, M.Biboy, J.Wilson, A.Cadby, I.T.Vollmer, W.Lambert, C.Lovering, A.L.Sockett, R.E.

(2022) Nat Commun 13: 1509-1509

  • DOI: https://doi.org/10.1038/s41467-022-29007-y
  • Primary Citation of Related Structures:  
    7O21

  • PubMed Abstract: 

    Peptidoglycan hydrolases contribute to the generation of helical cell shape in Campylobacter and Helicobacter bacteria, while cytoskeletal or periskeletal proteins determine the curved, vibrioid cell shape of Caulobacter and Vibrio. Here, we identify a peptidoglycan hydrolase in the vibrioid-shaped predatory bacterium Bdellovibrio bacteriovorus which invades and replicates within the periplasm of Gram-negative prey bacteria. The protein, Bd1075, generates cell curvature in B. bacteriovorus by exerting LD-carboxypeptidase activity upon the predator cell wall as it grows inside spherical prey. Bd1075 localizes to the outer convex face of B. bacteriovorus; this asymmetric localization requires a nuclear transport factor 2-like (NTF2) domain at the protein C-terminus. We solve the crystal structure of Bd1075, which is monomeric with key differences to other LD-carboxypeptidases. Rod-shaped Δbd1075 mutants invade prey more slowly than curved wild-type predators and stretch invaded prey from within. We therefore propose that the vibrioid shape of B. bacteriovorus contributes to predatory fitness.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized conserved
A, B
324Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: Bd1075
UniProt
Find proteins for Q6MNZ7 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MNZ7 
Go to UniProtKB:  Q6MNZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MNZ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
EA [auth B],
F [auth A],
J [auth A],
N [auth A],
O [auth B],
P [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
W [auth B],
Y [auth B],
Z [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth A]
L [auth A]
M [auth A]
G [auth A],
H [auth A],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
V [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
E [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.189α = 90
b = 100.631β = 108.07
c = 62.279γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
SOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Comision Nacional Cientifica y Technologica (CONICYT)Chile72180329

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references