Summary: Beta2-adaptin appendage, C-terminal sub-domain
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This is the Wikipedia entry entitled "B2-adapt-app C". More...
B2-adapt-app C Edit Wikipedia article
| B2-adapt-app_C | |||||||||
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beta2-adaptin appendage domain, from clathrin adaptor ap2
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| Identifiers | |||||||||
| Symbol | B2-adapt-app_C | ||||||||
| Pfam | PF09066 | ||||||||
| InterPro | IPR015151 | ||||||||
| SCOP | 1e42 | ||||||||
| SUPERFAMILY | 1e42 | ||||||||
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The C-terminal domain of Beta2-adaptin is a protein domain is involved in cell trafficking by aiding import and export of substances in and out of the cell.
Function
This is an adaptor protein which helps the formation of a clathrin coat around a vesicle.
Structure
This entry represents a subdomain of the appendage (ear) domain of beta-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet.[1] This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15).[2]
Cell trafficking
Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport.[3] Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors.[4][5]
AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes.[6] AP2 associates with the plasma membrane and is responsible for endocytosis.[7] AP3 is responsible for protein trafficking to lysosomes and other related organelles.[8] AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins.[9] One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface .[10]
More information about these proteins can be found at Protein of the Month: Clathrin .
References
- ^ Traub LM, Downs MA, Westrich JL, Fremont DH (August 1999). "Crystal structure of the alpha appendage of AP-2 reveals a recruitment platform for clathrin-coat assembly". Proc. Natl. Acad. Sci. U.S.A. 96 (16): 8907–12. PMC 17706
. PMID 10430869. doi:10.1073/pnas.96.16.8907. - ^ Owen DJ, Vallis Y, Pearse BM, McMahon HT, Evans PR (August 2000). "The structure and function of the beta 2-adaptin appendage domain". EMBO J. 19 (16): 4216–27. PMC 302036 . PMID 10944104. doi:10.1093/emboj/19.16.4216.
- ^ McMahon HT, Mills IG (August 2004). "COP and clathrin-coated vesicle budding: different pathways, common approaches". Curr. Opin. Cell Biol. 16 (4): 379–91. PMID 15261670. doi:10.1016/j.ceb.2004.06.009.
- ^ Voglmaier SM, Edwards RH (June 2007). "Do different endocytic pathways make different synaptic vesicles?". Curr. Opin. Neurobiol. 17 (3): 374–80. PMID 17449236. doi:10.1016/j.conb.2007.04.002.
- ^ Boehm M, Bonifacino JS (October 2001). "Adaptins: the final recount". Mol. Biol. Cell. 12 (10): 2907–20. PMC 60144 . PMID 11598180. doi:10.1091/mbc.12.10.2907.
- ^ Touz MC, Kulakova L, Nash TE (July 2004). "Adaptor protein complex 1 mediates the transport of lysosomal proteins from a Golgi-like organelle to peripheral vacuoles in the primitive eukaryote Giardia lamblia". Mol. Biol. Cell. 15 (7): 3053–60. PMC 452563 . PMID 15107467. doi:10.1091/mbc.E03-10-0744.
- ^ Conner SD, Schmid SL (September 2003). "Differential requirements for AP-2 in clathrin-mediated endocytosis". J. Cell Biol. 162 (5): 773–9. PMC 2172816 . PMID 12952931. doi:10.1083/jcb.200304069.
- ^ Gupta SN, Kloster MM, Rodionov DG, Bakke O (June 2006). "Re-routing of the invariant chain to the direct sorting pathway by introduction of an AP3-binding motif from LIMP II". Eur. J. Cell Biol. 85 (6): 457–67. PMID 16542748. doi:10.1016/j.ejcb.2006.02.001.
- ^ Haucke V, Wenk MR, Chapman ER, Farsad K, De Camilli P (November 2000). "Dual interaction of synaptotagmin with mu2- and alpha-adaptin facilitates clathrin-coated pit nucleation". EMBO J. 19 (22): 6011–9. PMC 305843 . PMID 11080148. doi:10.1093/emboj/19.22.6011.
- ^ Kanematsu T, Fujii M, Mizokami A, Kittler JT, Nabekura J, Moss SJ, Hirata M (May 2007). "Phospholipase C-related inactive protein is implicated in the constitutive internalization of GABAA receptors mediated by clathrin and AP2 adaptor complex". J. Neurochem. 101 (4): 898–905. PMID 17254016. doi:10.1111/j.1471-4159.2006.04399.x.
This article incorporates text from the public domain Pfam and InterPro IPR015151
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Beta2-adaptin appendage, C-terminal sub-domain Provide feedback
Members of this family adopt a structure consisting of a 5 stranded beta-sheet, flanked by one alpha helix on the outer side, and by two alpha helices on the inner side. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) [1].
Literature references
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Owen DJ, Vallis Y, Pearse BM, McMahon HT, Evans PR; , EMBO J. 2000;19:4216-4227.: The structure and function of the beta 2-adaptin appendage domain. PUBMED:10944104 EPMC:10944104
Internal database links
| SCOOP: | Alpha_adaptin_C |
| Similarity to PfamA using HHSearch: | Alpha_adaptin_C AP4E_app_platf Coatomer_g_Cpla |
External database links
| SCOP: | 1e42 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR015151
This entry represents a subdomain of the appendage (ear) domain of beta-adaptin. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet [PUBMED:10430869]. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) [PUBMED:10944104].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Cellular component | clathrin adaptor complex (GO:0030131) |
| Biological process | intracellular protein transport (GO:0006886) |
| vesicle-mediated transport (GO:0016192) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan APCOP-app_sub (CL0545), which has the following description:
This superfamily is characterised by subdomains from the clathrin and coatomer appendages. The superfamily possesses a single protein/protein interaction site that in yeast binds to the ARFGAP Glo3p, and in mammalian gamma-COP binds to a Glo3p orthologue, ARFGAP2 [1].
The clan contains the following 5 members:
Alpha_adaptin_C AP4E_app_platf B2-adapt-app_C Coatomer_b_Cpla Coatomer_g_CplaAlignments
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. 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 (90) |
Full (1652) |
Representative proteomes | UniProt (2827) |
NCBI (3848) |
Meta (3) |
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| RP15 (251) |
RP35 (647) |
RP55 (1169) |
RP75 (1668) |
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| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data 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.
| Seed (90) |
Full (1652) |
Representative proteomes | UniProt (2827) |
NCBI (3848) |
Meta (3) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (251) |
RP35 (647) |
RP55 (1169) |
RP75 (1668) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
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
| Seed source: | pdb_1e42 |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Sammut SJ 
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| Number in seed: | 90 |
| Number in full: | 1652 |
| Average length of the domain: | 107.50 aa |
| Average identity of full alignment: | 34 % |
| Average coverage of the sequence by the domain: | 13.24 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 112 | ||||||||||||
| Family (HMM) version: | 11 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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Viruses
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Unclassified sequence
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Interactions
There is 1 interaction for this family. More...
Alpha_adaptinC2Structures
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 B2-adapt-app_C domain has been found. There are 9 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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