PDBsum entry 5cer

Immune system

PDB id: 5cer

Contents

Protein chains

(+ 0 more) 401 a.a.

(+ 0 more) 193 a.a.

Ligands

EDO

Waters ×1356

PDB id:

5cer

Name:

Immune system

Title:

Bd0816 predatory endopeptidase from bdellovibrio bacteriovorus in complex with immunity protein bd3460

Structure:

Bd0816. Chain: a, c, e, g, i, k. Fragment: bd0816. Engineered: yes. Mutation: yes. Bd3460. Chain: b, d, f, h, j, l. Engineered: yes

Source:

Bdellovibrio bacteriovorus hd100. Organism_taxid: 264462. Gene: bd0816. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: bd3460.

Resolution:

2.48Å R-factor: 0.217 R-free: 0.249

Authors:

A.L.Lovering,I.T.Cadby,C.Lambert,R.E.Sockett

Key ref:

C.Lambert et al. (2015). Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus. Nat Commun, 6, 8884. PubMed id: 26626559 DOI: 10.1038/ncomms9884

Date:

07-Jul-15 Release date: 09-Dec-15

Protein chains

Q6MPN2  (Q6MPN2_BDEBA) -  D-alanyl-D-alanine carboxypeptidase from Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)

Seq: 436 a.a.

Struc: 401 a.a.*

Protein chains

Q6MHS9  (Q6MHS9_BDEBA) -  Uncharacterized protein from Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)

Seq: 220 a.a.

Struc: 193 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C, E, G, I, K: E.C.3.4.16.4 - serine-type D-Ala-D-Ala carboxypeptidase.
• Reaction: D-alanyl-D-alanine + H₂O = 2 D-alanine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/ncomms9884

Nat Commun 6:8884 (2015)

PubMed id: 26626559

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

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

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.