Potassium transporter family

Last updated
Potassium transporter TrkH/TrkA
Identifiers
SymbolTrk
Pfam PF02386
InterPro IPR003445
TCDB 2.A.38
OPM superfamily 8
OPM protein 4j7c

The K+Transporter (Trk) Family 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.

Contents

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. [1]

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. [2] Homology has been established between Trk carriers and VIC family channels. [3]

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. [4] and Trk2 of S. cerevisiae . [5] This folding pattern resembles quadruplicated primitive K+ channels of the VIC superfamily (TC #1.A.1) instead of typical 12 TMS carriers. [2] As homology has been established between Trk carriers and VIC family channels. [3] [6]

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. [7] 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. [8] The KTN domains of Kef channels interact dynamically with the transporter. The KTN conformation then controls permease activity. [8]

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. [4]

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

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

Related Research Articles

Reuptake

Reuptake is the reabsorption of a neurotransmitter by a neurotransmitter transporter located along the plasma membrane of an axon terminal or glial cell after it has performed its function of transmitting a neural impulse.

ATP-binding cassette transporter

The ATP-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans.

Mitochondrial carrier

Mitochondrial carriers are proteins from solute carrier family 25 which transfer molecules across the membranes of the mitochondria. Mitochondrial carriers are also classified in the Transporter Classification Database. The Mitochondrial Carrier (MC) Superfamily has been expanded to include both the original Mitochondrial Carrier (MC) family and the Mitochondrial Inner/Outer Membrane Fusion (MMF) family.

Betaine transporter Proteins

Proteins of the Betaine/Carnitine/Choline Transporter (BCCT) family are found in Gram-negative and Gram-positive bacteria and archaea. The BCCT family is a member a large group of secondary transporters, the APC superfamily. Their common functional feature is that they all transport molecules with a quaternary ammonium group [R-N (CH3)3]. The BCCT family proteins vary in length between 481 and 706 amino acyl residues and possess 12 putative transmembrane α-helical spanners (TMSs). The x-ray structures reveal two 5 TMS repeats with the total number of TMSs being 10. These porters catalyze bidirectional uniport or are energized by pmf-driven or smf-driven proton or sodium ion symport, respectively, or else by substrate:substrate antiport. Some of these permeases exhibit osmosensory and osmoregulatory properties inherent to their polypeptide chains.

The Nucleobase:Cation Symporter-1 (NCS1) Family (TC# 2.A.39) consists of over 1000 currently sequenced proteins derived from Gram-negative and Gram-positive bacteria, archaea, fungi and plants. These proteins function as transporters for nucleobases including purines and pyrimidines. Members of this family possess twelve transmembrane α-helical spanners (TMSs). At least some of them have been shown to function in uptake by substrate:H+ symport mechanism.

Sodium-solute symporter

Members of the Solute:Sodium Symporter (SSS) Family (TC# 2.A.21) catalyze solute:Na+ symport. The SSS family is within the APC Superfamily. The solutes transported may be sugars, amino acids, organo cations such as choline, nucleosides, inositols, vitamins, urea or anions, depending on the system. Members of the SSS family have been identified in bacteria, archaea and eukaryotes. Almost all functionally well-characterized members normally catalyze solute uptake via Na+ symport.

Proteins of the Proton-dependent Oligopeptide Transporter (POT) Family are found in animals, plants, yeast, archaea and both Gram-negative and Gram-positive bacteria, and are part of the major facilitator superfamily. The transport of peptides into cells is a well-documented biological phenomenon which is accomplished by specific, energy-dependent transporters found in a number of organisms as diverse as bacteria and humans. The proton-dependent oligopeptide transporter (PTR) family of proteins is distinct from the ABC-type peptide transporters and was uncovered by sequence analyses of a number of recently discovered peptide transport proteins. These proteins that seem to be mainly involved in the intake of small peptides with the concomitant uptake of a proton.

The Formate-Nitrite Transporter (FNT) Family belongs to the Major Intrinsic Protein (MIP) Superfamily. FNT family members have been sequenced from Gram-negative and Gram-positive bacteria, archaea, yeast, plants and lower eukaryotes. The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite.

The amino acid-polyamine-organocation (APC) superfamily is the second largest superfamily of secondary carrier proteins currently known, and it contains several Solute carriers. Originally, the APC superfamily consisted of subfamilies under the transporter classification number. This superfamily has since been expanded to include eighteen different families.

The cation-chloride cotransporter (CCC) family is part of the APC superfamily of secondary carriers. Members of the CCC family are found in animals, plants, fungi and bacteria. Most characterized CCC family proteins are from higher eukaryotes, but one has been partially characterized from Nicotiana tabacum, and homologous ORFs have been sequenced from Caenorhabditis elegans (worm), Saccharomyces cerevisiae (yeast) and Synechococcus sp.. The latter proteins are of unknown function. These proteins show sequence similarity to members of the APC family. CCC family proteins are usually large, and possess 12 putative transmembrane spanners (TMSs) flanked by large N-terminal and C-terminal hydrophilic domains.

The anion exchanger family is a member of the large APC superfamily of secondary carriers. Members of the AE family are generally responsible for the transport of anions across cellular barriers, although their functions may vary. All of them exchange bicarbonate. Characterized protein members of the AE family are found in plants, animals, insects and yeast. Uncharacterized AE homologues may be present in bacteria. Animal AE proteins consist of homodimeric complexes of integral membrane proteins that vary in size from about 900 amino acyl residues to about 1250 residues. Their N-terminal hydrophilic domains may interact with cytoskeletal proteins and therefore play a cell structural role. Some of the currently characterized members of the AE family can be found in the Transporter Classification Database.

The sulfate permease (SulP) family is a member of the large APC superfamily of secondary carriers. The SulP family is a large and ubiquitous family of proteins derived from archaea, bacteria, fungi, plants and animals. Many organisms including Bacillus subtilis, Synechocystis sp, Saccharomyces cerevisiae, Arabidopsis thaliana and Caenorhabditis elegans possess multiple SulP family paralogues. Many of these proteins are functionally characterized, and most are inorganic anion uptake transporters or anion:anion exchange transporters. Some transport their substrate(s) with high affinities, while others transport it or them with relatively low affinities. Others may catalyze SO2−
4:HCO−
3 exchange, or more generally, anion:anion antiport. For example, the mouse homologue, SLC26A6, can transport sulfate, formate, oxalate, chloride and bicarbonate, exchanging any one of these anions for another. A cyanobacterial homologue can transport nitrate. Some members can function as channels. SLC26A3 and SLC26A6 can function as carriers or channels, depending on the transported anion. In these porters, mutating a glutamate, also involved in transport in the CIC family, created a channel out of the carrier. It also changed the stoichiometry from 2Cl−/HCO−
3 to 1Cl−/HCO−
3.

Natural resistance-associated macrophage protein Family of transport proteins

Natural resistance-associated macrophage proteins (Nramps), also known as metal ion (Mn2+-iron) transporters (TC# 2.A.55), are a family of metal transport proteins found throughout all domains of life. Taking on an eleven-helix LeuT fold, the Nramp family is a member of the large APC Superfamily of secondary carriers. They transport a variety of transition metals such as manganese, cadmium, and manganese using an alternating access mechanism characteristic of secondary transporters.

The potassium (K+) uptake permease (KUP) family (TC# 2.A.72) is a member of the APC superfamily of secondary carriers. Proteins of the KUP/HAK/KT family include the KUP (TrkD) protein of E. coli and homologues in both Gram-positive and Gram-negative bacteria. High affinity (20 μM) K+ uptake systems (Hak1, TC# 2.A.72.2.1) of the yeast Debaryomyces occidentalis as well as the fungus, Neurospora crassa, and several homologues in plants have been characterized. Arabidopsis thaliana and other plants possess multiple KUP family paralogues. While many plant proteins cluster tightly together, the Hak1 proteins from yeast as well as the two Gram-positive and Gram-negative bacterial proteins are distantly related on the phylogenetic tree for the KUP family. All currently classified members of the KUP family can be found in the Transporter Classification Database.

The Ca2+:cation antiporter (CaCA) family (TC# 2.A.19) is a member of the cation diffusion facilitator (CDF) superfamily. This family should not be confused with the Ca2+:H+ Antiporter-2 (CaCA2) Family (TC# 2.A.106) which belongs to the Lysine Exporter (LysE) Superfamily. Proteins of the CaCA family are found ubiquitously, having been identified in animals, plants, yeast, archaea and divergent bacteria. Members of this family facilitate the antiport of calcium ion with another cation.

Lysine Exporters are a superfamily of transmembrane proteins which export amino acids, lipids and heavy metal ions. They provide ionic homeostasis, play a role in cell envelope assembly, and protect from excessive concentrations of heavy metals in cytoplasm. The superfamily was named based on the early discovery of the LysE carrier protein of Corynebacterium glutamicum.

Divalent anion:Na+ symporters were found in bacteria, archaea, plant chloroplasts and animals.

The Citrate-Mg2+:H+ (CitM) / Citrate-Ca2+:H+ (CitH) Symporter (CitMHS) Family (TC# 2.A.11) is a family of transport proteins belonging to the Ion transporter superfamily. Members of this family are found in Gram-positive and Gram-negative bacteria, archaea and possibly eukaryotes. These proteins all probably arose by an internal gene duplication event. Lensbouer & Doyle (2010) have reviewed these systems, classifying the porters with three superfamilies, according to ion-preference:

The NhaB family belongs to the ion transporter (IT) superfamily. A representative list of proteins belonging to the NhaB family can be found in the Transporter Classification Database.

The Reduced Folate Carrier (RFC) Family is a group of transport proteins that is part of the major facilitator superfamily. RFCs take up folate, reduced folate, derivatives of reduced folate and the drug, methotrexate.

References

  1. ↑ Saier MH, Eng BH, Fard S, Garg J, Haggerty DA, Hutchinson WJ, Jack DL, Lai EC, Liu HJ, Nusinew DP, Omar AM, Pao SS, Paulsen IT, Quan JA, Sliwinski M, Tseng TT, Wachi S, Young GB (February 1999). "Phylogenetic characterization of novel transport protein families revealed by genome analyses". Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes. 1422 (1): 1–56. doi:10.1016/s0304-4157(98)00023-9. PMID   10082980.
  2. 1 2 Matsuda N, Kobayashi H, Katoh H, Ogawa T, Futatsugi L, Nakamura T, Bakker EP, Uozumi N (December 2004). "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): 54952–62. doi: 10.1074/jbc.M407268200 . PMID   15459199.
  3. 1 2 Yu FH, Yarov-Yarovoy V, Gutman GA, Catterall WA (December 2005). "Overview of molecular relationships in the voltage-gated ion channel superfamily". Pharmacological Reviews. 57 (4): 387–95. doi:10.1124/pr.57.4.13. PMID   16382097. S2CID   2643413.
  4. 1 2 Kato Y, Sakaguchi M, Mori Y, Saito K, Nakamura T, Bakker EP, Sato Y, Goshima S, Uozumi N (May 2001). "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): 6488–93. Bibcode:2001PNAS...98.6488K. doi: 10.1073/pnas.101556598 . PMC   33495 . PMID   11344270.
  5. ↑ Zeng GF, Pypaert M, Slayman CL (January 2004). "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): 3003–13. doi: 10.1074/jbc.M309760200 . PMID   14570869.
  6. ↑ "2.A.38 The K+ Transporter (Trk) Family". TCDB. Retrieved 2016-04-16.
  7. ↑ Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL (January 2000). "The Pfam protein families database". Nucleic Acids Research. 28 (1): 263–6. doi:10.1093/nar/28.1.263. PMC   102420 . PMID   10592242.
  8. 1 2 Roosild TP, Miller S, Booth IR, Choe S (June 2002). "A mechanism of regulating transmembrane potassium flux through a ligand-mediated conformational switch". Cell. 109 (6): 781–91. doi: 10.1016/s0092-8674(02)00768-7 . PMID   12086676. S2CID   9265433.

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