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8  structures 7083  species 0  interactions 38248  sequences 198  architectures

Family: SSF (PF00474)

Summary: Sodium:solute 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-solute symporter". More...

Sodium-solute symporter Edit Wikipedia article

Sodium:solute symporter family
Identifiers
SymbolSSF
PfamPF00474
InterProIPR001734
PROSITEPDOC00429
TCDB2.A.21


Sodium/substrate symport (or co-transport) is a widespread mechanism of solute transport across cytoplasmic membranes of pro- and eukaryotic cells. Thereby the energy stored in an inwardly directed electrochemical sodium gradient (sodium motive force, SMF) is used to drive solute accumulation against a concentration gradient. The SMF is generated by primary sodium pumps (e.g. sodium/potassium ATPases, sodium translocating respiratory chain complexes) or via the action of sodium/proton antiporters. Sodium/substrate transporters are grouped in different families based on sequence similarities[1][2].

One of these families, known as the sodium:solute symporter family (SSSF), contains over a hundred members of pro- and eukaryotic origin[3]. The average hydropathy plot for SSSF proteins predicts 11 to 15 putative transmembrane domains (TMs) in alpha-helical conformation. A secondary structure model of PutP from Escherichia coli suggests the protein contains 13 TMs with the N-terminus located on the periplasmic side of the membrane and the C-terminus facing the cytoplasm. The results support the idea of a common topological motif for members of the SSSF. Transporters with a C-terminal extension are proposed to have an additional 14th TM.

An ordered binding model of sodium/substrate transport suggests that sodium binds to the empty transporter first, thereby inducing a conformational alteration which increases the affinity of the transporter for the solute. The formation of the ternary complex induces another structural change that exposes sodium and substrate to the other site of the membrane. Substrate and sodium are released and the empty transporter re-orientates in the membrane allowing the cycle to start again.

Subfamilies

Human proteins containing this domain

AIT; SLC5A1; SLC5A10; SLC5A11; SLC5A12; SLC5A2; SLC5A3; SLC5A4; SLC5A5; SLC5A6; SLC5A7; SLC5A8; SLC5A9;

References

  1. ^ Reizer J, Reizer A, Saier Jr MH (1990). "The Na+/pantothenate symporter (PanF) of Escherichia coli is homologous to the Na+/proline symporter (PutP) of E. coli and the Na+/glucose symporters of mammals". Res. Microbiol. 141 (9): 1069–1072. PMID 1965458.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ Reizer J, Reizer A, Saier Jr MH (1994). "A functional superfamily of sodium/solute symporters". Biochim. Biophys. Acta. 1197 (2): 133–136. PMID 8031825.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ Jung H (2002). "The sodium/substrate symporter family: structural and functional features". FEBS Lett. 529 (1): 73–77. PMID 12354616.
This article incorporates text from the public domain Pfam and InterPro: IPR001734

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:solute symporter family Provide feedback

This family includes P33413 which is not in the Prosite entry. Membership of this family is supported by a significant blast score.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001734

Sodium/substrate symport (or co-transport) is a widespread mechanism of solute transport across cytoplasmic membranes of pro- and eukaryotic cells. Thereby the energy stored in an inwardly directed electrochemical sodium gradient (sodium motive force, SMF) is used to drive solute accumulation against a concentration gradient. The SMF is generated by primary sodium pumps (e.g. sodium/potassium ATPases, sodium translocating respiratory chain complexes) or via the action of sodium/proton antiporters. Sodium/substrate transporters are grouped in different families based on sequence similarities [ PUBMED:1965458 , PUBMED:8031825 ].

One of these families, known as the sodium:solute symporter family (SSSF), contains over a hundred members of pro- and eukaryotic origin [ PUBMED:12354616 ]. The average hydropathy plot for SSSF proteins predicts 11 to 15 putative transmembrane domains (TMs) in alpha-helical conformation. A secondary structure model of PutP from Escherichia coli suggests the protein contains 13 TMs with the N terminus located on the periplasmic side of the membrane and the C terminus facing the cytoplasm. The results support the idea of a common topological motif for members of the SSSF. Transporters with a C-terminal extension are proposed to have an additional 14th TM.

An ordered binding model of sodium/substrate transport suggests that sodium binds to the empty transporter first, thereby inducing a conformational alteration which increases the affinity of the transporter for the solute. The formation of the ternary complex induces another structural change that exposes sodium and substrate to the other site of the membrane. Substrate and sodium are released and the empty transporter re-orientates in the membrane allowing the cycle to start again.

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 APC (CL0062), which has the following description:

This large superfamily contains a variety of transporters including amino acid permeases that according to TCDB belong to the APC (Amino acid-Polyamine-organoCation) superfamily.

The clan contains the following 21 members:

AA_permease AA_permease_2 AA_permease_C Aa_trans BCCT BenE Branch_AA_trans CstA DUF3360 HCO3_cotransp K_trans MFS_MOT1 Na_Ala_symp Nramp SNF Spore_permease SSF Sulfate_transp Transp_cyt_pur Trp_Tyr_perm Xan_ur_permease

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...

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
(10)
Full
(38248)
Representative proteomes UniProt
(146948)
RP15
(5939)
RP35
(17408)
RP55
(37194)
RP75
(60822)
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HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(10)
Full
(38248)
Representative proteomes UniProt
(146948)
RP15
(5939)
RP35
(17408)
RP55
(37194)
RP75
(60822)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(10)
Full
(38248)
Representative proteomes UniProt
(146948)
RP15
(5939)
RP35
(17408)
RP55
(37194)
RP75
(60822)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 10
Number in full: 38248
Average length of the domain: 345.7 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 70.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 406
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Selections

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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 SSF domain has been found. There are 8 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
A0A044TKP8 View 3D Structure Click here
A0A077Z158 View 3D Structure Click here
A0A077ZB02 View 3D Structure Click here
A0A077ZFC6 View 3D Structure Click here
A0A077ZK02 View 3D Structure Click here
A0A077ZQR5 View 3D Structure Click here
A0A0A0US36 View 3D Structure Click here
A0A0D2ENF2 View 3D Structure Click here
A0A0D2GLU5 View 3D Structure Click here
A0A0D2GPN3 View 3D Structure Click here
A0A0D2H163 View 3D Structure Click here
A0A0D2HAK9 View 3D Structure Click here
A0A0D2HJR7 View 3D Structure Click here
A0A0D2HMA0 View 3D Structure Click here
A0A0G2JY02 View 3D Structure Click here
A0A0G2K630 View 3D Structure Click here
A0A0G2K669 View 3D Structure Click here
A0A0G2KH46 View 3D Structure Click here
A0A0G2KQP1 View 3D Structure Click here
A0A0H2UJX9 View 3D Structure Click here
A0A0H3GIN9 View 3D Structure Click here
A0A0H3GQA8 View 3D Structure Click here
A0A0H3GQY7 View 3D Structure Click here
A0A0H3GX99 View 3D Structure Click here
A0A0H3GY78 View 3D Structure Click here
A0A0H5SLH5 View 3D Structure Click here
A0A0K0E742 View 3D Structure Click here
A0A0K0EGU3 View 3D Structure Click here
A0A0K0EI76 View 3D Structure Click here
A0A0N4UDU7 View 3D Structure Click here
A0A0N4UDU8 View 3D Structure Click here
A0A0N4UM12 View 3D Structure Click here
A0A0N4URP1 View 3D Structure Click here
A0A0R4IUP3 View 3D Structure Click here
A0A158Q301 View 3D Structure Click here
A0A175W9K4 View 3D Structure Click here
A0A175WGG2 View 3D Structure Click here
A0A1C1CME8 View 3D Structure Click here
A0A1C1CP50 View 3D Structure Click here
A0A1C1CUC5 View 3D Structure Click here