Summary

Syntaxin

Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteristic of and conserved in all syntaxins (PF05739), and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A (O35526) it is found as three alpha-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role. The function of syntaxins is determined by their localisation. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors [6].

Literature references

Jantti J, Aalto MK, Oyen M, Sundqvist L, Keranen S, Ronne H; , J Cell Sci 2002;115:409-420.: Characterization of temperature-sensitive mutations in the yeast syntaxin 1 homologues Sso1p and Sso2p, and evidence of a distinct function for Sso1p in sporulation. PUBMED:11839791
Marash M, Gerst JE; , EMBO J 2001;20:411-421.: t-SNARE dephosphorylation promotes SNARE assembly and exocytosis in yeast. PUBMED:11157748
Dulubova I, Yamaguchi T, Wang Y, Sudhof TC, Rizo J; , Nat Struct Biol 2001;8:258-264.: Vam3p structure reveals conserved and divergent properties of syntaxins. PUBMED:11224573
Carr CM; , Nat Struct Biol 2001;8:186-188.: The taming of the SNARE. PUBMED:11224554
Namy O, Hatin I, Stahl G, Liu H, Barnay S, Bidou L, Rousset JP; , Genetics 2002;161:585-594.: Gene overexpression as a tool for identifying new trans-acting factors involved in translation termination in Saccharomyces cerevisiae. PUBMED:12072456
Teng FY, Wang Y, Tang BL; , Genome Biol 2001;2:REVIEWS3012.: The syntaxins. PUBMED:11737951

InterPro entry IPR006011

Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family PUBMED:7690687. Members of the syntaxin family PUBMED:8493722, PUBMED:8490959 have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation.

Clan

This family is a member of clan SNARE-fusion (CL0445), which contains the following 3 members:

SNARE Synaptobrevin Syntaxin

Gene Ontology

Cellular component

membrane (GO:0016020)

External database links

HOMSTRAD:	Syntaxin
PANDIT:	PF00804
PROSITE:	PDOC00709
SCOP:	1sfc
SYSTERS:	Syntaxin

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

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (187) Full (735) NCBI (1146) Metagenomics (21)
Viewer:

Formatting options

Alignment:	Seed (187) Full (735)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (187) Full (735) NCBI (1146) Metagenomics (21)
Full length sequences	Full-sequences (735)

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 HMMER2.

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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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_1158 (release 2.1)

Previous IDs:

none

Type:

Domain

Author:

Bateman A

Number in seed:

187

Number in full:

735

Average length of the domain:

102.20 aa

Average identity of full alignment:

18 %

Average coverage of the sequence by the domain:

33.21 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.0	25.0
Trusted cut-off	25.0	25.0
Noise cut-off	24.9	24.9

Model length:

103

Family (HMM) version:

18

Download:

download the raw HMM for this family

Species distribution

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Species trees

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.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

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.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Interactions

There is 1 interaction for this family. More...

Syntaxin

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 Syntaxin domain has been found.

Loading structure mapping...

Family: Syntaxin (PF00804)

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Summary

Syntaxin

Literature references

InterPro entry IPR006011

Clan

Gene Ontology

External database links

Domain organisation

Alignments

Viewing

Downloading

View options

Formatting options

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures