5CER | pdb_00005cer

Bd0816 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460

PDB DOI: https://doi.org/10.2210/pdb5CER/pdb

Classification: IMMUNE SYSTEM
Organism(s): Bdellovibrio bacteriovorus HD100
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-07-07 Released: 2015-12-09
Deposition Author(s): Lovering, A.L., Cadby, I.T., Lambert, C., Sockett, R.E.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.249 (Depositor), 0.234 (DCC)
R-Value Work:
0.215 (Depositor)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 26626559 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms9884
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 390.49 kDa
Atom Count: 28,724
Modeled Residue Count: 3,561
Deposited Residue Count: 3,564
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bd0816	A, C, E, G, I A, C, E, G, I, K	401	Bdellovibrio bacteriovorus HD100	Mutation(s): 2 Gene Names: Bd0816 EC: 3.4.16.4
UniProt
Find proteins for Q6MPN2 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MPN2 Go to UniProtKB: Q6MPN2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6MPN2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bd3460	B, D, F, H, J B, D, F, H, J, L	193	Bdellovibrio bacteriovorus HD100	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6MHS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth I] MOL2 format, chain M [auth I] mmCIF format, chain M [auth I]	M [auth I]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth I] Interactions & Density Focus chain M [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.249 (Depositor), 0.234 (DCC)
R-Value Work: 0.215 (Depositor)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 237.45	α = 90
b = 212.32	β = 90
c = 90.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/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