Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
84  structures 2324  species 1  interaction 11073  sequences 25  architectures

Family: SNF (PF00209)

Summary: Sodium:neurotransmitter symporter family

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 "Sodium:neurotransmitter symporter". More...

Sodium:neurotransmitter symporter Edit Wikipedia article

Sodium:neurotransmitter symporter family
Identifiers
Symbol SNF
Pfam PF00209
InterPro IPR000175
PROSITE PDOC00533
SCOP 2a65
SUPERFAMILY 2a65
TCDB 2.A.22
OPM superfamily 67
OPM protein 2a65

Sodium:neurotransmitter symporters is a family of neurotransmitter transporters.

Neurotransmitter transport systems are responsible for the release, re-uptake and recycling of neurotransmitters at synapses.

High affinity transport proteins found in the plasma membrane of presynaptic nerve terminals and glial cells are responsible for the removal from the extracellular space of released-transmitters, thereby terminating their actions.[1] Plasma membrane neurotransmitter transporters fall into two structurally and mechanistically distinct families.

The majority of the transporters constitute an extensive family of homologous proteins that derive energy from the co-transport of Na+ and Cl, in order to transport neurotransmitter molecules into the cell against their concentration gradient. The family has a common structure of 12 presumed transmembrane helices and includes carriers for gamma-aminobutyric acid (GABA), noradrenaline/adrenaline, dopamine, serotonin, proline, glycine, choline, betaine and taurine.

They are structurally distinct from the second more-restricted family of plasma membrane transporters, which are responsible for excitatory amino acid transport. The latter couple glutamate and aspartate uptake to the cotransport of Na+ and the counter-transport of K+, with no apparent dependence on Cl.[2] In addition, both of these transporter families are distinct from the vesicular neurotransmitter transporters.[3][4]

Sequence analysis of the Na+/Cl neurotransmitter superfamily reveals that it can be divided into four subfamilies, these being transporters for monoamines, the amino acids proline and glycine, GABA, and a group of orphan transporters.[5]

Subfamilies[edit]

Human proteins containing this domain[edit]

SLC6A1, SLC6A2, SLC6A3, SLC6A4, SLC6A5, SLC6A6, SLC6A7, SLC6A8, SLC6A9, SLC6A11, SLC6A12, SLC6A13, SLC6A14, SLC6A15, SLC6A16, SLC6A17, SLC6A18, SLC6A19, SLC6A20

References[edit]

  1. ^ Attwell D, Bouvier M (1992). "Cloners quick on the uptake". Curr. Biol. 2 (10): 541–543. doi:10.1016/0960-9822(92)90024-5. PMID 15336049. 
  2. ^ Malandro MS, Kilberg MS (1996). "Molecular biology of mammalian amino acid transporters". Annu. Rev. Biochem. 65: 305–336. doi:10.1146/annurev.bi.65.070196.001513. PMID 8811182. 
  3. ^ Arriza JL, Amara SG (1993). "Neurotransmitter transporters: three distinct gene families". Curr. Opin. Neurobiol. 3 (3): 337–344. doi:10.1016/0959-4388(93)90126-J. PMID 8103691. 
  4. ^ Uhl GR, Johnson PS (1994). "Neurotransmitter transporters: three important gene families for neuronal function". J. Exp. Biol. 196: 229–236. PMID 7823024. 
  5. ^ Nelson N, Lill H (1998). "Homologies and family relationships among Na+/Cl neurotransmitter transporters". Meth. Enzymol. Methods in Enzymology 296: 425–436. doi:10.1016/S0076-6879(98)96030-X. ISBN 978-0-12-182197-5. PMID 9779464. 


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.

Sodium:neurotransmitter symporter family Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000175

Neurotransmitter transport systems are integral to the release, re-uptake and recycling of neurotransmitters at synapses. High affinity transport proteins found in the plasma membrane of presynaptic nerve terminals and glial cells are responsible for the removal from the extracellular space of released-transmitters, thereby terminating their actions [PUBMED:15336049]. Plasma membrane neurotransmitter transporters fall into two structurally and mechanistically distinct families. The majority of the transporters constitute an extensive family of homologous proteins that derive energy from the co-transport of Na+ and Cl-, in order to transport neurotransmitter molecules into the cell against their concentration gradient. The family has a common structure of 12 presumed transmembrane helices and includes carriers for gamma-aminobutyric acid (GABA), noradrenaline/adrenaline, dopamine, serotonin, proline, glycine, choline, betaine and taurine. They are structurally distinct from the second more-restricted family of plasma membrane transporters, which are responsible for excitatory amino acid transport. The latter couple glutamate and aspartate uptake to the cotransport of Na+ and the counter-transport of K+, with no apparent dependence on Cl- [PUBMED:8811182]. In addition, both of these transporter families are distinct from the vesicular neurotransmitter transporters [PUBMED:8103691, PUBMED:7823024].

Sequence analysis of the Na+/Cl- neurotransmitter superfamily reveals that it can be divided into four subfamilies, these being transporters for monoamines, the amino acids proline and glycine, GABA, and a group of orphan transporters [PUBMED:9779464].

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...

Loading domain graphics...

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...

View options

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
(15)
Full
(11073)
Representative proteomes NCBI
(8360)
Meta
(1447)
RP15
(1079)
RP35
(1659)
RP55
(2764)
RP75
(3409)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(15)
Full
(11073)
Representative proteomes NCBI
(8360)
Meta
(1447)
RP15
(1079)
RP35
(1659)
RP55
(2764)
RP75
(3409)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(15)
Full
(11073)
Representative proteomes NCBI
(8360)
Meta
(1447)
RP15
(1079)
RP35
(1659)
RP55
(2764)
RP75
(3409)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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.

Pfam alignments:

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
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 15
Number in full: 11073
Average length of the domain: 275.40 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 89.59 %

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 19.7 19.7
Trusted cut-off 19.7 19.7
Noise cut-off 19.4 19.5
Model length: 523
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

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

SNF

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 SNF domain has been found. There are 84 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.

Loading structure mapping...