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146  structures 113  species 6  interactions 296  sequences 1  architecture

Family: Porin_1 (PF00267)

Summary: Gram-negative porin

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This is the Wikipedia entry entitled "General bacterial porin family". More...

General bacterial porin family Edit Wikipedia article

Gram-negative porin
1pho opm.png
Identifiers
Symbol Porin_1
Pfam PF00267
Pfam clan CL0193
InterPro IPR001702
PROSITE PDOC00498
SCOP 1mpf
SUPERFAMILY 1mpf
TCDB 1.B.1
OPM superfamily 31
OPM protein 1pho
CDD cd01345

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.[1] 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.[2] It has been shown[3] that a number of porins are evolutionarily related, and these porins are:

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[2]. 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[4]

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[3].

Homologous Families

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).

Porin Superfamilies

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.

Subfamilies

References

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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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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.

Gene Ontology

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Domain organisation

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Alignments

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(11)
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(8058)
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(25518)
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(194)
RP15
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RP35
(105)
RP55
(367)
RP75
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(11)
Full
(296)
Representative proteomes UniProt
(8058)
NCBI
(25518)
Meta
(194)
RP15
(19)
RP35
(105)
RP55
(367)
RP75
(1297)
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  Seed
(11)
Full
(296)
Representative proteomes UniProt
(8058)
NCBI
(25518)
Meta
(194)
RP15
(19)
RP35
(105)
RP55
(367)
RP75
(1297)
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Seed source: Prosite
Previous IDs: Gram-ve_porins;
Type: Domain
Author: Finn RD
Number in seed: 11
Number in full: 296
Average length of the domain: 323.10 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 91.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.7 23.7
Trusted cut-off 23.8 23.7
Noise cut-off 23.6 23.6
Model length: 341
Family (HMM) version: 19
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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

Selections

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Interactions

There are 6 interactions for this family. More...

PDZ PDZ Transferrin Porin_1 Transferrin Cloacin

Structures

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 146 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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