PDBsum entry 4zqw

Toxin/inhibitor

PDB id: 4zqw

Contents

Protein chains

167 a.a.

13 a.a.

Metals

_CL ×2

Waters ×132

References listed in PDB file

Key reference

• Title: Diversification of β-Augmentation interactions between cdi toxin/immunity proteins.
• Authors: R.P.Morse, J.L.Willett, P.M.Johnson, J.Zheng, A.Credali, A.Iniguez, J.S.Nowick, C.S.Hayes, C.W.Goulding.
• Ref.: J Mol Biol, 2015, 427, 3766-3784. [DOI no: 10.1016/j.jmb.2015.09.020]
• PubMed id: 26449640

Abstract

Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition mediated by the CdiB/CdiA family of two-partner secretion proteins. CdiA effectors carry diverse C-terminal toxin domains (CdiA-CT), which are delivered into neighboring target cells to inhibit growth. CDI(+) bacteria also produce CdiI immunity proteins that bind specifically to cognate CdiA-CT toxins and protect the cell from auto-inhibition. Here, we compare the structures of homologous CdiA-CT/CdiI complexes from Escherichia coli EC869 and Yersinia pseudotuberculosis YPIII to explore the evolution of CDI toxin/immunity protein interactions. Both complexes share an unusual β-augmentation interaction, in which the toxin domain extends a β-hairpin into the immunity protein to complete a six-stranded anti-parallel sheet. However, the specific contacts differ substantially between the two complexes. The EC869 β-hairpin interacts mainly through direct H-bond and ion-pair interactions, whereas the YPIII β-hairpin pocket contains more hydrophobic contacts and a network of bridging water molecules. In accord with these differences, we find that each CdiI protein only protects target bacteria from its cognate CdiA-CT toxin. The compact β-hairpin binding pocket within the immunity protein represents a tractable system for the rationale design of small molecules to block CdiA-CT/CdiI complex formation. We synthesized a macrocyclic peptide mimic of the β-hairpin from EC869 toxin and solved its structure in complex with cognate immunity protein. These latter studies suggest that small molecules could potentially be used to disrupt CDI toxin/immunity complexes.