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11  structures 474  species 0  interactions 704  sequences 37  architectures

Family: OmpA_membrane (PF01389)

Summary: OmpA-like transmembrane domain

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This is the Wikipedia entry entitled "OmpA-like transmembrane domain". More...

OmpA-like transmembrane domain Edit Wikipedia article

OmpA-like transmembrane domain
1qjp opm.png
Pfam clanCL0193
OPM superfamily26
OPM protein1qjp

OmpA-like transmembrane domain is an evolutionarily conserved domain of bacterial outer membrane proteins. This domain consists of an eight-stranded beta barrel.[1] OmpA is the predominant cell surface antigen in enterobacteria found in about 100,000 copies per cell.[2] The expression of OmpA is tightly regulated by a variety of mechanisms. One mechanism by which OmpA expression is regulated in Vibrio species is by an antisense non-coding RNA called VrrA.[3]


The structure consists of an eight-stranded Up-And-Down Beta-Barrel. The strands are connected by four extracellular loops and three intracellular turns.[4]


Numerous OmpA-like membrane-spanning domains contribute to bacterial virulence by a variety of mechanisms such as binding to host cells or immune regulators such as Factor H. Notable examples include E. coli OmpA and Yersinia pestis Ail. Several of these proteins are vaccine candidates.

E. coli OmpA was shown to make specific interactions with the human glycoprotein Ecgp on brain microvascular endothelial cells.[5] Cronobacter sakazakii is a food borne pathogen causing meningitis in neonates and was shown to bind fibronectin via OmpA and this played a significant role in invasion of the blood brain barrier.[6] The Y. pestis protein Ail binds to laminin and heparin, therefore allowing bacterial attachment to host cells.[7] The Borrelia afzelii protein BAPKO_0422, is an OmpA-like transmembrane domain and binds to human Factor H.[8]

See also


  1. ^ Pautsch A, Schulz GE (Nov 1998). "Structure of the outer membrane protein A transmembrane domain". Nature Structural Biology. 5 (11): 1013–7. doi:10.1038/2983. PMID 9808047.
  2. ^ Smith SG, Mahon V, Lambert MA, Fagan RP (Aug 2007). "A molecular Swiss army knife: OmpA structure, function and expression". FEMS Microbiology Letters. 273 (1): 1–11. doi:10.1111/j.1574-6968.2007.00778.x. PMID 17559395.
  3. ^ Song T, Wai SN (July 2009). "A novel sRNA that modulates virulence and environmental fitness of Vibrio cholerae". RNA Biology. 6 (3): 254–8. doi:10.4161/rna.6.3.8371. PMID 19411843.
  4. ^ Fernández C, Hilty C, Wider G, Güntert P, Wüthrich K (Mar 2004). "NMR structure of the integral membrane protein OmpX". Journal of Molecular Biology. 336 (5): 1211–21. doi:10.1016/j.jmb.2003.09.014. PMID 15037080.
  5. ^ Prasadarao NV, Srivastava PK, Rudrabhatla RS, Kim KS, Huang SH, Sukumaran SK (Apr 2003). "Cloning and expression of the Escherichia coli K1 outer membrane protein A receptor, a gp96 homologue". Infection and Immunity. 71 (4): 1680–8. doi:10.1128/IAI.71.4.1680-1688.2003. PMC 152083. PMID 12654781.
  6. ^ Nair MK, Venkitanarayanan K, Silbart LK, Kim KS (May 2009). "Outer membrane protein A (OmpA) of Cronobacter sakazakii binds fibronectin and contributes to invasion of human brain microvascular endothelial cells". Foodborne Pathogens and Disease. 6 (4): 495–501. doi:10.1089/fpd.2008.0228. PMID 19415974.
  7. ^ Yamashita S, Lukacik P, Barnard TJ, Noinaj N, Felek S, Tsang TM, Krukonis ES, Hinnebusch BJ, Buchanan SK (Nov 2011). "Structural insights into Ail-mediated adhesion in Yersinia pestis". Structure. 19 (11): 1672–82. doi:10.1016/j.str.2011.08.010. PMC 3217190. PMID 22078566.
  8. ^ Dyer A, Brown G, Stejskal L, Laity PR, Bingham RJ (2015). "The Borrelia afzelii outer membrane protein BAPKO_0422 binds human factor-H and is predicted to form a membrane-spanning β-barrel". Bioscience Reports. 35 (4): e00240. doi:10.1042/BSR20150095. PMC 4613713. PMID 26181365.

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OmpA-like transmembrane domain Provide feedback

The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel [1]. This family includes some other distantly related outer membrane proteins with low scores.

Literature references

  1. Pautsch A, Schulz GE; , Nat Struct Biol 1998;5:1013-1017.: Structure of the outer membrane protein A transmembrane domain. PUBMED:9808047 EPMC:9808047

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000498

The ompA-like transmembrane domain is present in a number of different outer membrane proteins of several Gram-negative bacteria. Many of the proteins having this domain in the N-terminal also have the conserved bacterial outer membrane protein domain INTERPRO at the C terminus. The outer membrane protein A of Escherichia coli (OmpA), is one of the most studied proteins in this group [ PUBMED:10554771 ]. It has a multifunctional role. OmpA is required for the action of colicins K and L and for the stabilisation of mating aggregates in conjugation. It also serves as a receptor for a number of T-even like phages and can act as a porin with low permeability that allows slow penetration of small solutes [ PUBMED:1974149 ].

OmpA consists of a regular, extended eight-stranded beta-barrel and appears to be constructed like an inverse micelle with large water-filled cavities, but does not form a pore. The cavities seem to be highly conserved during evolution. The structure corroborates the concept that all outer membrane proteins consist of beta-barrels [ PUBMED:9808047 ]. The beta-barrel membrane anchor appears to be the outer membrane equivalent of the single-chain alpha-helix anchor of the inner membrane.

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 13
Number in full: 704
Average length of the domain: 174.00 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 40.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.1 20.1
Model length: 183
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the OmpA_membrane domain has been found. There are 11 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
P0A910 View 3D Structure Click here