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PROSITE documentation PDOC00819 [for PROSITE entry PS51123]

OmpA-like domain signature and profile





Description

The following Gram-negative outer membrane proteins share a domain of about 150 residues [1,2]:

  • Outer membrane protein ompA from enterobacteria such as Escherichia coli.
  • Outer membrane protein P5 from Haemophilus influenzae.
  • Outer membrane protein P.III/class IV from Neisseria.
  • Outer membrane porin F (gene oprF) from Pseudomonas.
  • Protein TpN50 from Treponema pallidum.
  • Peptidoglycan-associated lipoprotein (gene pal) from Escherichia coli, Haemophilus influenzae, Legionella pneumophila and Pseudomonas putida.
  • Outer membrane lipoprotein P6 from Haemophilus influenzae.
  • Escherichia coli hypothetical lipoprotein yiaD.
  • Vibrio parahaemolyticus sodium-type flagellar protein motY.

This domain is found in the C-terminal section of the above proteins. Apart from this domain, these proteins are not structurally related. Most of them are porin-like integral membrane proteins (such as ompA), but some are small lipid-anchored proteins (such as pal). In addition to being attached to the outer membrane, OmpA-like domains are also found attached to the inner membrane: MotB proteins, part of the flagellar motor/stator complex in Gram-positive and Gram-negative bacteria, span the inner membrane and contain OmpA-like domains in their periplasmic regions [3].

The OmpA-like domain is thought to be responsible for non-covalent interactions with peptidoglycan [3].

The OmpA-like domain adopts a β-α-β-α-β-β fold (see <PDB:1R1M>). The core OmpA-like domain consists of a mixed β-sheet formed from parallel and antiparallel β-strands (β1 to β4), which are flanked by two long α helices (α2 and α3). A short helix α1 is part of the segment connecting β1 to α2. An extension formed by two antiparallel α helices (α4 and α5), is stabilized by a disulphide bond. The domain fold creates a hydrophilic groove which could accomodate a glycan chain [3].

The signature pattern that we developed spans the central part of the OmpA-like domain. We also developed a profile which covers the entire domain.

Expert(s) to contact by email:

De Mot R.

Last update:

June 2005 / Profile added and text revised.

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Technical section

PROSITE methods (with tools and information) covered by this documentation:

OMPA_2, PS51123; OmpA-like domain profile  (MATRIX)

OMPA_1, PS01068; OmpA-like domain  (PATTERN)


References

1AuthorsDe Mot R. Proost P. van Damme J. Vanderleyden J.
TitleHomology of the root adhesin of Pseudomonas fluorescens OE 28.3 with porin F of P. aeruginosa and P. syringae.
SourceMol. Gen. Genet. 231:489-493(1992).
PubMed ID1538702

2AuthorsHardham J.M. Stamm L.V.
TitleIdentification and characterization of the Treponema pallidum tpn50 gene, an ompA homolog.
SourceInfect. Immun. 62:1015-1025(1994).
PubMed ID8112835

3AuthorsGrizot S. Buchanan S.K.
TitleStructure of the OmpA-like domain of RmpM from Neisseria meningitidis.
SourceMol. Microbiol. 51:1027-1037(2004).
PubMed ID14763978



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