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

BMC Structural Biology

Volumn 7, Issue , 2007, Pages

  Kim, In Kwon ^a   Kim, Min Kyu ^a   Kim, Ji Hye ^a   Yim, Hyung Soon ^a   Cha, Sun Shin ^b   Kang, Sa Ouk ^a  

^a Seoul National University   (South Korea)

^b Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

PEDIOCIN; BACTERIAL PROTEIN; BACTERIOCIN; ENTA PROTEIN, E COLI; ESCHERICHIA COLI PROTEIN; OXIDOREDUCTASE; PEDB PROTEIN, PEDIOCOCCUS PENTOSACEUS; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; IMMUNITY; MUTATIONAL ANALYSIS; NONHUMAN; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN STRUCTURE; STATISTICAL SIGNIFICANCE; CHEMICAL STRUCTURE; CHEMISTRY; GENE DELETION; IMMUNOLOGY; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

BACTERIAL PROTEINS; BACTERIOCINS; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI PROTEINS; IMMUNITY; MODELS, MOLECULAR; OXIDOREDUCTASES ACTING ON CH-CH GROUP DONORS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE DELETION;

EID: 34347400417     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-7-35     Document Type: Article

References (43)

1. Posttranslationally modified bacteriocins-the lantibiotics. A Guder I Wiedemann HG Sahl, Biopolymers 2000 55 1 62 73 10.1002/1097-0282(2000)55: 1<62::AID-BIP60>3.0.CO;2-Y 10931442
2. Ribosomally synthesized peptides with antimicrobial properties: biosynthesis, structure, function, and applications. M Papagianni, Biotechnol Adv 2003 21 6 465 499 10.1016/S0734-9750(03)00077-6 14499150
3. Nonlantibiotic antibacterial peptides from lactic acid bacteria. MJ van Belkum ME Stiles, Nat Prod Rep 2000 17 4 323 335 10.1039/a801347k 11014335
4. Biosynthesis and biological activities of lantibiotics with unique post-translational modifications. HG Sahl RW Jack G Bierbaum, Eur J Biochem 1995 230 3 827 853 10.1111/j.1432-1033.1995.tb20627.x 7601145
5. Class IIa bacteriocins: biosynthesis, structure and activity. S Ennahar T Sashihara K Sonomoto A Ishizaki, FEMS Microbiol Rev 2000 24 1 85 106 10.1111/j.1574-6976.2000.tb00534.x 10640600
6. Ribosomally synthesized antimicrobial peptides: their function, structure, biogenesis, and mechanism of action. J Nissen-Meyer IF Nes, Arch Microbiol 1997 167 2-3 67 77 9133328 10.1007/s002030050418
7. Mutational analysis of the role of tryptophan residues in an antimicrobial peptide. G Fimland VG Eijsink J Nissen-Meyer, Biochemistry 2002 41 30 9508 9515 10.1021/bi025856q 12135373
8. Pediocin PA-1, a bacteriocin from Pediococcus acidilactici PAC1.0, forms hydrophilic pores in the cytoplasmic membrane of target cells. ML Chikindas MJ Garcia-Garcera AJ Driessen AM Ledeboer J Nissen-Meyer IF Nes T Abee WN Konings G Venema, Appl Environ Microbiol 1993 59 11 3577 3584 8285666
9. Bacteriocins: mechanism of membrane insertion and pore formation. GN Moll WN Konings AJ Driessen, Antonie Van Leeuwenhoek 1999 76 1-4 185 198 10.1023/A:1002002718501 10532378
10. Three-dimensional structure in lipid micelles of the pediocin-like antimicrobial peptide sakacin P and a sakacin P variant that is structurally stabilized by an inserted C-terminal disulfide bridge. M Uteng HH Hauge PR Markwick G Fimland D Mantzilas J Nissen-Meyer C Muhle-Goll, Biochemistry 2003 42 39 11417 11426 10.1021/bi034572i 14516192
11. Three-dimensional structure of leucocin A in trifluoroethanol and dodecylphosphocholine micelles: spatial location of residues critical for biological activity in type IIa bacteriocins from lactic acid bacteria. NL Fregeau Gallagher M Sailer WP Niemczura TT Nakashima ME Stiles JC Vederas, Biochemistry 1997 36 49 15062 15072 10.1021/bi971263h 9398233
12. Solution structure of carnobacteriocin B2 and implications for structure-activity relationships among type IIa bacteriocins from lactic acid bacteria. Y Wang ME Henz NL Gallagher S Chai AC Gibbs LZ Yan ME Stiles DS Wishart JC Vederas, Biochemistry 1999 38 47 15438 15447 10.1021/bi991351x 10569926
13. Electrostatic interactions, but not the YGNGV consensus motif, govern the binding of pediocin PA-1 and its fragments to phospholipid vesicles. Y Chen RD Ludescher TJ Montville, Appl Environ Microbiol 1997 63 12 4770 4777 9406395
14. Mutational analysis of the role of charged residues in target-cell binding, potency and specificity of the pediocin-like bacteriocin sakacin P. M Kazazic J Nissen-Meyer G Fimland, Microbiology 2002 148 Pt 7 2019 2027 12101290
15. New biologically active hybrid bacteriocins constructed by combining regions from various pediocin-like bacteriocins: the C-terminal region is important for determining specificity. G Fimland OR Blingsmo K Sletten G Jung IF Nes J Nissen-Meyer, Appl Environ Microbiol 1996 62 9 3313 3318 8795220
16. Isolation and characterization of pediocin AcH chimeric protein mutants with altered bactericidal activity. KW Miller R Schamber O Osmanagaoglu B Ray, Appl Environ Microbiol 1998 64 6 1997 2005 9603806
17. The genes involved in production of and immunity to sakacin A, a bacteriocin from Lactobacillus sake Lb706. L Axelsson A Holck, J Bacteriol 1995 177 8 2125 2137 7721704
18. The putative immunity protein of the Gram-positive bacteria Leuconostoc mesenteroides is preferentially located in the cytoplasm compartment. MA Dayem Y Fleury G Devilliers E Chaboisseau R Girard P Nicolas A Delfour, FEMS Microbiol Lett 1996 138 2-3 251 259 10.1111/j.1574-6968.1996.tb08166.x 9026455
19. Analysis of the sakacin P gene cluster from Lactobacillus sake Lb674 and its expression in sakacin-negative Lb. sake strains. K Huhne L Axelsson A Holck L Krockel, Microbiology 1996 142 1437 1448 8704983
20. Characterization of the protein conferring immunity to the antimicrobial peptide carnobacteriocin B2 and expression of carnobacteriocins B2 and BM1. LE Quadri M Sailer MR Terebiznik KL Roy JC Vederas ME Stiles, J Bacteriol 1995 177 5 1144 1151 7868585
21. Characterization of a locus from Carnobacterium piscicola LV17B involved in bacteriocin production and immunity: evidence for global inducer-mediated transcriptional regulation. LE Quadri M Kleerebezem OP Kuipers WM de Vos KL Roy JC Vederas ME Stiles, J Bacteriol 1997 179 19 6163 6171 9324267
22. Comparative studies of class IIa bacteriocins of lactic acid bacteria. VG Eijsink M Skeie PH Middelhoven MB Brurberg IF Nes, Appl Environ Microbiol 1998 64 9 3275 3281 9726871
23. Comparative studies of immunity proteins of pediocin-like bacteriocins. G Fimland VG Eijsink J Nissen-Meyer, Microbiology 2002 148 Pt 11 3661 3670 12427956
24. The C-terminal domain of pediocin-like antimicrobial peptides (class IIa bacteriocins) is involved in specific recognition of the C-terminal part of cognate immunity proteins and in determining the antimicrobial spectrum. L Johnsen G Fimland J Nissen-Meyer, J Biol Chem 2005 280 10 9243 9250 10.1074/jbc.M412712200 15611086
25. Structure-function analysis of immunity proteins of pediocin-like bacteriocins: C-terminal parts of immunity proteins are involved in specific recognition of cognate bacteriocins. L Johnsen G Fimland D Mantzilas J Nissen-Meyer, Appl Environ Microbiol 2004 70 5 2647 2652 15128514 10.1128/AEM.70.5.2647-2652.2004
26. Functional analysis of the pediocin operon of Pediococcus acidilactici PAC1.0: PedB is the immunity protein and PedD is the precursor processing enzyme. K Venema J Kok JD Marugg MY Toonen AM Ledeboer G Venema ML Chikindas, Mol Microbiol 1995 17 3 515 522 10.1111/j.1365-2958.1995.mmi_17030515.x 8559070
27. 1.6 Å crystal structure of EntA-im. A bacterial immunity protein conferring immunity to the antimicrobial activity of the pediocin-like bacteriocin enterocin A. L Johnsen B Dalhus I Leiros J Nissen-Meyer, J Biol Chem 2005 280 19 19045 19050 10.1074/jbc.M501386200 15753083
28. NMR solution structure of ImB2, a protein conferring immunity to antimicrobial activity of the type IIa bacteriocin, carnobacteriocin B2. T Sprules KE Kawulka JC Vederas, Biochemistry 2004 43 37 11740 11749 10.1021/bi048854+ 15362858
29. Cloning, expression, and nucleotide sequence of genes involved in production of pediocin PA-1, and bacteriocin from Pediococcus acidilactici PAC1.0. JD Marugg CF Gonzalez BS Kunka AM Ledeboer MJ Pucci MY Toonen SA Walker LC Zoetmulder PA Vandenbergh, Appl Environ Microbiol 1992 58 8 2360 2367 1514784
30. Molecular cloning and nucleotide sequence of the superoxide dismutase gene and characterization of its product from Bacillus subtilis. T Inaoka Y Matsumura T Tsuchido, J Bacteriol 1998 180 14 3697 3703 9658017
31. SodA and manganese are essential for resistance to oxidative stress in growing and sporulating cells of Bacillus subtilis. T Inaoka Y Matsumura T Tsuchido, J Bacteriol 1999 181 6 1939 1943 10074093
32. The relation between the divergence of sequence and structure in proteins. C Chothia AM Lesk, EMBO J 1986 5 4 823 826 3709526
33. Computed circular dichroism spectra for the evaluation of protein conformation. N Greenfield GD Fasman, Biochemistry 1969 8 4108 4116 10.1021/bi00838a031 5346390
34. JPred: a consensus secondary structure prediction server. JA Cuff ME Clamp AS Siddiqui M Finlay GJ Barton, Bioinformatics 1998 14 10 892 893 10.1093/bioinformatics/14.10.892 9927721
35. Thermosensitive suicide vectors for gene replacement in Streptococcus suis. D Takamatsu M Osaki T Sekizaki, Plasmid 2001 46 2 140 148 10.1006/plas.2001.1532 11591139
36. Transformation of Lactobacillus by electroporation. TW Aukrust MB Brurberg IF Nes, Methods Mol Biol 1995 47 201 208 7550736
37. Crystallization and preliminary X-ray crystallographic analysis of the pediocin immunity protein (PedB) from Pediococcus pentosaceus at 1.35 Å resolution. IK Kim MK Kim HS Yim SS Cha SO Kang, Biochim Biophys Acta 2005 1751 2 205 208 16019271
38. Processing of X-ray diffraction data collected in oscillation mode. Z Otwinowski W Minor, Methods Enzymol 1997 276 307 326
39. Reciprocal-space solvent flattening. TC Terwilliger, Acta Crystallogr Sect D Biol Crystallogr 1999 55 11 1863 1871 10.1107/S0907444999010033
40. Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods. TC Terwilliger J Berendzen, Acta Crystallogr Sect D Biol Crystallogr 1999 55 Pt 2 501 505 10.1107/S0907444998012657
41. Crystallography & NMR system: A new software suite for macromolecular structure determination. AT Brunger PD Adams GM Clore WL DeLano P Gros RW Grosse-Kunstleve JS Jiang J Kuszewski M Nilges NS Pannu, Acta Crystallogr Sect D Biol Crystallogr 1998 54 Pt 5 905 921 10.1107/S0907444998003254
42. PROCHECK: a program to check the stereochemical quality of protein structures. RA Laskowski MW MacArthur DS Moss JM Thornton, J Appl Crystallogra 1993 26 283 291 10.1107/S0021889892009944
43. A novel lactococcal bacteriocin whose activity depends on the complementary action of two peptides. J Nissen-Meyer H Holo LS Havarstein K Sletten IF Nes, J Bacteriol 1992 174 17 5686 5692 1512201