Summary: Cation transport protein

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Wikipedia: Bacterial potassium transporter
Wikipedia: Potassium transporter family
Pfam
InterPro

This is the Wikipedia entry entitled "Bacterial potassium transporter". More...

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Bacterial potassium transporter Edit Wikipedia article

TrkH

Identifiers

Symbol

TrkH

Pfam clan

Available protein structures:
Pfam Â	structures / ECOD Â
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

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

^ SchlÃƒÂ¶sser 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): 1908â€“10. PMCÂ 176828. PMIDÂ 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...

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Potassium transporter family Edit Wikipedia article

The K⁺Â 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. cerevisiaeÂ possesses at least two paralogues, high- and low-affinity K⁺Â transporters. Folding pattern seen in Trk proteins resembles quadruplicated primitive K⁺Â 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, theÂ Triticum aestivum protein is 533 residues, and the yeast proteins vary between 841 and 1241 residues. These proteins possess 8 putative transmembrane Î±-helical spanners (TMSs). An 8 TMS topology with N- and C-termini on the inside, has been established for AtHKT1 ofÂ A. thaliana.^[5]Â and Trk2 ofÂ S. cerevisiae.^[6] This folding pattern resembles quadruplicated primitive K⁺Â 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⁺Â transporters in all three domains of life. These regulatory subunits are generally called K⁺Â transport/nucleotide binding subunits.^[8] TrkA domains can bind NAD⁺Â and NADH, possibly allowing K⁺Â transporters to be responsive to the redox state of the cell. The ratio of NADH/NAD⁺Â may control gating. Multiple crystal structures of two KTN domains complexed with NAD⁺Â 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⁺Â symport, but the wheat protein functions by K⁺:Na⁺Â 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⁺Â (out) + H⁺Â (out) â‡ŒÂ K⁺Â (in) + H⁺Â (in).

References

^ ^a ^b "2.A.38 The K+ Transporter (Trk) Family". TCDB. Retrieved 2016-04-16.
^ 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): 1â€“56. ISSNÂ 0006-3002. PMIDÂ 10082980.
^ 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): 54952â€“54962. doi:10.1074/jbc.M407268200. ISSNÂ 0021-9258. PMIDÂ 15459199.
^ ^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): 387â€“395. doi:10.1124/pr.57.4.13. ISSNÂ 1521-0081. PMIDÂ 16382097.
^ ^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): 6488â€“6493. doi:10.1073/pnas.101556598. ISSNÂ 0027-8424. PMCÂ 33495. PMIDÂ 11344270.
^ 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): 3003â€“3013. doi:10.1074/jbc.M309760200. ISSNÂ 0021-9258. PMIDÂ 14570869.
^ 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): 54952â€“54962. doi:10.1074/jbc.M407268200. ISSNÂ 0021-9258. PMIDÂ 15459199.
^ 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): 263â€“266. ISSNÂ 0305-1048. PMCÂ 102420. PMIDÂ 10592242.
^ ^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): 781â€“791. ISSNÂ 0092-8674. PMIDÂ 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

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
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
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

SCOOP:

KdpA

External database links

Transporter classification:

2.A.38

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.

Molecular function	cation transmembrane transporter activity (GO:0008324)
Biological process	transmembrane transport (GO:0055085)
Biological process	cation transport (GO:0006812)

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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

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You can see the alignments as HTML or in three different sequence viewers:

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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)
	Seed (9)	Full (12573)	RP15 (1724)	RP35 (6258)	RP55 (12053)	RP75 (19829)	UniProt (53854)
Jalview	View	View	View	View	View	View	View
HTML	View
PP/heatmap	₁

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

Key: available, not generated, — not available.

Format an alignment

	Seed (9)	Full (12573)	Representative proteomes				UniProt (53854)
	Seed (9)	Full (12573)	RP15 (1724)	RP35 (6258)	RP55 (12053)	RP75 (19829)	UniProt (53854)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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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)
	Seed (9)	Full (12573)	RP15 (1724)	RP35 (6258)	RP55 (12053)	RP75 (19829)	UniProt (53854)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
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

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

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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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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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order
family
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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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

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Family: TrkH (PF02386)

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Summary: Cation transport protein

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Bacterial potassium transporter Edit Wikipedia article

References

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Potassium transporter family Edit Wikipedia article

Homology

Structure

Function

References

Cation transport protein Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR003445

Gene Ontology

Domain organisation

Pfam Clan

Alignments

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Curation and family details

Curation

HMM information

Species distribution

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AlphaFold Structure Predictions

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