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7  structures 263  species 1  interaction 417  sequences 8  architectures

Family: Syntaxin-6_N (PF09177)

Summary: Syntaxin 6, N-terminal

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This is the Wikipedia entry entitled "Syntaxin 6 N terminal protein domain". More...

Syntaxin 6 N terminal protein domain Edit Wikipedia article

Syntaxin-6_N
PDB 1lvf EBI.jpg
syntaxin 6
Identifiers
Symbol Syntaxin-6_N
Pfam PF09177
InterPro IPR015260
SCOP 1lvf
SUPERFAMILY 1lvf

In molecular biology the protein domain Syntaxin 6 N terminal protein domain is a soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) found in endosomal transport vesicles. It is part of the family, of target SNAREs (t-SNAREs). It is a vital aid to exporting and importing cell cargo through a process called cell trafficking. Its SNARE motif shows significant homology to both syntaxin 1a and S25C, indicating similarity through evolutionary conservation. The structure of the syntaxin 6 N-terminal domain shows strong structural similarity with the N-terminal domains of syntaxin 1a, Sso1p, and Vam3p; despite a very low level of sequence similarity. SNARE functions essentially as a tether to hold the vesicle. The cytoplasmic regions of SNARE found on transport vesicles and target membranes interact, then a four-helix coiled coil forms. This links the cell membrane and vesicles together in such a way that it overcomes the energetic barrier to fusing two lipid bilayers. This is the way cell cargo is exchanged. This particular entry focuses on the N-terminal domain of Syntaxin 6.[1]

Structure[edit]

Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport.[2]

Function[edit]

SNAREs play a vital role in the trafficking of cell cargo. The vesicles fuse to the cell membrane with the help of SNARE proteinds. The SNARE motifs form a four-helix bundle that contributes to the fusion of two membranes. More specifically, the N-terminal domain binds to the SNARE motif, and this intramolecular interaction decreases the rate of association with the partner SNARE. However the N terminal domain's function still remains to fully elucidated.[2]



References[edit]

  1. ^ Jung JJ, Inamdar SM, Tiwari A, Choudhury A (2012). "Regulation of intracellular membrane trafficking and cell dynamics by syntaxin-6.". Biosci Rep 32 (4): 383–91. doi:10.1042/BSR20120006. PMC 3392101. PMID 22489884. 
  2. ^ a b Misura KM, Bock JB, Gonzalez LC, Scheller RH, Weis WI (July 2002). "Three-dimensional structure of the amino-terminal domain of syntaxin 6, a SNAP-25 C homolog". Proc. Natl. Acad. Sci. U.S.A. 99 (14): 9184–9. doi:10.1073/pnas.132274599. PMC 123115. PMID 12082176. 

This article incorporates text from the public domain Pfam and InterPro IPR015260

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Syntaxin 6, N-terminal Provide feedback

Members of this family, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport [1].

Literature references

  1. Misura KM, Bock JB, Gonzalez LC Jr, Scheller RH, Weis WI; , Proc Natl Acad Sci U S A. 2002;99:9184-9189.: Three-dimensional structure of the amino-terminal domain of syntaxin 6, a SNAP-25 C homolog. PUBMED:12082176 EPMC:12082176


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015260

Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport [PUBMED:12082176].

Gene Ontology

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Domain organisation

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Alignments

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(43)
Full
(417)
Representative proteomes NCBI
(389)
Meta
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(80)
RP35
(146)
RP55
(214)
RP75
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  Seed
(43)
Full
(417)
Representative proteomes NCBI
(389)
Meta
(2)
RP15
(80)
RP35
(146)
RP55
(214)
RP75
(271)
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  Seed
(43)
Full
(417)
Representative proteomes NCBI
(389)
Meta
(2)
RP15
(80)
RP35
(146)
RP55
(214)
RP75
(271)
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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.

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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...

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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.

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Curation and family details

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Curation View help on the curation process

Seed source: pdb_1lvf
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 43
Number in full: 417
Average length of the domain: 95.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 35.74 %

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 24.9 24.9
Trusted cut-off 25.0 25.5
Noise cut-off 24.8 24.8
Model length: 97
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Syntaxin-6_N

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-6_N domain has been found. There are 7 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 seqence.

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