PROSITE documentation PDOC00819OmpA-like domain signature and profile
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: Last update:June 2005 / Profile added and text revised.
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PROSITE methods (with tools and information) covered by this documentation:
| 1 | Authors | De Mot R. Proost P. van Damme J. Vanderleyden J. |
| Title | Homology of the root adhesin of Pseudomonas fluorescens OE 28.3 with porin F of P. aeruginosa and P. syringae. | |
| Source | Mol. Gen. Genet. 231:489-493(1992). | |
| PubMed ID | 1538702 |
| 2 | Authors | Hardham J.M. Stamm L.V. |
| Title | Identification and characterization of the Treponema pallidum tpn50 gene, an ompA homolog. | |
| Source | Infect. Immun. 62:1015-1025(1994). | |
| PubMed ID | 8112835 |
| 3 | Authors | Grizot S. Buchanan S.K. |
| Title | Structure of the OmpA-like domain of RmpM from Neisseria meningitidis. | |
| Source | Mol. Microbiol. 51:1027-1037(2004). | |
| PubMed ID | 14763978 |
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