title: Cloning and characterization of the gene encoding for OMP-PD porin: the major Photobacterium damsela outer membrane protein.
abstract: The outer membrane protein of Photobacterium damsela (OMP-PD) and the gene encoding for this porin protein were isolated and characterized. The deduced amino acid sequence of the OMP-PD monomer has 338 amino acids and a calculated molecular weight of 36,951 Da. This sequence includes a 22-amino acid signal peptide at the N-terminal, which is not found when the monomer is located in the outer membrane. Native OMP-PD protein forms a trimeric structure of approximately 110 kDa. It exhibits resistance to proteases, and it can be cleaved only following denaturation by SDS. The degree of identity of the OMP-PD amino acid sequence to porins from the Enterobacteriaceae was only 24%. Identity to Vibrio or Photobacterium porins was 38% and 48%, respectively. Nevertheless, the multiple alignment of this sequence with other structurally defined Enterobacteria porins demonstrated that the location of the 16 beta-strands and eight external loops, including a larger external L3 loop, are conserved in OMP-PD. These results, together with the previously known ability of OMP-PD to form an ion channel in artificial liposomes, strongly support its role as a porin in P. damsela and will help further investigations into the role of OMP-PD in P. damsela pathogenicity.
authors.affiliation: Health Sciences Research Center, Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Anna
authors.initials: A
authors.lastname: Gribun
authors.forename: Don J
authors.initials: DJ
authors.lastname: Katcoff
authors.forename: Gitit
authors.initials: G
authors.lastname: Hershkovits
authors.forename: Izabella
authors.initials: I
authors.lastname: Pechatnikov
authors.forename: Yeshayahu
authors.initials: Y
authors.lastname: Nitzan
mesh_terms: D000595:Amino Acid Sequence; D003001:Cloning, Molecular; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D010450:Endopeptidases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D005798:Genes, Bacterial; D057927:Hydrophobic and Hydrophilic Interactions; D008969:Molecular Sequence Data; D008970:Molecular Weight; D010776:Photobacterium / Q000737:chemistry / Q000235:genetics*; D018272:Porins / Q000737:chemistry* / Q000235:genetics* / Q000302:isolation & purification; D011489:Protein Denaturation; D021382:Protein Sorting Signals / Q000235:genetics; D017433:Protein Structure, Secondary; D021122:Protein Subunits; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012967:Sodium Dodecyl Sulfate; D014733:Vibrio / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D018272:Porins; D021382:Protein Sorting Signals; D021122:Protein Subunits; D012967:Sodium Dodecyl Sulfate; D010450:Endopeptidases