Summary: Pathogenesis-related protein Bet v I family
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Bet v I allergen Edit Wikipedia article
|Bet v I allergen|
Bet v I allergen is a family of protein allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms.
Trees within the order Fagales possess particularly potent allergens, e.g. the prototypical Bet v 1, the major white birch (Betula verrucosa) pollen antigen. Bet v 1 is the main cause of type I allergies observed in early spring. Type I, or immunoglobulin E-mediated (IgE-mediated) allergies affect 1 in 5 people in Europe and North America. Commonly observed symptoms are hay fever, dermatitis, asthma and, in severe cases, anaphylactic shock. First contact with these allergens results in sensitisation; subsequent contact produces a cross-linking reaction of IgE on mast cells and concomitant release of histamine. The inevitable symptoms of an allergic reaction ensue.
A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an Arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation.
The allergens in this family include allergens with the following designations: Bet v 1, Dau c 1, and Pru a 1. Other proteins belonging to this family include the major pollen allergens:
- Aln g I from Alnus glutinosa (Alder);
- Api G I from Apium graveolens (Celery);
- Car b I from Carpinus betulus (European hornbeam);
- Cor a I from Corylus avellana (European hazel);
- Mal d I from Malus domestica (Apple).
NMR analysis has confirmed earlier predictions of the protein structure and site of the major T-cell epitope. The Bet v 1 protein comprises 6 anti-parallel beta-strands and 3 alpha-helices. Four of the strands dominate the global fold, and 2 of the helices form a C-terminal amphipathic helical motif. This motif is believed to be the T-cell epitope. However, one very striking feature of the three-dimensional structure of Bet v 1 is the presence of a large hydrophobic cavity, which is open to the exterior and probably functions as a ligand binding site.
The motif is also found in:
- the wound-induced protein AoPR1 from Asparagus officinalis (Garden asparagus);
- the pathogenesis-related proteins from Phaseolus vulgaris (Kidney bean) and Petroselinum crispum (Parsley) (PR1-1 and PR1-3);
- the disease resistance response proteins, STH-2 and STH-21, from Solanum tuberosum (Potato) and pI49, pI176 and DRRG49-C from Pisum sativum (Garden pea);
- the P.sativum abscisic acid-responsive proteins ABR17 and ABR18;
- and the stress-induced protein SAM22 from Glycine max (Soybean).
Additionally, the core domain of Bet v 1 founds or is part of a superfamily of domains called SRPBCC (START/RHOalphaC/PITP/Bet v1/CoxG/CalC) that include the StAR-related lipid-transfer (START) domain.
The biological function of Bet v 1 is still under investigations. Bet v 1 harbors a large hydrophobic pocket and is able to bind a large spectra of ligands in it like hormones and siderophores like flavenols. It belongs to the pathogenesis-related (PR) proteins, which are usually expressed upon infections and stressful conditions, implicating a role in host defense. In vitro, Bet v 1 has been shown to be immune-suppressive, when its pocket was filled by a ligand, but was able to mount a Th2-response important in allergy development, when the pocket remained empty.
- Gajhede, M.; Osmark, P.; Poulsen, F. M.; Ipsen, H.; Larsen, J. N.; Joost Van Neerven, R. J.; Schou, C.; Løwenstein, H.; Spangfort, M. D. (1996). "X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy". Nature Structural Biology. 3 (12): 1040–1045. doi:10.1038/nsb1296-1040. PMID 8946858.
- [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]
- Rosch P, Kraft D, Faber C, Lindemann A, Sticht H, Ejchart A, Kungl A, Susani M, Frank RW, Breitenbach M (1996). "Secondary structure and tertiary fold of the birch pollen allergen Bet v 1 in solution". J. Biol. Chem. 271 (32): 19243–19250. doi:10.1074/jbc.271.32.19243. PMID 8702605.
- Kungl AJ, Kraft D, Lindemann A, Susani M, Breitenbach M, Scheiner O, Auer M, Machius M, Visser AJ (1996). "Evidence for an alpha helical T cell epitope in the C-terminus of the main birch pollen allergen Bet V 1". Biochem. Biophys. Res. Commun. 223 (1): 187–192. doi:10.1006/bbrc.1996.0867. PMID 8660368.
- Radauer, Christian; Lackner, Peter; Breiteneder, Heimo (2008-10-15). "The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands". BMC Evolutionary Biology. 8 (1): 286. doi:10.1186/1471-2148-8-286. PMC . PMID 18922149.
- Mogensen, Jesper E.; Wimmer, Reinhard; Larsen, Jørgen N.; Spangfort, Michael D.; Otzen, Daniel E. (2002-04-12). "The major birch allergen, Bet v 1, shows affinity for a broad spectrum of physiological ligands". Journal of Biological Chemistry. 277: 23684–92. doi:10.1074/jbc.M202065200. ISSN 0021-9258. PMID 11953433.
- Loon, L. C. van; Rep, M.; Pieterse, C. M. J. (2006-01-01). "Significance of Inducible Defense-related Proteins in Infected Plants". Annual Review of Phytopathology. 44 (1): 135–162. doi:10.1146/annurev.phyto.44.070505.143425. PMID 16602946.
- Roth-Walter, Franziska; Gomez-Casado, Cristina; Pacios, Luis F.; Mothes-Luksch, Nadine; Roth, Georg A.; Singer, Josef; Diaz-Perales, Araceli; Jensen-Jarolim, Erika (2014-06-20). "Bet v 1 from Birch Pollen Is a Lipocalin-like Protein Acting as Allergen Only When Devoid of Iron by Promoting Th2 Lymphocytes". Journal of Biological Chemistry. 289 (25): 17416–17421. doi:10.1074/jbc.M114.567875. ISSN 0021-9258. PMC . PMID 24798325.
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Pathogenesis-related protein Bet v I family Provide feedback
This family is named after Bet v 1, the major birch pollen allergen. This protein belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants . In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several subfamilies related to PR-10  - Pathogenesis-related proteins PR-10: These proteins were identified as major tree pollen allergens in birch and related species (hazel, alder), as plant food allergens expressed in high levels in fruits, vegetables and seeds (apple, celery, hazelnut), and as pathogenesis-related proteins whose expression is induced by pathogen infection, wounding, or abiotic stress. Hyp-1 (Q8H1L1), an enzyme involved in the synthesis of the bioactive naphthodianthrone hypericin in St. John's wort (Hypericum perforatum) also belongs to this family. Most of these proteins were found in dicotyledonous plants. In addition, related sequences were identified in monocots and conifers. - Cytokinin-specific binding proteins: These legume proteins bind cytokinin plant hormones . - (S)-Norcoclaurine synthases are enzymes catalysing the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine . -Major latex proteins and ripening-related proteins are proteins of unknown biological function that were first discovered in the latex of opium poppy (Papaver somniferum) and later found to be upregulated during ripening of fruits such as strawberry and cucumber . The occurrence of Bet v 1-related proteins is confined to seed plants with the exception of a cytokinin-binding protein from the moss Physcomitrella patens (Q9AXI3).
Wen J, Vanek-Krebitz M, Hoffmann-Sommergruber K, Scheiner O, Breiteneder H; , Mol Phylogenet Evol. 1997;8:317-333.: The potential of Betv1 homologues, a nuclear multigene family, as phylogenetic markers in flowering plants. PUBMED:9417891 EPMC:9417891
Fujimoto Y, Nagata R, Fukasawa H, Yano K, Azuma M, Iida A, Sugimoto S, Shudo K, Hashimoto Y; , Eur J Biochem. 1998;258:794-802.: Purification and cDNA cloning of cytokinin-specific binding protein from mung bean (Vigna radiata). PUBMED:9874249 EPMC:9874249
Samanani N, Liscombe DK, Facchini PJ; , Plant J. 2004;40:302-313.: Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis. PUBMED:15447655 EPMC:15447655
Samanani N, Liscombe DK, Facchini PJ; , Plant J. 2004;40:302-313.: Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis. PUBMED:15447655 EPMC:15447655
Internal database links
|Similarity to PfamA using HHSearch:||Polyketide_cyc2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000916
This domain is named after Bet v 1, the major birch pollen allergen. Bet v 1 belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants [PUBMED:9417891]. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several subfamilies related to PR-10 [PUBMED:18922149]:
- Pathogenesis-related proteins PR-10: These proteins were identified as major tree pollen allergens in birch and related species (hazel, alder), as plant food allergens expressed in high levels in fruits, vegetables and seeds (apple, celery, hazelnut), and as pathogenesis-related proteins whose expression is induced by pathogen infection, wounding, or abiotic stress. Hyp-1 (SWISSPROT), an enzyme involved in the synthesis of the bioactive naphthodianthrone hypericin in St. John's wort (Hypericum perforatum) also belongs to this family. Most of these proteins were found in dicotyledonous plants. In addition, related sequences were identified in monocots and conifers.
- Cytokinin-specific binding proteins: These legume proteins bind cytokinin plant hormones [PUBMED:9874249].
- (S)-Norcoclaurine synthases are enzymes catalysing the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine [PUBMED:15447655].
- Major latex proteins and ripening-related proteins are proteins of unknown biological function that were first discovered in the latex of opium poppy (Papaver somniferum) and later found to be upregulated during ripening of fruits such as strawberry and cucumber [PUBMED:15447655].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||defense response (GO:0006952)|
|response to biotic stimulus (GO:0009607)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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The Bet_V_I family is composed of sequences related to the major Birch (Betula verrucose) pollen antigen Betv1. This allergen is known to cause hayfever, dermatitis, asthma and occasionally anaphylactic shock. The other families in this clan share the same structure as Betv1 which is composed of antiparallel beta sheets and alpha helices. There is a cavity between the beta sheet and a long C terminal helix. The cavity appears to play roles in the binding of lipid molecules  which seems a common feature of the families in this clan.
The clan contains the following 19 members:AHSA1 Aromatic_hydrox Bet_v_1 COXG DAPG_hydrolase DUF1857 DUF2505 DUF3074 DUF3211 DUF3284 Fungal_KA1 IP_trans Lipoprotein_18 Polyketide_cyc Polyketide_cyc2 PRELI Ring_hydroxyl_A START VASt
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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We make a range of alignments for each Pfam-A family:
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You can see the alignments as HTML or in three different sequence viewers:
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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.
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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.
|Author:||Finn RD , Radauer C|
|Number in seed:||18|
|Number in full:||2560|
|Average length of the domain:||140.40 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||93.23 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|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.
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.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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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.
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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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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Bet_v_1 domain has been found. There are 164 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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