Summary: Synaptobrevin
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Synaptobrevin Edit Wikipedia article
| Synaptobrevin | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 Three different views of the high resolution structure of a truncated neuronal SNARE complex. Legend: synaptobrevin-2 (red), Syntaxin-1 (pink), SNAP-25 (purple). | |||||||||
| Identifiers | |||||||||
| Symbol | Synaptobrevin | ||||||||
| Pfam | PF00957 | ||||||||
| InterPro | IPR016444 | ||||||||
| PROSITE | PDOC00368 | ||||||||
| SCOPe | 1sfc / SUPFAM | ||||||||
| OPM superfamily | 197 | ||||||||
| OPM protein | 4wy4 | ||||||||
| Membranome | 351 | ||||||||
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Synaptobrevins (synaptobrevin isotypes 1-2) are small integral membrane proteins of secretory vesicles with molecular weight of 18 kilodalton (kDa) that are part of the vesicle-associated membrane protein (VAMP) family.[1][2][3][4][5]
Synaptobrevin is one of the SNARE proteins involved in formation of the SNARE complexes.
Contents
Structure
Out of four α-helices of the core SNARE complex one is contributed by synaptobrevin, one by syntaxin, and two by SNAP-25 (in neurons).
Function
SNARE proteins are the key components of the molecular machinery that drives fusion of membranes in exocytosis. Their function however is subject to fine-tuning by various regulatory proteins collectively referred to as SNARE masters.
Classification
In the Q/R nomenclature for organizing SNARE proteins, VAMP/synaptobrevin family members are classified as R-SNAREs, so named for the presence of an arginine at a specific location within the primary sequence of the protein (as opposed to the SNAREs of the target membrane, which contain a glutamine and are so named Q-SNAREs). Synaptobrevin is classified as a V-SNARE in the V/T nomenclature, an alternative classification scheme in which SNAREs are classified as V-SNAREs and T-SNAREs for their localization to vesicles and target membranes, respectively.[6]
Clinical significance
Synaptobrevin is degraded by tetanospasmin, a protein derived from the bacterium Clostridium tetani, which causes tetanus. A related bacterium, Clostridium botulinum, produces the botulinum toxin. Various botulinum toxin serotypes exist that each cleave specific peptide bonds of specific neuronal SNARE proteins, and synaptobrevin is this target protein for several of the serotypes.
Human proteins containing this domain
SEC22A; SEC22B; SYBL1; VAMP1; VAMP2; VAMP3; VAMP4; VAMP5; VAMP8; YKT6;
References and notes
- ^ Baumert M, Maycox PR, Navone F, De Camilli P, Jahn R (February 1, 1989). "Synaptobrevin: an integral membrane protein of 18,000 daltons present in small synaptic vesicles of rat brain". EMBO J. 8 (2): 379–84. doi:10.1002/j.1460-2075.1989.tb03388.x. PMC 400817. PMID 2498078.
- ^ Bock JB, Scheller RH (October 1999). "SNARE proteins mediate lipid bilayer fusion". Proc. Natl. Acad. Sci. U.S.A. 96 (22): 12227–9. doi:10.1073/pnas.96.22.12227. PMC 34255. PMID 10535902.
- ^ Ernst JA, Brunger AT (2003). "High resolution structure, stability, and synaptotagmin binding of a truncated neuronal SNARE complex". J Biol Chem. 278 (10): 8630–6. doi:10.1074/jbc.M211889200. PMID 12496247.
- ^ Fasshauer D, Sutton RB, Brunger AT, Jahn R (December 1998). "Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q- and R-SNAREs". Proc. Natl. Acad. Sci. U.S.A. 95 (26): 15781–6. doi:10.1073/pnas.95.26.15781. PMC 28121. PMID 9861047.
- ^ Weber T, Zemelman BV, McNew JA, Westermann B, Gmachl M, Parlati F, Sollner TH, Rothman JE (1998). "SNAREpins: minimal machinery for membrane fusion". Cell. 92 (6): 759–72. doi:10.1016/S0092-8674(00)81404-X. PMID 9529252.
- ^ Juan S. Bonifacino and Benjamin S. Glick. "The Mechanisms of Vesicle Budding and Fusion." Cell, Vol. 116, 153–166, January 23, 2004,
External links
- Synaptobrevin at the US National Library of Medicine Medical Subject Headings (MeSH)
- Myobloc (rimabotulinumtoxinB) Prescribing Information
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Internal database links
| SCOOP: | DUF5345 Ferlin_C MCU RIFIN SNARE Syntaxin |
External database links
| PROSITE: | PDOC00368 |
| SCOP: | 1sfc |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001388
Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [ PUBMED:2560644 ], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain [ PUBMED:1976629 ]. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins [ PUBMED:8406010 ]. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Cellular component | integral component of membrane (GO:0016021) |
| Biological process | 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 SNARE-fusion (CL0445), which has the following description:
The SNARE-fusion complex families are characterised by being tetrameric coiled-coil structures.
The clan contains the following 3 members:
Synaptobrevin Syntaxin Syntaxin_2Alignments
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 and the UniProtKB sequence database. More...
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| Seed (93) |
Full (10485) |
Representative proteomes | UniProt (18775) |
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| RP15 (2022) |
RP35 (5039) |
RP55 (8526) |
RP75 (11294) |
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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 (93) |
Full (10485) |
Representative proteomes | UniProt (18775) |
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|---|---|---|---|---|---|---|---|
| RP15 (2022) |
RP35 (5039) |
RP55 (8526) |
RP75 (11294) |
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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: | Pfam-B_303 (release 3.0) |
| Previous IDs: | synaptobrevin; |
| Type: | Family |
| Sequence Ontology: | SO:0100021 |
| Author: |
Finn RD  , Bateman A
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| Number in seed: | 93 |
| Number in full: | 10485 |
| Average length of the domain: | 79.80 aa |
| Average identity of full alignment: | 29 % |
| Average coverage of the sequence by the domain: | 35.76 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 89 | ||||||||||||
| Family (HMM) version: | 23 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Structures
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 Synaptobrevin domain has been found. There are 88 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
