{PDOC00819}
{PS01068; OMPA_1}
{PS51123; OMPA_2}
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* OmpA-like domain signature and profile *
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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  Beta-Alpha-Beta-Alpha-Beta-Beta  fold  (see
<PDB:1R1M>). The  core  OmpA-like domain consists of a mixed beta-sheet formed
from parallel  and  antiparallel  beta-strands  (beta1  to  beta4),  which are
flanked by two long alpha helices (alpha2 and alpha3). A short helix alpha1 is
part of  the  segment  connecting  beta1 to alpha2. An extension formed by two
antiparallel alpha  helices (alpha4 and alpha5), 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.

-Consensus pattern: [LIVMA]-x-[GT]-x-[TA]-[DAN]-x(2,3)-[DG]-[GSTPNKQ]-x(2)-
                    [LFYDEPAVI]-[NQS]-x(2)-[LI]-[SG]-[QEA]-[KRQENAD]-R-A-x(2)-
                    [LVAIT]-x(3)-[LIVMF]-x(4,5)-[LIVMF]-x(4)-[LIVM]-x(3)-
                    [SGW]-x-G
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for 4 sequences.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Expert(s) to contact by email:
           De Mot R.; Rene.DeMot@agr.kuleuven.ac.be

-Last update: June 2005 / Profile added and text revised.

[ 1] De Mot R., Proost P., van Damme J., Vanderleyden J.
     "Homology of the root adhesin of Pseudomonas fluorescens OE 28.3 with
     porin F of P. aeruginosa and P. syringae."
     Mol. Gen. Genet. 231:489-493(1992).
     PubMed=1538702
[ 2] Hardham J.M., Stamm L.V.
     "Identification and characterization of the Treponema pallidum tpn50
     gene, an ompA homolog."
     Infect. Immun. 62:1015-1025(1994).
     PubMed=8112835
[ 3] Grizot S., Buchanan S.K.
     "Structure of the OmpA-like domain of RmpM from Neisseria
     meningitidis."
     Mol. Microbiol. 51:1027-1037(2004).
     PubMed=14763978

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