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0  structures 42  species 0  interactions 136  sequences 5  architectures

Family: Synapsin_N (PF10581)

Summary: Synapsin N-terminal

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Synapsin N-terminal Provide feedback

This highly conserved domain of synapsin proteins has a serine at position 9 or 10 which is a phosphorylation site. The domain appears to be the part of the molecule that binds to calmodulin [3].

Literature references

  1. Heierhorst J, Mitchelhill KI, Mann RJ, Tiganis T, Czernik AJ, Greengard P, Kemp BE; , Biochem J. 1999;344:577-583.: Synapsins as major neuronal Ca2+/S100A1-interacting proteins. PUBMED:10567243 EPMC:10567243

  2. Gitler D, Xu Y, Kao HT, Lin D, Lim S, Feng J, Greengard P, Augustine GJ; , J Neurosci. 2004;24:3711-3720.: Molecular determinants of synapsin targeting to presynaptic terminals. PUBMED:15071120 EPMC:15071120

  3. Benfenati F, Ferrari R, Onofri F, Arcuri C, Giambanco I, Donato R; , J Neurochem. 2004;89:1260-1270.: S100A1 codistributes with synapsin I in discrete brain areas and inhibits the F-actin-bundling activity of synapsin I. PUBMED:15147519 EPMC:15147519


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019736

The synapsins are a family of neuron-specific phosphoproteins that coat synaptic vesicles and are involved in the binding between these vesicles and the cytoskeleton (including actin filaments). The family comprises 5 homologous proteins Ia, Ib, IIa, IIb and III. Synapsins I, II, and III are encoded by 3 different genes. The a and b isoforms of synapsin I and II are splice variants of the primary transcripts [PUBMED:10940454].

Synapsin I is mainly associated with regulation of neurotransmitter release from presynaptic neuron terminals [PUBMED:2859595]. Synapsin II, as well as being involved in neurotransmitter release, has a role in the synaptogenesis and synaptic plasticity responsible for long term potentiation [PUBMED:7777057]. Recent studies implicate synapsin III with a developmental role in neurite elongation and synapse formation that is distinct from the functions of synapsins I and II [PUBMED:10804215].

Structurally, synapsins are multidomain proteins, of which 3 domains are common to all the mammalian forms. The N-terminal `A' domain is ~30 residues long and contains a serine residue that serves as an acceptor site for protein kinase-mediated phosphorylation. This is followed by the `B' linker domain, which is ~80 residues long and is relatively poorly conserved. Domain `C' is the longest, spanning approximately 300 residues. This domain is highly conserved across all the synapsins (including those from Drosophila) and is possessed by all splice variants. The remaining six domains, D-I, are not shared by all the synapsins and differ both between the primary transcripts and the splice variants.

This entry represents a conserved octapeptide in the immediate N-terminal domain, which contains the phosphorylated serine residue.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

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(5)
Full
(136)
Representative proteomes NCBI
(160)
Meta
(0)
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(5)
RP35
(11)
RP55
(28)
RP75
(56)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(5)
Full
(136)
Representative proteomes NCBI
(160)
Meta
(0)
RP15
(5)
RP35
(11)
RP55
(28)
RP75
(56)
Alignment:
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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
(5)
Full
(136)
Representative proteomes NCBI
(160)
Meta
(0)
RP15
(5)
RP35
(11)
RP55
(28)
RP75
(56)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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 View help on the curation process

Seed source: PROSITE_PS00415
Previous IDs: none
Type: Domain
Author: Finn R, Coggill P
Number in seed: 5
Number in full: 136
Average length of the domain: 31.30 aa
Average identity of full alignment: 77 %
Average coverage of the sequence by the domain: 6.20 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.5 25.5
Noise cut-off 22.5 21.5
Model length: 32
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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