1.A.2 The Inward Rectifier K+ Channel (IRK-C) Family
IRK or GIRK channels possess the ''minimal channel-forming structure'' with only a P domain, characteristic of the channel proteins of the VIC family (TC #1.A.1), and two flanking transmembrane spanners. They may exist in the membrane as homo- or heterooligomers. They have a greater tendency to let K flow into the cell than out. Voltage-dependence may be regulated by external K+ , by internal Mg2+ , by internal ATP and/or by G-proteins. The P domains of IRK channels exhibit limited sequence similarity to those of the VIC family. Inward rectifiers play a role in setting cellular membrane potentials, and closing of these channels upon depolarization permits the occurrence of long duration action potentials with a plateau phase. Inward rectifiers lack the intrinsic voltage sensing helices found in many VIC family channels. In a few cases, those of Kir1.1a, Kir6.1 and Kir6.2, for example, direct interaction with a member of the ABC superfamily has been proposed to confer unique functional and regulatory properties to the heteromeric complex, including sensitivity to ATP. These ATP-sensitive channels are found in many body tissues. They render channel activity responsive to the cytoplasmic ATP/ADP ratio (increased ATP/ADP closes the channel). The human SUR1 and SUR2 sulfonylurea receptors (spQ09428 and Q15527, respectively) are the ABC proteins that regulate both the Kir6.1 and Kir6.2 channels in response to ATP, and CFTR (TC #3.A.1.208.4) may regulate Kir1.1a.
Mutations in SUR1 are the cause of familial persistent hyperinsulinemic hypoglycemia in infancy (PHHI), an autosomal recessive disorder characterized by unregulated insulin secretion in the pancreas. SUR1 has two nucleotide binding domains, NBD1 (binds ATP) and NBD2 (binds Mg-ADP). Both NBDs mediate nucleotide regulation of pore activity. Kir6.2, unlike many other Kir channels, cannot form plasma membrane functional channels when expressed without SUR1. This is due to a trafficking signal in SUR1 (Partridge et al., 2001). Epsilon toxin from Clostridium perfringens causes inhibition of potassium inward rectifier (Kir) channels, possibly by an indirect mechanism, in oligodendrocytes (Bossu et al. 2020).
The crystal structure (Kuo et al., 2003) and function (Enkvetchakul et al., 2004) of bacterial members of the IRK-C family have been determined. KirBac1.1, from Burkholderia pseudomallei, is 333 aas long with two N-terminal TMSs flanking a P-loop (residues 1-150), and the C-terminal half of the protein is hydrophilic. It transports monovalent cations with the selectivity: K ~ Rb ~ Cs >> Li ~ Na ~ NMGM (protonated N-methyl-D-glucamine). Activity is inhibited by Ba2* , Ca2+ and low pH (Enkvetchakul et al., 2004).
Kir3 channels control heart rate and neuronal excitability through GTP-binding (G) proteins and phosphoinositide signaling pathways (Doupnik 2008). These channels were the first characterized effectors of the betagamma subunits of G proteins. The crystal structure of a chimera between the cytosolic domain of a mammalian Kir3.1 and the transmembrane region of a prokaryotic KirBac1.3 (Kir3.1 chimera) provided structural insight. This channel has been functionally reconstituted in planar lipid bilayers (Leal-Pinto et al. 2010). The chimera behaved like a Kir channel, displaying a requirement for PIP(2) and Mg2+-dependent inward rectification. The channel was blocked by external tertiapin Q. The three-dimensional reconstruction of the chimera by single particle electron microscopy revealed a structure consistent with the crystal structure. Channel activity could be stimulated by ethanol and activated G proteins but the presence of both activated G-alpha and G-betagamma subunits was required for gating.
GIRK (Kir3) channels are members of the large family of inwardly rectifying potassium channels (Kir1-Kir7). GIRK channels, like all other Kir channels, possess an extrinsic mechanism of inward rectification involving intracellular Mg2+ and polyamines that occlude the conduction pathway at membrane potentials positive to EK. More than 20 high-resolution atomic structures containing GIRK channel cytoplasmic domains and transmembrane domains have been solved. These structures have provided valuable insight into the structural determinants of many of the properties common to all inward rectifiers, such as permeation and rectification, as well as revealing the structural bases for GIRK channel gating (Glaaser and Slesinger 2015).
GIRK channels are abundantly expressed in the heart and require that phosphatidylinositol bisphosphate (PIP2) is present so that intracellular channel-gating regulators such as Gbetagamma (Gβγ)and Na+ ions maintain the channel-open state. Li et al. 2019 determined how each regulator uses the channel domain movements to control gate transitions. Na+ controls the cytosolic gate of the channel through an anti-clockwise rotation, whereas Gbetagamma stabilizes the transmembrane gate in the open state through a rocking movement of the cytosolic domain. Both effects altered the way by which the channel interacts with PIP2 and thereby stabilized the open states of the respective gates (Li et al. 2019).
The generalized transport reaction catalyzed by IRK-C family proteins is:
K+ (out) K+ (in)
ATP-activated inward rectifier K+ channel, IRK1 (also called ROMK or KIR1.1) (regulated by Sur1, allowing ATP sensitivity; also activated by phosphatidylinositol 4,5-bisphosphate (PIP) with affinity to PIP controlled by protein kinase A phosphorylation (which increases affinity for PIP) and protein kinase C phosphorylation (which decreases affinity for PIP (Zeng et al., 2003). The mechanism of voltage sensitivity of IRK1 inward-rectifier K+ channel block by the polyamine, spermine, has been proposed (Shin and Lu 2005). A putative pH sensor has been identified (Rapedius et al. 2006). Closure of the Kir1.1 pH gate results from steric occlusion of the permeation path by the convergence of four leucines (or phenylalanines) at the cytoplasmic apex of the inner transmembrane helices. In the open state, K+ crosses the pH gate together with its hydration shell (Sackin et al. 2005). Alternariol (AOH), the most important mycotoxin produced by Alternaria species, which are the most common mycoflora infecting small grain cereals worldwide, causes loss of cell viability by inducing apoptosis. AOH-induced apoptosis through a mitochondria-dependent pathway is characterized by p53 activation, an opening of the mitochondrial permeability transition pore (PTP), loss of mitochondrial transmembrane potential (ΔΨm), a downstream generation of O2- and caspase 9 and 3 activation (Bensassi et al., 2012). Pharmacological inhibition of renal ROMK causes diuresis and natriuresis in the absence of kaliuresis (Garcia et al. 2013). Cholesterol binding sites in KIR channels have been identified (Rosenhouse-Dantsker 2019). The ubiquitously expressed family of inward rectifier potassium (KIR) channels, encoded by KCNJ genes, is primarily involved in cell excitability and potassium homeostasis. Disease-associated mutations in KIR proteins have been linked to aberrant inward rectifier channel trafficking (Zangerl-Plessl et al. 2019).
IRK1 of Homo sapiens (P48048)
G-protein-activated inward rectifying K+ channel, Kir3.2, KATP2, KCNJ7 or GIRK2 of 423 aas (Inanobe et al., 2011; Yokogawa et al. 2011). Important in regulating heart rate and neuronal excitability. Activated by binding of the βγ-subunit complex to the cytoplasmic pore gate (Yokogawa et al. 2011). Chen et al. 2017 found that the G-protein-gated inwardly rectifying K+ (GIRK) channel is activated by Ivermectin (IVM) directly. Cholesterol binds to and upregulates GIRK channels (GIRK2 and 4), and the binding sites have been determined (Rosenhouse-Dantsker 2018). An inherited gain-of-function mutation in the human GIRK3.4 causes familial human sinus node dysfunction (SND). The increased activity of GIRK channels is likely to lead to a sustained hyperpolarization of pacemaker cells and thereby reduces heart rate (Kuß et al. 2019). GIRK2 channels are abundantly expressed in the heart and require that phosphatidylinositol bisphosphate (PIP2) is present so that intracellular channel-gating regulators such as Gbetagamma (Gβγ)and Na+ ions maintain the channel-open state. Li et al. 2019 determined how each regulator uses the channel domain movements to control gate transitions. Na+ controls the cytosolic gate of the channel through an anti-clockwise rotation, whereas Gbetagamma stabilizes the transmembrane gate in the open state through a rocking movement of the cytosolic domain. Both effects altered the way by which the channel interacts with PIP2 and thereby stabilized the open states of the respective gates (Li et al. 2019).
Kir3.2 of Homo sapiens (P48051)
Inward rectifying potassium channel 16, Kir5.1 or KCNJ16. (Potassium channel subfamily J member 16). Involved in pH and fluid regulation. Forms heteromers with Kir4.1/KCNJ10 or Kir2.1/KCNJ2. MAGI-1 anchors Kir4.1 channels (Kir4.1 homomer and Kir4.1/Kir5.1 heteromer) and contributes to basolateral K+ recycling. The Kir4.1 A167V mutation is associated with EAST/SeSAME syndrome caused by mistrafficking of the mutant channels and inhibiting their expression on the basolateral surface of tubular cells. These findings suggest that mislocalization of the Kir4.1 channels contributes to renal salt wasting. (Tanemoto et al. 2014).
KCNJ16 of Homo sapiens
G protein-activated inward rectifying K+ channel 1 (Kir3.1; IRK3; KCNJ3; GIRK1). Regulates the heartbeat in humans. Phosphatidylinositol bisphosphate (PIP2) activates by opening the intracelluar G-loop gate (Meng et al., 2012). Along the ion permeation pathway, three relatively narrow regions (the selectivity filter, the inner helix bundle crossing, and the cytosolic G loop) may serve as gates to control ion permeation (Meng et al. 2016). Cholesterol up-regulates neuronal GIRK channel activity (Bukiya et al. 2017). Changes in the levels of cholesterol and PI(4,5)P2 may act in concert to provide fine-tuning of Kir3 channel function (Bukiya et al. 2017). Kir3.1 forms oligomers with Kir3.4 (TC# 1.A.2.1.3) and transporters Rb+ and spermine. It has been suggested that the selectivity filter is responsible for inward rectification and agonist activation as well as permeation and block (Makary et al. 2006). Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification (Pegan et al. 2005).
Kir3.1 (IRK3) of Homo sapiens (P48549)
ATP-sensitive inward rectifying K+ channel 8, KCNJ8 or Kir6.1. It acts with Sur2B (3.A.1.208.23). Channel activity is inhibited in oxidative stress via S-glutathionylation (Yang et al., 2011). Oxidative sensitivity is dependent on Cys176 (Yang et al., 2011). These proteins comprise part of a glucose sensing mechanism (Rufino et al. 2013). It may play a role in limb wound repair and regeneration (Zhang et al. 2020). It is inhibited by glibenclamide (glyburide), an antidiabetic sulfonylurea used in the treatment of type II diabetes (Fernandes et al. 2004).
Kir6.1 of Homo sapiens (Q15842)
Inward rectifying potassium (K+) (IRK) channel of 426 aas and 2 TMSs, AgaP.
AgaP of Anopheles gambiae (African malaria mosquito)
Kir1 (AgaP) K+ channel of 444 aas and 2 TMSs.
Kir1 of Anopheles gambiae (African malaria mosquito)
Inward rectifying K+ channel, Kir4.1, encoded by the KCNJ10 gene, of 379 aas and 2 TMSs. It is inhibited by chloroethylclonidine and pentamidine which bind in the channel (Rodríguez-Menchaca et al. 2016; Aréchiga-Figueroa et al. 2017). It is also inhibited by chloropuine which inhibits by an open pore blocking mecnanism (Marmolejo-Murillo et al. 2017). Loss-of-function mutations in the pore-forming Kir4.1 subunit cause an autosomal recessive disorder characterized by epilepsy, ataxia, sensorineural deafness and tubulopathy (SeSAME/EST syndrome) Pentamidine potently inhibited Kir4.1 channels when applied to the cytoplasmic side under inside-out patch clamp configuration (IC50 = 97nM). The block was voltage dependent. Molecular modeling predicted the binding of pentamidine to the transmembrane pore region of Kir4.1 at amino acids T127, T128 and E158. Mutation of each of these residues reduced the potency of pentamidine to block Kir4.1 channels (Aréchiga-Figueroa et al. 2017). Mutations in the KCNJ10 gene are associated with a distinctive ataxia, sensorineural hearing loss and a spasticity (Morin et al. 2020).
Kir4.1 of Homo sapiens
KCNJ11 or Kir6.2 or KATP of 390 aas; 96% identical to the rat homologue, TC# 1.A.2.1.7. Congenital hyperinsulinism (CHI) is characterized by persistent insulin secretion despite severe hypoglycemia. Mutations in the pancreatic ATP-sensitive K+ (K(ATP)) channel proteins sulfonylurea receptor 1 (SUR1) and Kir6.2, encoded by ABCC8 and KCNJ11, respectively, is the most common cause of the disease. Many mutations in SUR1 render the channel unable to traffic to the cell surface, thereby reducing channel function. Many studies have shown that for some SUR1 trafficking mutants, the defects could be corrected by treating cells with sulfonylureas or diazoxide (Yan et al. 2007). Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. Their voltage dependence is regulated by the concentration of extracellular potassium; as external potassium is raised, the voltage range of the channel opening shifts to more positive voltages. The inward rectification is mainly due to the blockage of outward current by internal magnesium (Tammaro and Ashcroft 2007). Kir6.2 is an ATP-sensitive potassium (KATP) channel coupling cell metabolism to electrical activity by regulating K+ fluxes across the plasma membrane. Channel closure is facilitated by ATP, which binds to the pore-forming subunit (Kir6.2). Conversely, channel opening is potentiated by phosphoinositol bisphosphate (PIP2), which binds to Kir6.2 and reduces channel inhibition by ATP. The PIP2 binding site has been identified (Haider et al. 2007). KATP channels are metabolic sensors that couple cell energetics to membrane excitability. In pancreatic beta-cells, channels formed by SUR1 and Kir6.2 regulate insulin secretion and are the targets of antidiabetic sulfonylureas. Martin et al. 2017 used cryo-EM to elucidate the structural basis of channel assembly and gating. The structure, determined in the presence of ATP and the sulfonylurea, glibenclamide, at ~6 Å resolution, revealed a closed Kir6.2 tetrameric core with four peripheral SUR1s, each anchored to a Kir6.2 by its N-terminal transmembrane domain (TMD0). Intricate interactions between TMD0, the loop following TMD0, and Kir6.2 near the proposed PIP2 binding site, and where ATP density is observed, suggest that SUR1 may contribute to ATP and PIP2 binding to enhance Kir6.2 sensitivity to both. The SUR1-ABC core is found in an unusual inward-facing conformation whereby the two nucleotide binding domains are misaligned along a two-fold symmetry axis, revealing a possible mechanism by which glibenclamide inhibits channel activity (Martin et al. 2017). a cryo-EM structure of a hamster SUR1/rat Kir6.2 channel bound to a high-affinity sulfonylurea drug glibenclamide and ATP has been solved at 3.63 Å resolution. The structure shows that glibenclamide is lodged in the transmembrane bundle of the SUR1-ABC core connected to the first nucleotide binding domain near the inner leaflet of the lipid bilayer (Martin et al. 2017). The activation of K(ATP) channels contributes to the shortening of action potential duration but is not the primary cause of extracellular K+ accumulation during early myocardial ischemia (Saito et al. 2005).
Kir6.2 of Homo sapiens
Inward rectifier potassium channel 4, KCNJ4, IRK3 or 4, of 445 aas. Its voltage dependence is regulated by the concentration of extracellular potassium; as external potassium is raised, the voltage range of the channel opening shifts to more positive voltages. The inward rectification is mainly due to the blockage of outward current by internal magnesium, and it can be blocked by extracellular barium and cesium. It may play a role in the control of polyamine-mediated channel gating and in the blocking by intracellular magnesium. Overexpression of KCNJ4 correlates with cancer progression and nfavorable prognosis in lung adenocarcinoma (Wu and Yu 2019).
KMCJ4 of Homo sapiens
G protein-activated inward rectifier potassium channel 3, GIRK3 or KCNJ9 of 393 aas and 2 TMSs. It is expressed in sensory neurons and spinal cord and has uses both anterograde and retrograde axonal transport (Lyu et al. 2020).
GIRK3 of Homo sapiens
G-protein enhanced inward rectifier K channel 2, IRK1, IRK2, KCNJ2, KCNJ5, Kir2.1 (Andersen-Tawil Syndrome (ATS-1) protein; the V302M mutation causing the syndrome, alters the G-loop cytoplasmic K conduction pathway) (Bendahhou et al., 2003; Ma et al., 2007). (Blocked by chloroquine which binds in the cytoplasmic pore domain (Rodriguez-Menchaca et al., 2008)). Forms heteromultimers with Kir3.1 and Kir3.4 (Ishihara et al., 2009). A C-terminal domain is critical for the sensitivity of Kir2.1 to cholesterol (Epshtein et al., 2009). Flecainide increases Kir2.1 currents by interacting with cysteine 311, decreasing the polyamine-induced rectification (Caballero et al., 2010). The inhibitory cholesterol binding site has been identified (Fürst et al. 2014). Polyamines and Mg2+ block ion flux synergistically (Huang and Kuo 2016). Long polyamines serve a dual role as both blockers and coactivators (with PIP2) of Kir2.1 channels (Xie et al. 2005). Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification (Pegan et al. 2005). Loss-of-function mutations are a rare cause of long QT syndrome (Fodstad et al. 2004).
IRK2 of Homo sapiens (P63252)
G-protein activated IRK5 (Kir3.4, KCNJ5, GIRK4) channel. The p75 neurotrophin receptor mediates cell death by activating GIRK channels through phosphatidylinositol 4,5-bisphosphate (Coulson et al., 2008). Cholesterol up-regulates neuronal GIRK channel activity (Bukiya et al. 2017). Forms an oligomeric channel with Kir3.1, transporting K+, Rb+ and spermine. The selectivity filter may be responsible for inward rectification and agonist activation as well as permeation and block by Cs+ (Makary et al. 2006). Ivermictin activates GIRK channels in a PIP2-dependent manner (Chen et al. 2017).
IRK5 of Homo sapiens (P48544)
Hepatocyte basolateral inwardly rectifying K+ channel, Kir4.2, involved in bile secretion (Hill et al., 2002). This protein is 96% identical to the human KCNJ14 or KCNJ15 of 375 aas (Q99712).
Kir4.2 of Rattus norvegicus (Q91ZF1)
Cranial nerve inward rectifying K+ channel, Kir2.4 (IRK4) (Töpert et al., 1998). The human ortholog, of 436 aas, is 94% identical and is called KCMJ14 or IRK4.
Kir2.4 of Rattus norvegicus (O70596)
Kidney/pancreas/muscle ATP-senstive, ER/Golgi K+ channel, KATP or ROMK (Kir6.2) (Boim et al., 1995) (three alternatively spliced isoforms are called ROMK1-3). Involved in congenital hyperinsulinism (Lin et al., 2008). Regulated by Ankyrin-B (Li et al., 2010). ATP activates ATP-sensitive potassium channels composed of mutant sulfonylurea receptor 1 (SUR1) and Kir6.2 with diminished PIP2 sensitivity (Pratt and Shyng, 2011). This channel protects the myocardium from hypertrophy induced by pressure-overloading (Alvin et al., 2011). Domain organization studies show which domains in Sur and Kir6.2 interact (Wang et al. 2012). KATP channels consisting of Kir6.2 and SUR1 couple cell metabolism to membrane excitability and regulate insulin secretion in pancreatic beta cells, and mutations in the former protein can compensate for mutations in the latter (Zhou et al. 2013). Mutations cause inactivation of channel function by disrupting PIP2-dependent gating (Bushman et al. 2013). Thus, these proteins comprise part of the glucose sensing mechanism (Rufino et al. 2013). A single point mutation can confer voltage sensitivity (Kurata et al. 2010). Its involvement in type II diabetes has been reviewed by Bonfanti et al. 2015. KATP channels (Kir6.2/SUR1) in the brain and endocrine
pancreas couple metabolic status to the membrane potential. In beta-cells, increases in
cytosolic [ATP/ADP] inhibit KATP channel activity, leading to membrane depolarization and
exocytosis of insulin granules. Mutations in ABCC8 (SUR1) or KCNJ11 (Kir6.2) can result in gain or
loss of channel activity and cause neonatal diabetes (ND) or congenital hyperinsulinism (CHI),
respectively. Nucleotide binding without hydrolysis switches SUR1 to stimulatory conformations. Increased affinity for ATP gives rise to ND while decreased affinty gives rise to CHI (Ortiz and Bryan 2015). Kir6.2 can associate with either SUR1 (TC# 3.A.1.208.4) or SUR2A (TC# 3.A.1.208.23) to form heteroctamers, leading to different locations and consequences (Principalli et al. 2015). IATP channels and Ca2+ influx play roles in purinergic vasotoxicity and cell death (Shibata et al. 2018).
A cryo-EM structure of a hamster SUR1/rat Kir6.2 channel bound to a high-affinity sulfonylurea drug, glibenclamide, and ATP at 3.63 A resolution revealed details of the ATP and glibenclamide binding sites (Martin et al. 2017). The structure showed that glibenclamide lodges in the transmembrane bundle of the SUR1-ABC core connected to the first nucleotide binding domain near the inner leaflet of the lipid bilayer. Mutation of residues predicted to interact with glibenclamide led to reduced sensitivity to this drug (Martin et al. 2017).
ROMK of Rattus norvegicus (P70673)
The inward rectifier potassium channel 13, Kir 7.1, Kir1.4, or KCNJ13, of 360 aas and 2 TMSs. A splice variant expressed in mouse tissues shares organisational and functional properties with human leber amaurosis-causing mutations of this channel (Vera et al. 2019). In fact, mutations in KCNJ13 are associated with two retinal disorders; Leber congenital amaurosis (LCA) and snowflake vitreoretinal degeneration (SVD) (Toms et al. 2019). Pinacidil is a channel opener (Sun et al. 2019). It may play a role in the control of polyamine-mediated channel gating and in the blocking by intracellular magnesium.
Kir 7.1 or KCNJ13 of Homo sapiens (O60928)
The inward-rectifier K+ channel, Kir2.2, KCNJ12, KCNJN1, KCNJ18, IRK2, of 433 aas and 2 TMSs. The 3-d structure at 3.1 Å resolution is available (Tao et al., 2009). (It is 70% identical to Kir2.1 (TC # 1.A.2.1.2)). The structural basis of PIP2 activation of Kir2.2 has been presented (Hansen et al., 2011).
Kir2.2 of Homo sapiens (Q14500)
Prokaryotic K+-selective Kir channel KirBac1.1 (selectivity: K+ = Rb+ = Cs+ >> Li+, Na+ or NMGM) (Enkvetchakul et al., 2004), inward rectifying (Cheng et al., 2009). Closure of the Kir1.1 pH gate results from steric occlusion of the permeation path by the convergence of four leucines (or phenylalanines) at the cytoplasmic apex of the inner transmembrane helices. In the open state, K+ crosses the pH gate together with its hydration shell (Sackin et al. 2005). The inhibitory cholesterol binding site has been identified (Fürst et al. 2014). Conformational changes associated with an open activation gate have been identified, and these suggest a unique allosteric pathway that ties the selectivity filter to the activation gate through interactions between both transmembrane helices, the turret, the selectivity filter loop, and the pore helix. Specific residues involved in this conformational exchange that are highly conserved among human Kir channels have also been identified (Amani et al. 2020).
KirBac1.1 OF Burkholderia pseudomallei (IP7BA; gi33357898)
The KirBac3.1 K+ channel (a dimer of dimers with gating visualized by atomic force microscopy, Jaroslawski et al., 2007) (regulated by binding lipids, G-proteins, nucleotides, and ions (H+, Ca2+, and Mg2+)). The 3-D structure is available (1XL6_A). The inhibitory cholesterol binding site has been identified (Fürst et al. 2014).
KirBac3.1 of Magnetospirillum magnetotacticum (D9N164)
ATP-sensitive inward rectifying Kir K channel (Choi et al. 2010).
Kir K+ channel of Chromobacterium violaceum
Putative K+ channel
K+ channel of Synechocystis PCC 6803
Inward rectifier potassium channel
K+ channel of Burkholderia xenovorans