High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins.
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.


CONCLUSIONS
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.
Kim
In-Kwon
IK
Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea. ikkim33@snu.ac.kr <ikkim33@snu.ac.kr>
Kim
Min-Kyu
MK
Kim
Ji-Hye
JH
Yim
Hyung-Soon
HS
Cha
Sun-Shin
SS
Kang
Sa-Ouk
SO
D001426:Bacterial Proteins / Q000737:chemistry* / Q000276:immunology*; D001430:Bacteriocins / Q000737:chemistry* / Q000276:immunology*; D018360:Crystallography, X-Ray; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000276:immunology; D007109:Immunity; D008958:Models, Molecular; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000737:chemistry / Q000276:immunology; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D017384:Sequence Deletion
D001426:Bacterial Proteins; D001430:Bacteriocins; D029968:Escherichia coli Proteins; C504668:PedB protein, Pediococcus pentosaceus; D044925:Oxidoreductases Acting on CH-CH Group Donors; C061899:entA protein, E coli