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71  structures 1444  species 0  interactions 7041  sequences 139  architectures

Family: Syntaxin (PF00804)

Summary: Syntaxin

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Syntaxin". More...

Syntaxin Edit Wikipedia article

Syntaxin
PDB 1br0 EBI.jpg
Structure of an evolutionarily conserved N-terminal domain of syntaxin 1A.[1]
Identifiers
SymbolSyntaxin
PfamPF00804
InterProIPR006011
SMARTSM00503
SCOPe1br0 / SUPFAM
OPM superfamily197
OPM protein2xhe
Membranome349

Syntaxins are a family of membrane integrated Q-SNARE proteins participating in exocytosis.[2]

Domains

Syntaxins possess a single C-terminal transmembrane domain, a SNARE domain (known as H3), and an N-terminal regulatory domain (Habc). Syntaxin 17 may have two transmembrane domains.

  • The SNARE (H3) domain binds to both synaptobrevin and SNAP-25 forming the core SNARE complex. Formation of this stable SNARE core complex is believed to generate the free energy required to initiate fusion between the vesicle membrane and plasma membrane.[3]
  • The N-terminal Habc domain is formed by 3 α-helices and when collapsed onto its own H3 helix forms an inactive "closed" syntaxin conformation. This closed conformation of syntaxin is believed to be stabilized by binding of Munc-18 (nSec1), although more recent data suggests that nSec1 may bind to other conformations of syntaxin, as well. The "open" syntaxin conformation is the conformation that is competent to form into SNARE core complexes.

Function

Molecular machinery driving exocytosis in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and SNAP-25, synaptotagmin serves as a Ca2+ sensor and regulates intimately the SNARE zipping.[4]

In vitro syntaxin per se is sufficient to drive spontaneous calcium independent fusion of synaptic vesicles containing v-SNAREs.[5]

More recent and somewhat controversial amperometric data suggest that the transmembrane domain of Syntaxin1A may form part of the fusion pore of exocytosis.[6]

Binding

Syntaxins bind synaptotagmin in a calcium-dependent fashion and interact with voltage dependent calcium and potassium channels via the C-terminal H3 domain. Direct syntaxin-channel interaction is a suitable molecular mechanism for proximity between the fusion machinery and the gates of Ca2+ entry during depolarization of the presynaptic axonal boutons.

The Sec1/Munc18 protein family is known to bind to Syntaxin and regulate Syntaxins machinery. Munc18-1 binds to Syntaxin 1A via two distinct sites referred as N-terminus binding and "closed" conformation that incorporates both the central Habc domain and the SNARE core domain. Munc18-1 binding to the N-terminus of Syntaxin-1 is thought to facilitate Syntaxin-1 interaction with another SNARE, while binding to the "closed" conformation of Syntaxin-1 is believed to be inhibitory.

Recently published data show that alternative spliced Syntaxin 1 (STX1B) which lacks the transmembrane domain localizes in the nuclei.[7]

Genes

Human genes encoding syntaxin proteins include:

See also

  • Tomosyn, a syntaxin binding protein

References

  1. ^ Fernandez I, Ubach J, Dulubova I, Zhang X, Südhof TC, Rizo J (Sep 1998). "Three-dimensional structure of an evolutionarily conserved N-terminal domain of syntaxin 1A". Cell. 94 (6): 841–9. doi:10.1016/S0092-8674(00)81742-0. PMID 9753330.
  2. ^ Bennett MK, García-Arrarás JE, Elferink LA, Peterson K, Fleming AM, Hazuka CD, Scheller RH (Sep 1993). "The syntaxin family of vesicular transport receptors". Cell. 74 (5): 863–73. doi:10.1016/0092-8674(93)90466-4. PMID 7690687.
  3. ^ Lam AD, Tryoen-Toth P, Tsai B, Vitale N, Stuenkel EL (2008). "SNARE-catalyzed fusion events are regulated by Syntaxin1A-lipid interactions". Molecular Biology of the Cell. 19 (2): 485–97. doi:10.1091/mbc.E07-02-0148. PMC 2230580. PMID 18003982.
  4. ^ Georgiev DD, Glazebrook JF (2007). "Subneuronal processing of information by solitary waves and stochastic processes". In Lyshevski SE (ed.). Nano and Molecular Electronics Handbook. Nano and Microengineering Series. CRC Press. pp. 17–1–17-41. ISBN 978-0-8493-8528-5.
  5. ^ Woodbury DJ, Rognlien K (2000). "The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes". Cell Biology International. 24 (11): 809–18. doi:10.1006/cbir.2000.0631. PMID 11067766.
  6. ^ Han X, Wang CT, Bai J, Chapman ER, Jackson MB (Apr 2004). "Transmembrane segments of syntaxin line the fusion pore of Ca2+-triggered exocytosis". Science. 304 (5668): 289–92. doi:10.1126/science.1095801. PMID 15016962.
  7. ^ Pereira S, Massacrier A, Roll P, Vérine A, Etienne-Grimaldi MC, Poitelon Y, Robaglia-Schlupp A, Jamali S, Roeckel-Trevisiol N, Royer B, Pontarotti P, Lévêque C, Seagar M, Lévy N, Cau P, Szepetowski P (Nov 2008). "Nuclear localization of a novel human syntaxin 1B isoform". Gene. 423 (2): 160–71. doi:10.1016/j.gene.2008.07.010. PMID 18691641.

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Syntaxin Provide feedback

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

  1. 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 EPMC:11839791

  2. Marash M, Gerst JE; , EMBO J 2001;20:411-421.: t-SNARE dephosphorylation promotes SNARE assembly and exocytosis in yeast. PUBMED:11157748 EPMC:11157748

  3. 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 EPMC:11224573

  4. Carr CM; , Nat Struct Biol 2001;8:186-188.: The taming of the SNARE. PUBMED:11224554 EPMC:11224554

  5. 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 EPMC:12072456

  6. Teng FY, Wang Y, Tang BL; , Genome Biol 2001;2:REVIEWS3012.: The syntaxins. PUBMED:11737951 EPMC:11737951


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006011

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 , and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A ( SWISSPROT ) 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 [ PUBMED:11737951 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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_2

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 (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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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
(68)
Full
(7041)
Representative proteomes UniProt
(11833)
RP15
(1098)
RP35
(3129)
RP55
(5838)
RP75
(7816)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(68)
Full
(7041)
Representative proteomes UniProt
(11833)
RP15
(1098)
RP35
(3129)
RP55
(5838)
RP75
(7816)
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
(68)
Full
(7041)
Representative proteomes UniProt
(11833)
RP15
(1098)
RP35
(3129)
RP55
(5838)
RP75
(7816)
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Gzipped Download   Download   Download   Download   Download   Download   Download  

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 View help on the curation process

Seed source: Pfam-B_1158 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 68
Number in full: 7041
Average length of the domain: 182.50 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 60.29 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.7 26.7
Trusted cut-off 26.7 26.7
Noise cut-off 26.6 26.6
Model length: 199
Family (HMM) version: 27
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 Syntaxin domain has been found. There are 71 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.

Protein Predicted structure External Information
A0A0G2K516 View 3D Structure Click here
A0A0G2K528 View 3D Structure Click here
A0A0P0X6V1 View 3D Structure Click here
A0A0P0Y804 View 3D Structure Click here
A0A0R0ILG9 View 3D Structure Click here
A0A0R0ILG9 View 3D Structure Click here
A0A0R0KZ25 View 3D Structure Click here
A0A0R4ICQ9 View 3D Structure Click here
A0A1D6GG21 View 3D Structure Click here
A0A1D6GG21 View 3D Structure Click here
A0A1D6GG22 View 3D Structure Click here
A0A1D6GI53 View 3D Structure Click here
A0A1D6HSW4 View 3D Structure Click here
A0A1D6HSW4 View 3D Structure Click here
A0A1D6L384 View 3D Structure Click here
A0A1D6L6W5 View 3D Structure Click here
A0A1D6LFH1 View 3D Structure Click here
A0A1D6LSK3 View 3D Structure Click here
A0A1D6MXV0 View 3D Structure Click here
A0A1D6QQM6 View 3D Structure Click here
A0A1R3QVV0 View 3D Structure Click here
A0A1R3QVV0 View 3D Structure Click here
A0A2R8QH11 View 3D Structure Click here
A0A2R8QH11 View 3D Structure Click here
A0A2R8RWS3 View 3D Structure Click here
A4I3M6 View 3D Structure Click here
A4I905 View 3D Structure Click here
A5PMK2 View 3D Structure Click here
B6TDM3 View 3D Structure Click here
C6THU9 View 3D Structure Click here
D3ZUH2 View 3D Structure Click here
E7F2P0 View 3D Structure Click here
E9AHG5 View 3D Structure Click here
E9QCC0 View 3D Structure Click here
F1QX22 View 3D Structure Click here
I1J8T7 View 3D Structure Click here
I1JD32 View 3D Structure Click here
I1JGG8 View 3D Structure Click here
I1JGG9 View 3D Structure Click here
I1JQ97 View 3D Structure Click here
I1KQP4 View 3D Structure Click here
I1L9L2 View 3D Structure Click here
I1L9L3 View 3D Structure Click here
I1LHU2 View 3D Structure Click here
I1LU69 View 3D Structure Click here
I1M2C2 View 3D Structure Click here
I1MEA9 View 3D Structure Click here
I1MNS3 View 3D Structure Click here
I1MNV4 View 3D Structure Click here
I1NAV2 View 3D Structure Click here
K7KQY1 View 3D Structure Click here
K7VES8 View 3D Structure Click here
O04378 View 3D Structure Click here
O14662 View 3D Structure Click here
O16000 View 3D Structure Click here
O35526 View 3D Structure Click here
O64791 View 3D Structure Click here
O75558 View 3D Structure Click here
O96189 View 3D Structure Click here
P32851 View 3D Structure Click here
P32856 View 3D Structure Click here
P32867 View 3D Structure Click here
P39926 View 3D Structure Click here
P50279 View 3D Structure Click here
P61264 View 3D Structure Click here
P61265 View 3D Structure Click here
P61266 View 3D Structure Click here
P70452 View 3D Structure Click here
P91409 View 3D Structure Click here
Q00262 View 3D Structure Click here
Q08849 View 3D Structure Click here
Q08850 View 3D Structure Click here
Q12846 View 3D Structure Click here
Q13277 View 3D Structure Click here
Q16623 View 3D Structure Click here
Q1MTI1 View 3D Structure Click here
Q20024 View 3D Structure Click here
Q20574 View 3D Structure Click here
Q24547 View 3D Structure Click here
Q42374 View 3D Structure Click here
Q4CYJ1 View 3D Structure Click here
Q4D8X0 View 3D Structure Click here
Q54HM5 View 3D Structure Click here
Q551H5 View 3D Structure Click here
Q55DR2 View 3D Structure Click here
Q59YF0 View 3D Structure Click here
Q5RGD4 View 3D Structure Click here
Q5VRF6 View 3D Structure Click here
Q64704 View 3D Structure Click here
Q69X85 View 3D Structure Click here
Q6F3B4 View 3D Structure Click here
Q6H8D0 View 3D Structure Click here
Q6PHV0 View 3D Structure Click here
Q7KVY7 View 3D Structure Click here
Q7XIE2 View 3D Structure Click here
Q84R43 View 3D Structure Click here
Q8BVI5 View 3D Structure Click here
Q8ILE4 View 3D Structure Click here
Q8N4C7 View 3D Structure Click here
Q8R1Q0 View 3D Structure Click here
Q8VZU2 View 3D Structure Click here
Q9D3G5 View 3D Structure Click here
Q9SRV7 View 3D Structure Click here
Q9SVC2 View 3D Structure Click here
Q9SXB0 View 3D Structure Click here
Q9USH7 View 3D Structure Click here
Q9ZPV9 View 3D Structure Click here
Q9ZQZ8 View 3D Structure Click here
Q9ZSD4 View 3D Structure Click here
X1WEE0 View 3D Structure Click here