Summary: Gram-negative porin
This is the Wikipedia entry entitled "General bacterial porin family". More...
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General bacterial porin family Edit Wikipedia article
General bacterial porins are a family of proteins from the outer membrane of Gram-negative bacteria. The porins act as molecular filters for hydrophilic compounds. They are responsible for the 'molecular sieve' properties of the outer membrane. Porins form large water-filled channels which allow the diffusion of hydrophilic molecules into the periplasmic space. Some porins form general diffusion channels that allow any solutes up to a certain size (that size is known as the exclusion limit) to cross the membrane, while other porins are specific for one particular solute and contain a binding site for that solute inside the pores (these are known as selective porins). As porins are the major outer membrane proteins, they also serve as receptor sites for the binding of phages and bacteriocins.
General diffusion porins usually assemble as a trimer in the membrane and the transmembrane core of these proteins is composed exclusively of beta strands. It has been shown that a number of general porins are evolutionarily related, and these porins are:
- Enterobacteria PhoE, OmpC, OmpF, NmpC.
- Bacteriophage PA-2 LC.
- Neisseria PI.A, PI.B
- Benz R, Bauer K (1988). "Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria. Review on bacterial porins". Eur. J. Biochem. 176 (1): 1–19. doi:10.1111/j.1432-1033.1988.tb14245.x. PMID 2901351.
- Jap BK, Walian PJ (1990). "Biophysics of the structure and function of porins". Q. Rev. Biophys. 23 (4): 367–403. doi:10.1017/S003358350000559X. PMID 2178269.
- Pattus F, Jeanteur D, Lakey JH (1991). "The bacterial porin superfamily: sequence alignment and structure prediction". Mol. Microbiol. 5 (9): 2153–2164. doi:10.1111/j.1365-2958.1991.tb02145.x. PMID 1662760.
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Internal database links
|Similarity to PfamA using HHSearch:||Porin_4|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001702
Porins are found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts, where they form ion-selective channels for small hydrophilic molecules (up to ~600 D) [PUBMED:2178269, PUBMED:1373213]. X-ray structure analyses of several bacterial porins [PUBMED:1707373, PUBMED:1725488, PUBMED:7525973] have revealed a large 16-stranded anti-parallel beta-barrel structure enclosing the transmembrane pore, by contrast with all other integral membrane proteins described to date, which are alpha-helical. Three subunits form a trimer; the 3-fold axis is approximately parallel to the barrel axes and is assumed to be perpendicular to the membrane plane [PUBMED:].
From the range of porins now known, similarities have been observed between porins from different species, and between porins of different specificity within the same species. But most porins cannot be related to each other on the basis of sequence alone, and this is reflected in the lengths of the known porin sequences, which range from 282-483 residues/monomer.This entry represents porins from Gram-negative bacteria.
|Cellular component||membrane (GO:0016020)|
|Molecular function||transporter activity (GO:0005215)|
|Biological process||transport (GO:0006810)|
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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 54 members:Ail_Lom Autotransporter Bac_surface_Ag Campylo_MOMP Channel_Tsx CopB DUF1302 DUF1597 DUF2320 DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3374 DUF3575 DUF4289 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL Phenol_MetA_deg Porin_1 Porin_2 Porin_4 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ
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Curation and family details
|Number in seed:||18|
|Number in full:||5868|
|Average length of the domain:||301.00 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||93.43 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
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We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Porin_1 domain has been found. There are 89 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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