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 membranes 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 solute 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 porins are evolutionarily related, and these porins are:
- E.Coli PhoE phosphoporin (Phosphate anion selective TC# 1.B.1.1.2), OmpC(TC# 1.B.1.1.3) OmpF(general porins of differing pore diameter TC# 1.B.1.1.1), NmpC (TC# 1.B.1.1.4 anion selective, transporting a variety of drugs and small neutral compounds)
- Bacteriophage PA.2 LC Porin(TC# 1.B.1.1.5) (not well characterized).
- Neisseria PorA(TC# 1.B.1.5.2), PorB(TC# 1.B.1.5.4)
Structure of Porins
Porins are composed of β-strands, which are, in general, linked together by beta turns on the periplasmic side of the outer membrane and long loops on the external side of the membrane. The β strand lie in an antiparallel fashion and form a cylindrical tube, called a β-barrel. The amino acid composition of the porin β-strands are unique in that polar and non-polar residues alternate along them. This means that the non-polar residues face outwards so as to interact with the non-polar lipid membrane, whereas the polar residues face inwards into the center of the β-barrel to form the aqueous channel. The phospholipids that comprise the outer membrane give it the same semi-permeable characteristics as the cytoplasmic membrane
The porin channel is partially blocked by a loop, called the eyelet, which projects into the cavity. In general, it is found between strands 5 and 6 of each barrel, and it defines the size of solute that can traverse the channel. It is lined almost exclusively with charged amino acyl residues arranged on opposite sides of the channel, creating a transversal electric field across the pore. The eyelet has a local surplus of negative charges from four glutamic acid and seven aspartic acid residues (in contrast to one histidine, two lysine and three arginine residues) is partially compensated for by two bound calcium atoms, and this asymmetric arrangement of molecules is thought to have an influence in the selection of molecules that can pass through the channel.
Three dimensional structural analyses show that there are many(at-least 48) other families which share sufficient sequence similarity to the General Bacterial Porin(GBP) family. are homologous in structure and function to General bacterial porin family. One such family is The Sugar Porin (SP) Family. (TC# 1.B.3) The SP family includes the well characterized maltoporin of E. coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 β-stranded β-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family(TC# 1.B.7)) which consist of 16 β-stranded β-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP (TC# 1.B.1) and RPP families(TC# 1.B.7), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
The Rhodobacter PorCa Protein, the only well characterized member of the RPP family, was the first porin to yield its three-dimensional structure by X-ray crystallography. It has a 16-stranded β-barrel structure similar to that of the members of the GBP (TC #1.B.1) family. Paupit et al. (1991) presented crystal structures of phosphoporin (PhoE; TC# 1.B.1.1.2), maltoporin (LamB; TC# 1.B.3.1.1) and Matrixporin (OmpF), all of E. coli, and found these have 3-d folds similar to that of the Rhodobacter porin, PorCa. Structural and sequence analysis provide firm evidence that the GBP, SP and RPP families together with 44 additional families in TCDB belong to a single superfamily. However, we have been able to demonstrate homology between members of families GBP and RPP using statistical means (M. Saier, unpublished results).
General bacterial porin family belongs to Porin Superfamily I. The homologous families Sugar Porin(SP) family and Rhodobacter PorCa Porin (RPP) Family also belong to the Porin Superfamily I.
- 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.
- Van Gelder P, Saint N, van Boxtel R, Rosenbusch JP, Tommassen J. (1997). "Pore functioning of outer membrane protein PhoE of Escherichia col". Protein Eng. 10 (6): 699–706. doi:10.1093/protein/10.6.6. PMID 9278284.
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Gram-negative porin Provide feedback
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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.
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||porin activity (GO:0015288)|
|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 63 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 Lipoprot_C MDM10 MipA MSP 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_3 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
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Curation and family details
|Number in seed:||11|
|Number in full:||220|
|Average length of the domain:||323.50 aa|
|Average identity of full alignment:||42 %|
|Average coverage of the sequence by the domain:||91.91 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
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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 Porin_1 domain has been found. There are 134 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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