Summary: Putative beta-barrel porin 2
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Porin (protein) Edit Wikipedia article
Porins are beta barrel proteins that cross a cellular membrane and act as a pore, through which molecules can diffuse. 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.
- 1 Structure
- 2 Cellular Roles
- 3 Diversity
- 4 Antibiotic Resistance
- 5 Discoverer
- 6 Porin superfamilies
- 7 See also
- 8 References
- 9 External links
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. 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. The majority of porins are monomers, however some dimeric porins have been discovered, as well as an octameric porin. 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. 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). 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:
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.
Porins are water-filled pores and channels found in the membranes of bacteria and eukaryotes. Porin-like channels have also been discovered in archaea. 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. 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. Additionally, porins can regulate permeability and prevent lysis by limiting the entry of detergents into the cell.
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. 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.
In gram-negative bacteria, the inner membrane is the major permeability barrier. The outer membrane is more permeable to hydrophilic substances, due to the presence of porins. 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.
Porins were first discovered in gram-negative bacteria, but gram-positive bacteria with both types of porins have been found. They exhibit similar transport functions but have a more limited variety of porins, compared to the distribution found in gram-negative bacteria. Gram-positive bacteria lack outer membranes, so these porin channels are instead bound to specific lipids within the cell walls.
Porins are also found in eukaryotes, specifically in the outer membranes of mitochondria and chloroplasts. 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. However, eukaryotic porins exhibit the same limited diversity as gram-positive porins, and also display a greater voltage-dependent role during metabolism.
Archaea also contain ion channels that have originated from general porins. 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.
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. Specific antibiotics have been designed to travel through porins in order to inhibit cellular processes.
However, due to selective pressure, bacteria can develop resistance through mutations in the porin gene. 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.
The discovery of porins has been attributed to Hiroshi Nikaido, nicknamed "the porinologist."
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.
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
- Porins at the US National Library of Medicine Medical Subject Headings (MeSH)
- 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.
- 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.
- Faller, M. (20 February 2004). "The Structure of a Mycobacterial Outer-Membrane Channel". Science. 303 (5661): 1189–1192. doi:10.1126/science.1094114.
- 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.
- Benz, ed. by Roland (2004). Bacterial and eukaryotic porins : structure, function, mechanism. Weinheim: Wiley-VCH. pp. 26–29. ISBN 9783527307753.
- 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.
- 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.
- 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.
- 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.
- 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.
- Klebba PE (December 2005). "The porinologist". J. Bacteriol. 187 (24): 8232–6. doi:10.1128/JB.187.24.8232-8236.2005. PMC . PMID 16321927.
- 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.
- 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.
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
|SCOOP:||DUF560 OMP_b-brl OmpA_membrane Porin_4|
|Similarity to PfamA using HHSearch:||DUF560 MtrB_PioB MtrB_PioB|
External database links
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
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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 89 members:Ail_Lom Alginate_exp Autotransporter Bac_surface_Ag BBP2 BBP2_2 BBP7 BCSC_C Campylo_MOMP Caps_assemb_Wzi Channel_Tsx Chlam_OMP CopB CymA DUF2219 DUF2490 DUF2715 DUF2860 DUF3078 DUF3138 DUF3187 DUF3373 DUF3573 DUF3575 DUF4421 DUF4595 DUF481 DUF5020 DUF560 Gcw_chp HP_OMP HP_OMP_2 HpuA IAT_beta KdgM LamB Legionella_OMP Lipoprot_C MDM10 MipA MOSP_C 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 PLA1 Pom Porin_1 Porin_10 Porin_2 Porin_3 Porin_4 Porin_5 Porin_6 Porin_7 Porin_8 Porin_O_P Porin_OmpG Porin_OmpG_1_2 Porin_OmpL1 PorP_SprF ShlB Surface_Ag_2 TbpB_B_D Toluene_X TonB_dep_Rec TraF_2 TSA UPF0164 Usher Usher_TcfC YadA_anchor YfaZ YjbH
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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
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 UniProtKB sequence database using the family HMM
- 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:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
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You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
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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.
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.
|Seed source:||COGs (COG5338)|
|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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
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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.