PDBsum entry 5cec

Protein binding

PDB id: 5cec

Contents

Protein chains

401 a.a.

193 a.a.

Ligands

SO4 ×6

Waters ×493

PDB id:

5cec

Name:

Protein binding

Title:

Bd3459 predatory endopeptidase from bdellovibrio bacteriovorus in complex with immunity protein bd3460

Structure:

Bd3459. Chain: a. Fragment: bd3459. Engineered: yes. Mutation: yes. Bd3460. Chain: b. Engineered: yes

Source:

Bdellovibrio bacteriovorus (strain atcc 15356 / dsm 50701 / ncib 9529 / hd100). Organism_taxid: 264462. Gene: bd3459. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: bd3460.

Resolution:

1.36Å R-factor: 0.143 R-free: 0.169

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:

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

Protein chain

Q6MHT0  (Q6MHT0_BDEBA) -  D-alanyl-D-alanine carboxypeptidase from Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)

Seq: 446 a.a.

Struc: 401 a.a.*

Protein chain

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 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chain A: 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.