Summary: OmpA-like transmembrane domain
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OmpA-like transmembrane domain Edit Wikipedia article
|OmpA-like transmembrane domain|
OmpA-like transmembrane domain is an evolutionarily conserved domain of bacterial outer membrane proteins. This domain consists of an eight-stranded beta barrel. OmpA is the predominant cell surface antigen in enterobacteria found in about 100,000 copies per cell. 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.
- Pautsch A, Schulz GE (November 1998). "Structure of the outer membrane protein A transmembrane domain". Nat. Struct. Biol. 5 (11): 1013â€“7. doi:10.1038/2983. PMID 9808047.
- Smith SG, Mahon V, Lambert MA, Fagan RP (August 2007). "A molecular Swiss army knife: OmpA structure, function and expression". FEMS Microbiol. Lett. 273 (1): 1â€“11. doi:10.1111/j.1574-6968.2007.00778.x. PMID 17559395.
- Song T, Wai SN (July 2009). "A novel sRNA that modulates virulence and environmental fitness of Vibrio cholerae". RNA Biol 6 (3): 254â€“8. doi:10.4161/rna.6.3.8371. PMID 19411843.
|This membrane proteinâ€“related article is a stub. You can help Wikipedia by expanding it.|
OmpA-like transmembrane domain Provide feedback
The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel . This family includes some other distantly related outer membrane proteins with low scores.
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.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||cell outer membrane (GO:0009279)|
|integral component of membrane (GO:0016021)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.
The clan contains the following 59 members:Ail_Lom Autotransporter Bac_surface_Ag BBP2 BBP2_2 Campylo_MOMP Channel_Tsx CopB DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3575 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA MtrB_PioB Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL PagP Phenol_MetA_deg Porin_1 Porin_10 Porin_2 Porin_4 Porin_7 Porin_8 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 TcfC Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||13|
|Number in full:||4656|
|Average length of the domain:||172.30 aa|
|Average identity of full alignment:||63 %|
|Average coverage of the sequence by the domain:||50.22 %|
|HMM build commands:||
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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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 9 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 seqence.
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