High Resolution Crystal Structure of PedB: a Structural Basis for the Classification of Pediocin-like Immunity Proteins

Overview

Journal BMC Struct Biol

Publisher Biomed Central

Specialties Biochemistry
Molecular Biology

Date 2007 Jun 1

PMID 17537233

Citations 4

Authors

In-Kwon Kim

Min-Kyu Kim

Ji-Hye Kim

Hyung-Soon Yim

Sun-Shin Cha

Sa-Ouk Kang

Affiliations

Soon will be listed here.

Abstract

Background: Pediocin-like bacteriocins, ribosomally-synthesized antimicrobial peptides, are generally coexpressed with cognate immunity proteins in order to protect the bacteriocin-producer from its own bacteriocin. As a step for understanding the mode of action of immunity proteins, we determined the crystal structure of PedB, a pediocin-like immunity protein conferring immunity to pediocin PP-1.

Results: The 1.6 A crystal structure of PedB reveals that PedB consists of an antiparallel four-helix bundle with a flexible C-terminal end. PedB shows structural similarity to an immunity protein against enterocin A (EntA-im) but some disparity to an immunity protein against carnobacteriocin B2 (ImB2) in both the C-terminal conformation and the local structure constructed by alpha3, alpha4, and their connecting loop. Structure-inspired mutational studies reveal that deletion of the last seven residues of the C-terminus of PedB almost abolished its immunity activity.

Conclusion: The fact that PedB, EntA-im, and ImB2 share a four-helix bundle structure strongly suggests the structural conservation of this motif in the pediocin-like immunity proteins. The significant difference in the core structure and the C-terminal conformation provides a structural basis for the classification of pediocin-like immunity proteins. Our mutational study using C-terminal-shortened PedBs and the investigation of primary sequence of the C-terminal region, propose that several polar or charged residues in the extreme C-terminus of PedB which is crucial for the immunity are involved in the specific recognition of pediocin PP-1.

Citing Articles

Structural Basis of Pore Formation in the Mannose Phosphotransferase System by Pediocin PA-1.

Zhu L, Zeng J, Wang C, Wang J Appl Environ Microbiol. 2021; 88(3):e0199221.

PMID: 34851716 PMC: 8824269. DOI: 10.1128/AEM.01992-21.

Site-directed mutagenesis identifies the positively charged residue lysine-46 essential for the function of the immunity protein PedB.

Wang C, Douillard F, Zhou W, Hao Y Curr Microbiol. 2014; 69(4):423-8.

PMID: 24838664 DOI: 10.1007/s00284-014-0596-6.

Class IIa bacteriocins: diversity and new developments.

Cui Y, Zhang C, Wang Y, Shi J, Zhang L, Ding Z Int J Mol Sci. 2012; 13(12):16668-707.

PMID: 23222636 PMC: 3546714. DOI: 10.3390/ijms131216668.

The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes.

Chang C, Coggill P, Bateman A, Finn R, Cymborowski M, Otwinowski Z BMC Struct Biol. 2009; 9:75.

PMID: 20017931 PMC: 2806384. DOI: 10.1186/1472-6807-9-75.

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