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24  structures 5983  species 0  interactions 12573  sequences 52  architectures

Family: TrkH (PF02386)

Summary: Cation transport protein

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 "Bacterial potassium transporter". More...

Bacterial potassium transporter Edit Wikipedia article

TrkH
Identifiers
SymbolTrkH
PfamPF02386
Pfam clanCL0030
InterProIPR003445
TCDB2.A.38
OPM superfamily8
OPM protein3pjz

This protein family consists of various potassium transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J (EC). These proteins are involved in active sodium up-take utilizing ATP in the process. TrkH from Escherichia coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in this organism.[1] This protein interacts with TrkA and requires TrkE for transport activity.

References

  1. ^ Schlösser A, Meldorf M, Stumpe S, Bakker EP, Epstein W (1995). "TrkH and its homolog, TrkG, determine the specificity and kinetics of cation transport by the Trk system of Escherichia coli". J. Bacteriol. 177 (7): 1908–10. PMC 176828. PMID 7896723. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR003445

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

This is the Wikipedia entry entitled "Potassium transporter family". More...

Potassium transporter family Edit Wikipedia article

The K+ Transporter (Trk) Family (TC# 2.A.38) is a member of the voltage-gated ion channel (VIC) superfamily. The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and plants. A representative list of proteins belonging to the Trk family can be found in the Transporter Classification Database.[1]

Homology

The phylogenetic tree reveals that the proteins cluster according to phylogeny of the source organism with (1) the Gram-negative bacterial Trk proteins, (2) the Gram-negative and Gram-positive bacterial Ktr proteins, (3) the yeast proteins and (4) the plant proteins comprising four distinct clusters.[2] S. cerevisiae possesses at least two paralogues, high- and low-affinity K+ transporters. Folding pattern seen in Trk proteins resembles quadruplicated primitive K+ channels of the VIC superfamily (TC #1.A.1) instead of typical 12 TMS carriers.[3] Homology has been established between Trk carriers and VIC family channels.[4]

Structure

The sizes of the Trk family members vary from 423 residues to 1235 residues. The bacterial proteins are of 423-558 residues, the Triticum aestivum protein is 533 residues, and the yeast proteins vary between 841 and 1241 residues. These proteins possess 8 putative transmembrane α-helical spanners (TMSs). An 8 TMS topology with N- and C-termini on the inside, has been established for AtHKT1 of A. thaliana.[5] and Trk2 of S. cerevisiae.[6] This folding pattern resembles quadruplicated primitive K+ channels of the VIC superfamily (TC #1.A.1) instead of typical 12 TMS carriers.[7] As homology has been established between Trk carriers and VIC family channels.[1][4]

Function

Trk family members regulate various K+ transporters in all three domains of life. These regulatory subunits are generally called K+ transport/nucleotide binding subunits.[8] TrkA domains can bind NAD+ and NADH, possibly allowing K+ transporters to be responsive to the redox state of the cell. The ratio of NADH/NAD+ may control gating. Multiple crystal structures of two KTN domains complexed with NAD+ or NADH reveal that these ligands control the oligomeric (tetrameric) state of KTN. The results suggest that KTN is inherently flexible, undergoing a large conformational change through a hinge motion.[9] The KTN domains of Kef channels interact dynamically with the transporter. The KTN conformation then controls permease activity.[9]

Both yeast transport systems are believed to function by K+:H+ symport, but the wheat protein functions by K+:Na+ symport. It is possible that some of these proteins can function by a channel-type mechanism. Positively charged residues in TMS8 of several ktr/Trk/HKT transporters probably face the channel and block a conformational change that is essential for channel activity while allowing secondary active transport.[5]

The generalized transport reaction catalyzed by the Trk family members is therefore probably:

K+ (out) + H+ (out) ⇌ K+ (in) + H+ (in).

References

  1. ^ a b "2.A.38 The K+ Transporter (Trk) Family". TCDB. Retrieved 2016-04-16.
  2. ^ Saier, M. H.; Eng, B. H.; Fard, S.; Garg, J.; Haggerty, D. A.; Hutchinson, W. J.; Jack, D. L.; Lai, E. C.; Liu, H. J. (1999-02-25). "Phylogenetic characterization of novel transport protein families revealed by genome analyses". Biochimica Et Biophysica Acta. 1422 (1): 1–56. ISSN 0006-3002. PMID 10082980.
  3. ^ Matsuda, Nobuyuki; Kobayashi, Hiroshi; Katoh, Hirokazu; Ogawa, Teruo; Futatsugi, Lui; Nakamura, Tatsunosuke; Bakker, Evert P.; Uozumi, Nobuyuki (2004-12-24). "Na+-dependent K+ uptake Ktr system from the cyanobacterium Synechocystis sp. PCC 6803 and its role in the early phases of cell adaptation to hyperosmotic shock". The Journal of Biological Chemistry. 279 (52): 54952–54962. doi:10.1074/jbc.M407268200. ISSN 0021-9258. PMID 15459199.
  4. ^ a b Yu, Frank H.; Yarov-Yarovoy, Vladimir; Gutman, George A.; Catterall, William A. (2005-12-01). "Overview of Molecular Relationships in the Voltage-Gated Ion Channel Superfamily". Pharmacological Reviews. 57 (4): 387–395. doi:10.1124/pr.57.4.13. ISSN 1521-0081. PMID 16382097.
  5. ^ a b Kato, Y.; Sakaguchi, M.; Mori, Y.; Saito, K.; Nakamura, T.; Bakker, E. P.; Sato, Y.; Goshima, S.; Uozumi, N. (2001-05-22). "Evidence in support of a four transmembrane-pore-transmembrane topology model for the Arabidopsis thaliana Na+/K+ translocating AtHKT1 protein, a member of the superfamily of K+ transporters". Proceedings of the National Academy of Sciences of the United States of America. 98 (11): 6488–6493. doi:10.1073/pnas.101556598. ISSN 0027-8424. PMC 33495. PMID 11344270.
  6. ^ Zeng, Ge-Fei; Pypaert, Marc; Slayman, Clifford L. (2004-01-23). "Epitope tagging of the yeast K(+) carrier Trk2p demonstrates folding that is consistent with a channel-like structure". The Journal of Biological Chemistry. 279 (4): 3003–3013. doi:10.1074/jbc.M309760200. ISSN 0021-9258. PMID 14570869.
  7. ^ Matsuda, Nobuyuki; Kobayashi, Hiroshi; Katoh, Hirokazu; Ogawa, Teruo; Futatsugi, Lui; Nakamura, Tatsunosuke; Bakker, Evert P.; Uozumi, Nobuyuki (2004-12-24). "Na+-dependent K+ uptake Ktr system from the cyanobacterium Synechocystis sp. PCC 6803 and its role in the early phases of cell adaptation to hyperosmotic shock". The Journal of Biological Chemistry. 279 (52): 54952–54962. doi:10.1074/jbc.M407268200. ISSN 0021-9258. PMID 15459199.
  8. ^ Bateman, A.; Birney, E.; Durbin, R.; Eddy, S. R.; Howe, K. L.; Sonnhammer, E. L. (2000-01-01). "The Pfam protein families database". Nucleic Acids Research. 28 (1): 263–266. ISSN 0305-1048. PMC 102420. PMID 10592242.
  9. ^ a b Roosild, Tarmo P.; Miller, Samantha; Booth, Ian R.; Choe, Senyon (2002-06-14). "A mechanism of regulating transmembrane potassium flux through a ligand-mediated conformational switch". Cell. 109 (6): 781–791. ISSN 0092-8674. PMID 12086676.

As of this edit, this article uses content from "2.A.38 The K+ Transporter (Trk) Family", which is licensed in a way that permits reuse under the Creative Commons Attribution-ShareAlike 3.0 Unported License, but not under the GFDL. All relevant terms must be followed.

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.

Cation transport protein Provide feedback

This family consists of various cation transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J EC:3.6.1.34. These proteins are involved in active sodium up-take utilising ATP in the process. TrkH a member of the family P76769 from E. coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in E. coli [2].

Literature references

  1. Cziepluch C, Kordes E, Pujol A, Jauniaux JC; , Yeast 1996;12:1471-1474.: Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon. PUBMED:8948101 EPMC:8948101

  2. Schlosser A, Meldorf M, Stumpe S, Bakker EP, Epstein W; , J Bacteriol 1995;177:1908-1910.: TrkH and its homolog, TrkG, determine the specificity and kinetics of cation transport by the Trk system of Escherichia coli. PUBMED:7896723 EPMC:7896723

  3. Calero F, Gomez N, Arino J, Ramos J; , J Bacteriol 2000;182:394-399.: Trk1 and Trk2 define the major K(+) transport system in fission yeast. PUBMED:10629185 EPMC:10629185


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003445

This family consists of various potassium transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J ( EC ). These proteins are involved in active sodium up-take utilizing ATP in the process. TrkH from Escherichia coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in this organism [ PUBMED:7896723 ]. This protein interacts with TrkA and requires TrkE for transport activity.

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 Ion_channel (CL0030), which has the following description:

This superfamily contains a diverse range of ion channels that share a pair of transmembrane helices in common. This clan is classified as the VIC (Voltage-gated Ion Channel) superfamily in TCDB.

The clan contains the following 8 members:

Ion_trans Ion_trans_2 IRK KdpA Lig_chan PKD_channel Polycystin_dom TrkH

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
(9)
Full
(12573)
Representative proteomes UniProt
(53854)
RP15
(1724)
RP35
(6258)
RP55
(12053)
RP75
(19829)
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  Seed
(9)
Full
(12573)
Representative proteomes UniProt
(53854)
RP15
(1724)
RP35
(6258)
RP55
(12053)
RP75
(19829)
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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
(9)
Full
(12573)
Representative proteomes UniProt
(53854)
RP15
(1724)
RP35
(6258)
RP55
(12053)
RP75
(19829)
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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_529 (release 5.2)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A , Eberhardt R
Number in seed: 9
Number in full: 12573
Average length of the domain: 380.5 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 79.67 %

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 27.0 27.0
Trusted cut-off 27.5 27.0
Noise cut-off 26.8 26.9
Model length: 502
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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 TrkH domain has been found. There are 24 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
A0A0D2GFM6 View 3D Structure Click here
A0A0D2GT60 View 3D Structure Click here
A0A0H3GLP4 View 3D Structure Click here
A0A0R0LDQ5 View 3D Structure Click here
A0A175WGE5 View 3D Structure Click here
A0A1C1C785 View 3D Structure Click here
A0A1C1CBE0 View 3D Structure Click here
A0A1D6E031 View 3D Structure Click here
A0A1D6GV20 View 3D Structure Click here
A0A1D6MRU0 View 3D Structure Click here
A0A1D8PTL7 View 3D Structure Click here
A2WNZ9 View 3D Structure Click here
A2YGP9 View 3D Structure Click here
A4IAQ9 View 3D Structure Click here
C0NH13 View 3D Structure Click here
C0NT93 View 3D Structure Click here
C0NV51 View 3D Structure Click here
C1H2U6 View 3D Structure Click here
C1H952 View 3D Structure Click here
E1V6C5 View 3D Structure Click here
E1V6K4 View 3D Structure Click here
I1KEI5 View 3D Structure Click here
I1LSK8 View 3D Structure Click here
K7L1F4 View 3D Structure Click here
O31658 View 3D Structure Click here
O32081 View 3D Structure Click here
P0AFZ7 View 3D Structure Click here
P0AFZ8 View 3D Structure Click here
P0AFZ9 View 3D Structure Click here
P12685 View 3D Structure Click here
P23849 View 3D Structure Click here
P28584 View 3D Structure Click here
P44843 View 3D Structure Click here
P47564 View 3D Structure Click here
P47946 View 3D Structure Click here
P75323 View 3D Structure Click here
Q0D9S3 View 3D Structure Click here
Q0JNB6 View 3D Structure Click here
Q0P8X4 View 3D Structure Click here
Q10065 View 3D Structure Click here