Cloning and characterization of the gene encoding for OMP-PD porin: the major Photobacterium damsela outer membrane protein

Curr Microbiol. 2004 Mar;48(3):167-74. doi: 10.1007/s00284-003-4111-8.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Cloning, Molecular
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / isolation & purification
  • Endopeptidases / metabolism
  • Escherichia coli / genetics
  • Genes, Bacterial
  • Hydrophobic and Hydrophilic Interactions
  • Molecular Sequence Data
  • Molecular Weight
  • Photobacterium / chemistry
  • Photobacterium / genetics*
  • Porins / chemistry*
  • Porins / genetics*
  • Porins / isolation & purification
  • Protein Denaturation
  • Protein Sorting Signals / genetics
  • Protein Structure, Secondary
  • Protein Subunits
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology
  • Sodium Dodecyl Sulfate
  • Vibrio / genetics


  • DNA, Bacterial
  • Porins
  • Protein Sorting Signals
  • Protein Subunits
  • Sodium Dodecyl Sulfate
  • Endopeptidases

Associated data

  • GENBANK/AF411938