WORKLIST ENTRIES (1): KV34CHANNEL View alignment Kv3.4 voltage-gated K+ channel signature Type of fingerprint: COMPOUND with 5 elements Links: PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL; PR01495 SHABCHANNEL PRINTS; PR01496 SHAKERCHANEL; PR01497 SHALCHANNEL; PR01492 KV6CHANNEL PRINTS; PR01493 KV8CHANNEL; PR01494 KV9CHANNEL; PR01498 SHAWCHANNEL PRINTS; PR01581 KV31CHANNEL; PR01582 KV33CHANNEL Creation date 11-SEP-2001 1. MILLER, C. An overview of the potassium channel family. GENOME BIOL. 1(4) 1-5 (2000). 2. ASHCROFT, F.M. Voltage-gated K+ channels. IN ION CHANNELS AND DISEASE, ACADEMIC PRESS, 2000, PP.97-123. 3. SANSOM, M.S. Putting the parts together. CURR.BIOL. 9(19) R738-R741 (1999). 4. CONLEY, E.C. AND BRAMMAR, W.J. Shaw. IN THE ION CHANNEL FACTSBOOK, VOLUME IV, ACADEMIC PRESS, 1999, PP.559-614. Potassium ion (K+) channels are a structurally diverse group of proteins that facilitate the flow of K+ ions across cell membranes. They are ubiquitous, being present in virtually all cell types. Activation of K+ channels tends to hyperpolarise cells, reducing the membrane's electrical resistance, dampening nervous activity. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, and act as effectors in signal transduction pathways involving G protein- coupled receptors (GPCRs). In prokaryotic cells, they play a role in the maintenance of ionic homeostasis . Structurally, Kv channels belong to the subfamily of K+ channels whose subunits contain 6 transmembrane (TM) domains: these are the voltage- gated K+ (Kv) channels, the KCNQ channels, the EAG-like K+ channels and 3 kinds of Ca2+-activated K+ channels (BK, IK and SK) . All K+ channels share a characteristic sequence feature: a TMxTVGYG motif that resides between the 2 C-terminal membrane spanning helices, and forms the K+-selective pore domain [1-2]. The Kv family can be divided into 4 subfamilies on the basis of sequence similarity and function: Shaker (Kv1), Shab (Kv2), Shaw (Kv3) and Shal (Kv4). All consist of pore-forming alpha subunits that associate with different types of beta subunit. To form a functional K+ channel pore, 4 alpha subunits and 4 beta subunits are required. The alpha subunits have 6 well-conserved TM domains, a pore loop region and variable length N- and C-termini. TM domains 5 and 6, and the loop region, form the K+ channel pore through which the K+ ions pass . The shaw gene was first isolated from Drosophila. Several vertebrate K+ channels with similar amino acid sequences were subsequently found and, together with the Drosophila Shaw channel, now constitute the Shaw (Kv3) family. These channels are thought to play a role in shortening of action potential durations and modulating pre-synaptic neurotransmitter release. In mammals, the family consists of 4 genes (Kv3.1, Kv3.2, Kv3.3 and Kv3.4). Each gene product has its own subcellular location and function . Kv3.4 channels are expressed in cells that surround the cerebellar Purkinje cells. In the presence of protein kinase C, rapid inactivation is eliminated, resulting in a non-inactivating delayed rectifying current. The implications of this are seen for signal encoding in the central nervous system . KV34CHANNEL is a 5-element fingerprint that provides a signature for the Kv3.4 voltage-gated K+ channel. The fingerprint was derived from an initial alignment of 3 sequences: the motifs were drawn from conserved regions spanning the full alignment length - motifs 1-4 lie in the N-terminus; and motif 5 is situated in the C-terminus. A single iteration on SPTR39.22_17.3f was required to reach convergence, no further sequences being identified beyond the starting set. SUMMARY INFORMATION 3 codes involving 5 elements 0 codes involving 4 elements 0 codes involving 3 elements 0 codes involving 2 elements COMPOSITE FINGERPRINT INDEX 5| 3 3 3 3 3 4| 0 0 0 0 0 3| 0 0 0 0 0 2| 0 0 0 0 0 --+-------------------------- | 1 2 3 4 5 True positives.. CIKG_HUMAN Q9H1V7 CIKG_RAT PROTEIN TITLES CIKG_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 (KSHIIIC) - Ho Q9H1V7 DJ1003J2.3.1 (POTASSIUM VOLTAGE-GATED CHANNEL, SHAW-RELATED CIKG_RAT VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 (RAW3) - Rattu
SCAN HISTORY SPTR39.22_17.3f 1 100 NSINGLE INITIAL MOTIF SETS KV34CHANNEL1 Length of motif = 14 Motif number = 1 Kv3.4 voltage-gated K+ channel motif I - 1 PCODE ST INT KPPSKTCLKEEMAK CIKG_HUMAN 18 18 KPPSKTCLKEEMAK CIKG_RAT 18 18 KPPSKTCLKEEMAK Q9H1V7 18 18 KV34CHANNEL2 Length of motif = 12 Motif number = 2 Kv3.4 voltage-gated K+ channel motif II - 1 PCODE ST INT DPDGGGRPETDG CIKG_HUMAN 67 35 DPDGGGRPESDG CIKG_RAT 67 35 DPDGGGRPETDG Q9H1V7 67 35 KV34CHANNEL3 Length of motif = 12 Motif number = 3 Kv3.4 voltage-gated K+ channel motif III - 1 PCODE ST INT DEAGDDERELAL CIKG_HUMAN 175 96 DEAGDDERELAL CIKG_RAT 176 97 DEAGDDERELAL Q9H1V7 175 96 KV34CHANNEL4 Length of motif = 17 Motif number = 4 Kv3.4 voltage-gated K+ channel motif IV - 1 PCODE ST INT RLGPHEGGAGHGAGSGG CIKG_HUMAN 188 1 RLGPHEGGSGPGAGSGG CIKG_RAT 189 1 RLGPHEGGAGHGAGSGG Q9H1V7 188 1 KV34CHANNEL5 Length of motif = 17 Motif number = 5 Kv3.4 voltage-gated K+ channel motif V - 1 PCODE ST INT SEETSPRDSTCSDTSPP CIKG_HUMAN 510 305 SEETSPRDSTYSDTSPP CIKG_RAT 511 305 SEETSPRDSTCSDTSPP Q9H1V7 510 305 FINAL MOTIF SETS KV34CHANNEL1 Length of motif = 14 Motif number = 1 Kv3.4 voltage-gated K+ channel motif I - 1 PCODE ST INT KPPSKTCLKEEMAK CIKG_HUMAN 18 18 KPPSKTCLKEEMAK Q9H1V7 18 18 KPPSKTCLKEEMAK CIKG_RAT 18 18 KV34CHANNEL2 Length of motif = 12 Motif number = 2 Kv3.4 voltage-gated K+ channel motif II - 1 PCODE ST INT DPDGGGRPETDG CIKG_HUMAN 67 35 DPDGGGRPETDG Q9H1V7 67 35 DPDGGGRPESDG CIKG_RAT 67 35 KV34CHANNEL3 Length of motif = 12 Motif number = 3 Kv3.4 voltage-gated K+ channel motif III - 1 PCODE ST INT DEAGDDERELAL CIKG_HUMAN 175 96 DEAGDDERELAL Q9H1V7 175 96 DEAGDDERELAL CIKG_RAT 176 97 KV34CHANNEL4 Length of motif = 17 Motif number = 4 Kv3.4 voltage-gated K+ channel motif IV - 1 PCODE ST INT RLGPHEGGAGHGAGSGG CIKG_HUMAN 188 1 RLGPHEGGAGHGAGSGG Q9H1V7 188 1 RLGPHEGGSGPGAGSGG CIKG_RAT 189 1 KV34CHANNEL5 Length of motif = 17 Motif number = 5 Kv3.4 voltage-gated K+ channel motif V - 1 PCODE ST INT SEETSPRDSTCSDTSPP CIKG_HUMAN 510 305 SEETSPRDSTCSDTSPP Q9H1V7 510 305 SEETSPRDSTYSDTSPP CIKG_RAT 511 305
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