Summary: Eukaryotic porin
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Voltage-dependent anion channel Edit Wikipedia article
Crystal Structure of the Human Voltage-Dependent Anion Channel. The arrows denote the antiparallel beta sheets that form the characteristic beta-barrel
Voltage-dependent anion channels, or mitochondrial porins, are a class of porin ion channel located on the outer mitochondrial membrane. There is debate as to whether or not this channel is expressed in the cell surface membrane.
This major protein of the outer mitochondrial membrane of eukaryotes forms a voltage-dependent anion-selective channel (VDAC) that behaves as a general diffusion pore for small hydrophilic molecules. The channel adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30â€“40 mV. VDAC facilitates the exchange of ions and molecules between mitochondria and cytosol and is regulated by the interactions with other proteins and small molecules.
Since its discovery in 1976, extensive function and structure analysis of VDAC proteins has been conducted. A prominent feature of the pore emerged: when reconstituted into planar lipid bilayers, there is a voltage-dependent switch between an anion-selective high-conductance state with high metabolite flux and a cation-selective low-conductance state with limited passage of metabolites.
More than 30 years after its initial discovery, in 2008, three independent structural projects of VDAC-1 were completed. The first was solved by multi-dimensional NMR spectroscopy. The second applied a hybrid approach using crystallographic data. The third was for mouse VDAC-1 crystals determined by X-ray crystallographic techniques. The three projects of the 3D structures of VDAC-1 revealed many structural features. First, VDAC-1 represents a new structural class of outer membrane Î²-barrel proteins with an odd number of strands. Another aspect is that the negatively charged side chain of residue E73 is oriented towards the hydrophobic membrane environment. The 19-stranded 3D structure obtained under different experimental sources by three different laboratories fits the EM and AFM data from native membrane sources and represents a biologically relevant state of VDAC-1.
At membrane potentials exceeding 30 mV (positive or negative), VDAC assumes a closed state, and transitions to its open state once the voltage drops below this threshold. Although both states allow passage of simple salts, VDAC is much more stringent with organic anions, a category into which most metabolites fall. The precise mechanism for coupling voltage changes to conformational changes within the protein has not yet been worked out, but studies by Thomas et al. suggest that when the protein transitions to the closed form, voltage changes lead to the removal of a large section of the protein from the channel and decrease effective pore radius. Several lysine residues, as well as Glu-152, have been implicated as especially important sensor residues within the protein.
The voltage-dependent ion channel plays a key role in regulating metabolic and energetic flux across the outer mitochondrial membrane. It is involved in the transport of ATP, ADP, pyruvate, malate, and other metabolites, and thus communicates extensively with enzymes from metabolic pathways. The ATP-dependent cytosolic enzymes hexokinase, glucokinase, and glycerol kinase, as well as the mitochondrial enzyme creatine kinase, have all been found to bind to VDAC. This binding puts them in close proximity to ATP released from the mitochondria. In particular, the binding of hexokinase is presumed to play a key role in coupling glycolysis to oxidative phosphorylation. Additionally, VDAC is an important regulator of Ca2+ transport in and out of the mitochondria. Because Ca2+ is a cofactor for metabolic enzymes such as pyruvate dehydrogenase and isocitrate dehydrogenase, energetic production and homeostasis are both affected by VDACâ€™s permeability to Ca2+.
VDAC has also been shown to play a role in apoptosis. During apoptosis, increased permeability of VDAC allows for the release of apoptogenic factors such as cytochrome c. Although cyt. c plays an essential role in oxidative phosphorylation within the mitochondrion, in the cytosol it activates proteolytic enzymes called caspases, which play a major role in cell death. Although the mechanism for VDAC-facilitated cyt. c release has not yet been fully elucidated, some research suggests that oligomerization between individual subunits may create a large flexible pore through which cyt. c can pass. A more important factor is that release of cyt c. is also regulated by the Bcl-2 protein family: Bax interacts directly with VDAC to increase pore size and promote cyt. c release, while anti-apoptotic Bcl-xL produces the exact opposite effect. In fact, it has been shown that antibodies that inhibit VDAC also interfere with Bax-mediated cyt. c release in both isolated mitochondria and whole cells. This key role in apoptosis suggests VDAC as a potential target for chemotherapeutic drugs.
Yeast contains two members of this family (genes POR1 and POR2); vertebrates have at least three members (genes VDAC1, VDAC2 and VDAC3).
Plants have the largest number of VDACs. Arabidopsis encode four different VDACs but this number can be larger in other species.
- Hoogenboom BW, Suda K, Engel A, Fotiadis D (2007). "The supramolecular assemblies of voltage-dependent anion channels in the native membrane". J. Mol. Biol. 370 (2): 246â€“55. doi:10.1016/j.jmb.2007.04.073. PMID 17524423.
- Blachly-Dyson, E; Forte, M (September 2001). "VDAC channels". IUBMB Life. 52 (3â€“5): 113â€“8. doi:10.1080/15216540152845902. PMID 11798022.
- Sabirov RZ, Merzlyak PG (June 2012). "Plasmalemmal VDAC controversies and maxi-anion channel puzzle". Biochim. Biophys. Acta. 1818 (6): 1570â€“80. doi:10.1016/j.bbamem.2011.09.024. PMID 21986486.
- De Pinto, V.; Messina, A.; Lane, D. J. R.; Lawen, A. (2010). "Voltage-dependent anion-selective channel (VDAC) in the plasma membrane". FEBS Letters. 584 (9): 1793â€“1799. doi:10.1016/j.febslet.2010.02.049. PMID 20184885.
- Niehage, C.; Steenblock, C.; Pursche, T.; BornhÃ¤user, M.; Corbeil, D.; Hoflack, B. (2011). Borlongan, Cesario V (ed.). "The Cell Surface Proteome of Human Mesenchymal Stromal Cells". PLoS ONE. 6 (5): e20399. Bibcode:2011PLoSO...620399N. doi:10.1371/journal.pone.0020399. PMC 3102717. PMID 21637820.
- Benz R (1994). "Permeation of hydrophilic solutes through mitochondrial outer membranes: review on mitochondrial porins". Biochim. Biophys. Acta. 1197 (2): 167â€“196. doi:10.1016/0304-4157(94)90004-3. PMID 8031826.
- Mannella CA (1992). "The 'ins' and 'outs' of mitochondrial membrane channels". Trends Biochem. Sci. 17 (8): 315â€“320. doi:10.1016/0968-0004(92)90444-E. PMID 1384178.
- Dihanich M (1990). "The biogenesis and function of eukaryotic porins". Experientia. 46 (2): 146â€“153. doi:10.1007/BF02027310. PMID 1689252.
- Forte M, Guy HR, Mannella CA (1987). "Molecular genetics of the VDAC ion channel: structural model and sequence analysis" (PDF). J. Bioenerg. Biomembr. 19 (4): 341â€“350. doi:10.1007/BF00768537. PMID 2442148.
- Hiller S, Abramson J, Mannella C, Wagner G, Zeth K (September 2010). "The 3D structures of VDAC represent a native conformation". Trends Biochem. Sci. 35 (9): 514â€“21. doi:10.1016/j.tibs.2010.03.005. PMC 2933295. PMID 20708406.
- Sampson MJ, Lovell RS, Davison DB, Craigen WJ (1996). "A novel mouse mitochondrial voltage-dependent anion channel gene localizes to chromosome 8". Genomics. 36 (1): 192â€“196. doi:10.1006/geno.1996.0445. PMID 8812436.
- Zeth K (2010). "Structure and evolution of mitochondrial outer membrane proteins of beta-barrel topology". Biochim. Biophys. Acta. 1797 (6â€“7): 1292â€“9. doi:10.1016/j.bbabio.2010.04.019. PMID 20450883.
- Blachly-Dyson, E. & Forte, M. (2001). "VDAC Channels". IUBMB Life. 52 (3â€“5): 113â€“18. doi:10.1080/15216540152845902. PMID 11798022.
- Colombini M, Blachly-Dyson E, Forte M (1996). "VDAC, a channel in the outer mitochondrial membrane". Ion Channels. 4: 169â€“202. PMID 8744209.
- Thomas L, Blachly-Dyson E, Colombini M, Forte M (June 1993). "Mapping of residues forming the voltage sensor of the voltage-dependent anion-selective channel". Proc. Natl. Acad. Sci. U.S.A. 90 (12): 5446â€“9. Bibcode:1993PNAS...90.5446T. doi:10.1073/pnas.90.12.5446. PMC 46737. PMID 7685903.
- Shoshan-Barmatz V; Gincel D. (2003). "The voltage-dependent anion channel: characterization, modulation, and role in mitochondrial function in cell life and death". Cell Biochem. Biophys. 39 (3): 279â€“92. doi:10.1385/CBB:39:3:279. PMID 14716081.
- Lemasters JJ; Holmuhamedov E. (2006). "Voltage-dependent anion channel (VDAC) as mitochondrial governator--thinking outside the box". Biochim. Biophys. Acta. 1762 (2): 181â€“90. doi:10.1016/j.bbadis.2005.10.006. PMID 16307870.
- Tsujimoto Y, Shimizu S (2002). "The voltage-dependent anion channel: an essential player in apoptosis". Biochimie. 84 (2â€“3): 187â€“93. doi:10.1016/S0300-9084(02)01370-6. PMID 12022949.
- Zalk R; Israelson A; Garty ES; Azoulay-Zohar H; Shoshan-Barmatz V. (2005). "Oligomeric states of the voltage-dependent anion channel and cytochrome c release from mitochondria". Biochem. J. 386 (1): 73â€“83. doi:10.1042/BJ20041356. PMC 1134768. PMID 15456403.
- Shimizu S; Narita M; Tsujimoto Y. (1999). "Bcl-2 family proteins regulate the release of apoptogenic cytochrome c by the mitochondrial channel VDAC". Nature. 399 (6735): 483â€“7. Bibcode:1999Natur.399..483S. doi:10.1038/20959. PMID 10365962.
- Shimizu S; Matsuoka Y; Shinohara Y; Yoneda Y; Tsujimoto Y. (2001). "Essential role of voltage-dependent anion channel in various forms of apoptosis in mammalian cells". J. Cell Biol. 152 (2): 237â€“50. doi:10.1083/jcb.152.2.237. PMC 2199613. PMID 11266442.
- Bay DC, Hafez M, Young MJ, Court DA (June 2012). "Phylogenetic and coevolutionary analysis of the Î²-barrel protein family comprised of mitochondrial porin (VDAC) and Tom40". Biochim. Biophys. Acta. 1818 (6): 1502â€“19. doi:10.1016/j.bbamem.2011.11.027. PMID 22178864.
- HomblÃ© F, Krammer E, Prevost M (June 2012). "Plant VDAC: facts and speculations". Biochim. Biophys. Acta. 1818 (6): 1486â€“501. doi:10.1016/j.bbamem.2011.11.028. PMID 22155681.
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.
Eukaryotic porin Provide feedback
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|Transporter classification:||1.B.8 3.A.8|
This tab holds annotation information from the InterPro database.
InterPro entry IPR027246
This entry represents both eukaryotic mitochondrial porins and Tom40 proteins.
Eukaryotic mitochondrial porins are voltage-dependent anion-selective channels (VDAC) that behave as general diffusion pores for small hydrophilic molecules [PUBMED:8031826, PUBMED:1384178, PUBMED:1689252, PUBMED:2442148]. The channels adopt an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The eukaryotic mitochondrial porins are beta-barrel proteins, composed of between 12 to 16 beta-strands that span the mitochondrial outer membrane. Yeast contains two members of this family (genes POR1 and POR2); vertebrates have at least three members (genes VDAC1, VDAC2 and VDAC3) [PUBMED:8812436]. They are related to the mitochondrial import receptor subunit Tom40 proteins, sharing a common evolutionary origin and structure [PUBMED:22178864].
Tom40 is a mitochondrion outer membrane protein and a component of the TOM (translocator of the outer mitochondrial membrane) complex, which is essential for import of protein precursors into mitochondria [PUBMED:10427088]. In Saccharomyces cerevisiae, TOM complex is composed of the subunits Tom70, Tom40, Tom22, Tom20, Tom7, Tom6, and Tom5 [PUBMED:1327874, PUBMED:9774667]. Tom40 is an integral membrane protein and the main structural component of the protein-conducting channel formed by the TOM complex [PUBMED:14595396]. It is stabilised by other components, such as Tom5, Tom6, and Tom7 [PUBMED:11866524].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||mitochondrial outer membrane (GO:0005741)|
|Biological process||transmembrane transport (GO:0055085)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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 92 members:Ail_Lom Alginate_exp Autotransporter 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 DUF5777 Gcw_chp HP_OMP HP_OMP_2 HpuA IAT_beta KdgM LamB Legionella_OMP Lipoprot_C LptD MDM10 MipA MOSP_C MSP MtrB_PioB Omp85 Omp85_2 Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF 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 TbpB_C 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...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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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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|Seed source:||Prodom_3211 (release 99.1) & Pfam-B__3211 (release 7.5)|
|Number in seed:||70|
|Number in full:||5214|
|Average length of the domain:||241.60 aa|
|Average identity of full alignment:||23 %|
|Average coverage of the sequence by the domain:||84.27 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||23|
|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:
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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.
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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.
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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.
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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.
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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_3 domain has been found. There are 25 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 sequence.
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