Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 473  species 0  interactions 596  sequences 9  architectures

Family: BBP2_2 (PF10082)

Summary: Putative beta-barrel porin 2

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Porin (protein)". More...

Porin (protein) Edit Wikipedia article

A single monomer of the same protein in side view, illustrating the antiparallel beta barrel structure.
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

Porins are beta barrel proteins that cross a cellular membrane and act as a pore, through which molecules can diffuse.[1] Unlike other membrane transport proteins, porins are large enough to allow passive diffusion, i.e., they act as channels that are specific to different types of molecules. They are present in the outer membrane of gram-negative bacteria and some gram-positive bacteria of the group Mycolata (mycolic acid-containing actinomycetes), the mitochondria, and the chloroplast.

Structure

Porins are composed of β strands, which are linked together by beta turns on the cytoplasmic side and long loops of amino acids on the other. The β strands 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 nonpolar residues alternate along them. This means that the nonpolar residues face outward so as to interact with the nonpolar lipids of outer membrane, whereas the polar residues face inwards into the center of the beta barrel to create the aqueous channel. The specific amino acids in the channel determine the specificity of the porin to different molecules.

The β barrels that make up a porin are composed of as few as eight β strands to as many as twenty-two β strands. The individual strands are joined together by loops and turns.[3] The majority of porins are monomers, however some dimeric porins have been discovered, as well as an octameric porin.[4] Depending on the size of the porin, the interior of the protein may either be filled with water, have up to two β strands folded back into the interior, or contain a "stopper" segment composed of β strands.

All porins form homotrimers in the outer membrane, meaning that three identical porin subunits associate together to form a porin super-structure with three channels.[5] Hydrogen bonding and dipole-dipole interactions between each monomer in the homotrimer ensure that they do not dissociate, and remain together in the outer membrane.

Several parameters have been used to describe the structure of a porin protein. They include the tilting angle (α), shear number (S), strand number (n), and barrel radius (R).[6] The tilting angle refers to the angle relative to the membrane. The shear number (S) is the number of amino acid residues found in each β strands. Strand number (n) is the amount of β strands in the porin, and barrel radius (R) refers to the radius of the opening of the porin. These parameters are related via the following formulas:

and,

Using these formulas, the structure of a porin can be determined by knowing only a few of the available parameters. While the structure of many porins have been determined using X-ray crystallography, the alternative method of sequencing protein primary structure may also be used instead.

Cellular Roles

Porins are water-filled pores and channels found in the membranes of bacteria and eukaryotes. Porin-like channels have also been discovered in archaea.[7] Note that the term "nucleoporin" refers to unrelated proteins that facilitate transport through nuclear pores in the nuclear envelope.

Porins are primarily involved in passively transporting hydrophilic molecules of various sizes and charges across the membrane.[8] For survival, certain required nutrients and substrates must be transported into the cells. Likewise, toxins and wastes must be transported out to avoid toxic accumulation.[9] Additionally, porins can regulate permeability and prevent lysis by limiting the entry of detergents into the cell.[8]

Two types of porins exist to transport different materials– general and selective. General porins have no substrate specificities, though some exhibit slight preferences for anions or cations.[8] Selective porins are smaller than general porins, and have specificities for chemical species. These specificities are determined by the threshold sizes of the porins, and the amino acid residues lining them.[10]

In gram-negative bacteria, the inner membrane is the major permeability barrier.[11] The outer membrane is more permeable to hydrophilic substances, due to the presence of porins.[10] Porins have threshold sizes of transportable molecules that depend on the type of bacteria and porin. Generally, only substances less than 600 Daltons in size can diffuse through.[8]

Diversity

Porins were first discovered in gram-negative bacteria, but gram-positive bacteria with both types of porins have been found.[9] They exhibit similar transport functions but have a more limited variety of porins, compared to the distribution found in gram-negative bacteria.[9] Gram-positive bacteria lack outer membranes, so these porin channels are instead bound to specific lipids within the cell walls.[7]

Porins are also found in eukaryotes, specifically in the outer membranes of mitochondria and chloroplasts.[9][11] The organelles contain general porins that are structurally and functionally similar to bacterial ones. These similarities have supported the Endosymbiotic theory, through which eukaryotic organelles arose from gram-negative bacteria.[11] However, eukaryotic porins exhibit the same limited diversity as gram-positive porins, and also display a greater voltage-dependent role during metabolism.[9][11]

Archaea also contain ion channels that have originated from general porins.[7] The channels are found in the cell envelope and help facilitate solute transfer. They have similar characteristics as bacterial and mitochondrial porins, indicating physiological overlaps over all three domains of life.[7]

Antibiotic Resistance

Many porins are targets for host immune cells, resulting in signaling pathways that lead to bacterial degradation. Therapeutic treatments, like vaccinations and antibiotics, are used to supplement this immune response.[10] Specific antibiotics have been designed to travel through porins in order to inhibit cellular processes.[8]

However, due to selective pressure, bacteria can develop resistance through mutations in the porin gene.[10] The mutations may lead to a loss of porins, resulting in the antibiotics having a lower permeability or being completely excluded from transport. These changes have contributed to the global emergence of antibiotic resistance, and an increase in mortality rates from infections.[10]

Discoverer

The discovery of porins has been attributed to Hiroshi Nikaido, nicknamed "the porinologist."[12]

Porin superfamilies

There are five evolutionarily independent superfamilies of porins. Porin superfamily I includes 47 families of porins with a range of numbers of trans-membrane β-strands (β-TMS). These include the GBP, SP and RPP porin families. While PSF I includes 47 families, PSF II-V each contain only 2 families. While PSF I derives members from gram-negative bacteria primarily one family of eukaryotic mitochondrial porins, PSF II and V porins are derived from Actinobacteria. PSF III and V are derived from eukaryotic organelle. See TCDB for more details.[13][14]

Porin Superfamily I

1.B.1 - The General Bacterial Porin (GBP) Family
1.B.2 - The Chlamydial Porin (CP) Family
1.B.3 - The Sugar Porin (SP) Family
1.B.4 - The Brucella-Rhizobium Porin (BRP) Family
1.B.5 - The Pseudomonas OprP Porin (POP) Family
1.B.6 - The OmpA-OmpF Porin (OOP) Family
1.B.7 - The Rhodobacter PorCa Porin (RPP) Family
1.B.8 - The Mitochondrial and Plastid Porin (MPP) Family
1.B.9 - The FadL Outer Membrane Protein (FadL) Family
1.B.10 - The Nucleoside-specific Channel-forming Outer Membrane Porin (Tsx) Family
1.B.11 - The Outer Membrane Fimbrial Usher Porin (FUP) Family
1.B.12 - The Autotransporter-1 (AT-1) Family
1.B.13 - The Alginate Export Porin (AEP) Family
1.B.14 - The Outer Membrane Receptor (OMR) Family
1.B.15 - The Raffinose Porin (RafY) Family
1.B.16 - The Short Chain Amide and Urea Porin (SAP) Family
1.B.17 - The Outer Membrane Factor (OMF) Family
1.B.18 - The Outer Membrane Auxiliary (OMA) Protein Family
1.B.19 - The Glucose-selective OprB Porin (OprB) Family
1.B.20 - The Two-Partner Secretion (TPS) Family
1.B.21 - The OmpG Porin (OmpG) Family
1.B.22 - The Outer Bacterial Membrane Secretin (Secretin) Family
1.B.23 - The Cyanobacterial Porin (CBP) Family
1.B.25 - The Outer Membrane Porin (Opr) Family
1.B.26 - The Cyclodextrin Porin (CDP) Family
1.B.31 - The Campylobacter jejuni Major Outer Membrane Porin (MomP) Family
1.B.32 - The Fusobacterial Outer Membrane Porin (FomP) Family
1.B.33 - The Outer Membrane Protein Insertion Porin (Bam Complex) (OmpIP) Family
1.B.35 - The Oligogalacturonate-specific Porin (KdgM) Family
1.B.39 - The Bacterial Porin, OmpW (OmpW) Family
1.B.42 - The Outer Membrane Lipopolysaccharide Export Porin (LPS-EP) Family
1.B.43 - The Coxiella Porin P1 (CPP1) Family
1.B.44 - The Probable Protein Translocating Porphyromonas gingivalis Porin (PorT) Family
1.B.49 - The Anaplasma P44 (A-P44) Porin Family
1.B.54 - The Intimin/Invasin (Int/Inv) or Autotransporter-3 (AT-3) Family
1.B.55 - The Poly Acetyl Glucosamine Porin (PgaA) Family
1.B.57 - The Legionella Major-Outer Membrane Protein (LM-OMP) Family
1.B.60 - The Omp50 Porin (Omp50 Porin) Family
1.B.61 - The Delta-Proteobacterial Porin (Delta-Porin) Family
1.B.62 - The Putative Bacterial Porin (PBP) Family
1.B.66 - The Putative Beta-Barrel Porin-2 (BBP2) Family
1.B.67 - The Putative Beta Barrel Porin-4 (BBP4) Family
1.B.68 - The Putative Beta Barrel Porin-5 (BBP5) Superfamily
1.B.70 - The Outer Membrane Channel (OMC) Family
1.B.71 - The Proteobacterial/Verrucomicrobial Porin (PVP) Family
1.B.72 - The Protochlamydial Outer Membrane Porin (PomS/T) Family
1.B.73 - The Capsule Biogenesis/Assembly (CBA) Family
1.B.78 - The DUF3374 Electron Transport-associated Porin (ETPorin) Family

Porin Superfamily II (MspA Superfamily)

1.B.24 - The Mycobacterial Porin (MBP) Family
1.B.58 - Nocardial Hetero-oligomeric Cell Wall Channel (NfpA/B) Family

Porin Superfamily III

1.B.28 - The Plastid Outer Envelope Porin of 24 kDa (OEP24) Family
1.B.47 - The Plastid Outer Envelope Porin of 37 kDa (OEP37) Family

Porin Superfamily IV (Tim17/OEP16/PxMPL (TOP) Superfamily)

This superfamily includes protein that comprise pores in multicomponent protein translocases as follows: 3.A.8 - [Tim17 (P39515) Tim22 (Q12328) Tim23 (P32897)]; 1.B.69 - [PXMP4 (Q9Y6I8) PMP24 (A2R8R0)]; 3.D.9 - [NDH 21.3 kDa component (P25710)]

1.B.30 - The Plastid Outer Envelope Porin of 16 kDa (OEP16) Family
1.B.69 - The Peroxysomal Membrane Porin 4 (PxMP4) Family
3.A.8 - The Mitochondrial Protein Translocase (MPT) Family

Porin Superfamily V (Corynebacterial PorA/PorH Superfamily)

1.B.34 - The Corynebacterial Porin A (PorA) Family 1.B.59 - The Outer Membrane Porin, PorH (PorH) Family

See also

References

  1. ^ Porins at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. ^ Schirmer T (1998). "General and specific porins from bacterial outer membranes". J. Struct. Biol. 121 (2): 101–9. doi:10.1006/jsbi.1997.3946. PMID 9615433. 
  3. ^ Tamm, Lukas K.; Hong, Heedeok; Liang, Binyong (November 2004). "Folding and assembly of β-barrel membrane proteins". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1666 (1-2): 250–263. doi:10.1016/j.bbamem.2004.06.011. 
  4. ^ Faller, M. (20 February 2004). "The Structure of a Mycobacterial Outer-Membrane Channel". Science. 303 (5661): 1189–1192. doi:10.1126/science.1094114. 
  5. ^ Galdiero, Stefania; Falanga, Annarita; Cantisani, Marco; Tarallo, Rossella; Elena Della Pepa, Maria; D'Oriano, Virginia; Galdiero, Massimiliano (1 December 2012). "Microbe-Host Interactions: Structure and Role of Gram-Negative Bacterial Porins". Current Protein and Peptide Science. 13 (8): 843–854. doi:10.2174/138920312804871120. 
  6. ^ Benz, ed. by Roland (2004). Bacterial and eukaryotic porins : structure, function, mechanism. Weinheim: Wiley-VCH. pp. 26–29. ISBN 9783527307753. 
  7. ^ a b c d Besnard M, Martinac B, Ghazi A (1997). "Voltage-dependent Porin-like Ion Channels in the Archaeon Haloferax volcanii". Journal of Biological Chemistry. 2 (272): 992–995. doi:10.1074/jbc.272.2.992. PMID 8995393. 
  8. ^ a b c d e Novikova OD, Solovyeva TF (2009). "Nonspecific Porins of the Outer Membrane of Gram-Negative Bacteria: Structure and Functions". Biologicheskie Membrany. 3 (1): 3–15. doi:10.1134/S1990747809010024. 
  9. ^ a b c d e Yen MR, Peabody CR, Partovi SM, Zhai Y, Tseng YH, Saier Jr MH (2002). "Protein-translocating outer membrane porins of Gram-negative bacteria". BBA − Biomembranes. 1562 (1-2): 6–31. 
  10. ^ a b c d e Galdiero S, Falanga A, Cantisani M, Tarallo R, Della Pepa ME, D’Oriano V, Galdiero M (2012). "Microbe-Host Interactions: Structure and Role of Gram-Negative Bacterial Porins". Curr Protein Pept Sci. 8 (13): 843–854. 
  11. ^ a b c d Benz R (1989). "Porins from Mitochondrial and Bacterial Outer Membranes: Structural and Functional Aspects". Anion Carriers of Mitochondrial Membranes: 199–214. doi:10.1007/978-3-642-74539-3_16. 
  12. ^ Klebba PE (December 2005). "The porinologist". J. Bacteriol. 187 (24): 8232–6. doi:10.1128/JB.187.24.8232-8236.2005. PMC 1317029Freely accessible. PMID 16321927. 
  13. ^ Niederweis, Michael (2003-09-01). "Mycobacterial porins--new channel proteins in unique outer membranes". Molecular Microbiology. 49 (5): 1167–1177. doi:10.1046/j.1365-2958.2003.03662.x. ISSN 0950-382X. PMID 12940978. 
  14. ^ Rath, Parthasarathi; Saurel, Olivier; Tropis, Maryelle; Daffé, Mamadou; Demange, Pascal; Milon, Alain (2013-11-15). "NMR localization of the O-mycoloylation on PorH, a channel forming peptide from Corynebacterium glutamicum". FEBS Letters. 587 (22): 3687–3691. doi:10.1016/j.febslet.2013.09.032. ISSN 1873-3468. PMID 24100136. 

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Putative beta-barrel porin 2 Provide feedback

This domain is a putative beta-barrel porin type 2.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018759

This entry represents a putative beta-barrel porin type 2.

Domain organisation

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

Loading domain graphics...

Alignments

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(39)
Full
(596)
Representative proteomes UniProt
(1513)
NCBI
(3286)
Meta
(42)
RP15
(119)
RP35
(353)
RP55
(623)
RP75
(960)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(39)
Full
(596)
Representative proteomes UniProt
(1513)
NCBI
(3286)
Meta
(42)
RP15
(119)
RP35
(353)
RP55
(623)
RP75
(960)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(39)
Full
(596)
Representative proteomes UniProt
(1513)
NCBI
(3286)
Meta
(42)
RP15
(119)
RP35
(353)
RP55
(623)
RP75
(960)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

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.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: COGs (COG5338)
Previous IDs: DUF2320;
Type: Family
Author: COGs, Finn RD, Sammut SJ
Number in seed: 39
Number in full: 596
Average length of the domain: 299.40 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 68.38 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.7 23.7
Trusted cut-off 23.7 23.7
Noise cut-off 23.6 23.5
Model length: 379
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.