WORKLIST ENTRIES (1): KCNE2CHANNEL View alignment KCNE voltage-gated K+ channel subfamily E2 signature Type of fingerprint: COMPOUND with 4 elements Links: PRINTS; PR01491 KVCHANNEL; PR00168 KCNECHANNEL; PR01604 KCNE1CHANNEL PRINTS; PR01606 KCNE3CHANNEL Creation date 12-SEP-2001 1. MILLER, C. An overview of the potassium channel family. GENOME BIOL. 1(4) 1-5 (2000). 2. CONLEY, E.C. AND BRAMMAR, W.J. MinK. IN THE ION CHANNEL FACTSBOOK, VOLUME IV, ACADEMIC PRESS, 1999, PP.703-767. 3. ABBOT, G.W., SESTI, F., SPLAWSKI, I., BUCK, M.E., LEHMANN, M.H., TIMOTHY, K.W., KEATING, M.T. AND GOLDSTEIN, S.A.N. MiRP1 forms IKr potassium channels with HERG and is associated with cardiac arrhythmia. CELL 97 175-187 (1999). 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 . Some types of K+ channel are closed at the resting potential of the cell, but open on membrane depolarisation, and are thus known as voltage-gated channels. Each of these types of channel typically comprises 4 pore-forming alpha subunits that may associate with one of a number of different types of beta subunit. Two types of beta subunit (KCNE and KCNAB) are presently known to associate with voltage-gated alpha subunits (Kv, KCNQ and eag-like). However, not all combinations of alpha and beta subunits are possible. The KCNE family of K+ channel subunits are membrane glycoproteins that possess a single transmembrane (TM) domain. They share no structural relationship with the alpha subunit proteins, which possess pore forming domains. The subunits appear to have a regulatory function, modulating the kinetics and voltage dependence of the alpha subunits of voltage-dependent K+ channels . KCNE subunits are formed from short polypeptides of ~130 amino acids, and are divided into five subfamilies: KCNE1 (MinK/IsK), KCNE2 (MiRP1), KCNE3 (MiRP2), KCNE4 (MiRP3) and KCNE1L (AMMECR2). KCNE2 subunits associate with the eag-like HERG alpha subunits, which are the pore-forming subunits of cardiac IKr channels. Channels formed solely from HERG subunits display similar properties to native IKr channels; however, they differ in their gating and single channel conductance. Channels formed from both KCNE2 and HERG exhibit properties that are identical to those seen in native IKr channels. Three mutations in the KCNE2 gene are associated with long QT syndrome and ventricular fibrillation. These mutations result in channels that open slower and close more rapidly, the net effect being a reduced K+ current . KCNE2CHANNEL is a 4-element fingerprint that provides a signature for the KCNE voltage-gated K+ channel subfamily E2. The fingerprint was derived from an initial alignment of 2 sequences: the motifs were drawn from conserved regions spanning the N- and C-terminal portions of the alignment, focusing on those sections that characterise the KCNE2 subunits but distinguish them from the rest of the KCNE family - motifs 1-3 lie in the extracellular N-terminus; and motif 4 resides in the cytoplasmic C-terminus. Two iterations on SPTR39.22_17.3f were required to reach convergence, at which point a true set comprising 3 sequences was identified. SUMMARY INFORMATION 3 codes involving 4 elements 0 codes involving 3 elements 0 codes involving 2 elements COMPOSITE FINGERPRINT INDEX 4| 3 3 3 3 3| 0 0 0 0 2| 0 0 0 0 --+--------------------- | 1 2 3 4 True positives.. MIR1_RAT Q9D808 MIR1_HUMAN PROTEIN TITLES MIR1_RAT MINIMUM POTASSIUM ION CHANNEL-RELATED PEPTIDE 1 (MIRP1) (MIN Q9D808 2200002I16RIK PROTEIN - Mus musculus (Mouse). MIR1_HUMAN MINIMUM POTASSIUM ION CHANNEL-RELATED PEPTIDE 1 (MIRP1) (MIN
SCAN HISTORY SPTR39.22_17.3f 2 200 NSINGLE INITIAL MOTIF SETS KCNE2CHANNEL1 Length of motif = 15 Motif number = 1 KCNE voltage-gated K+ channel subfamily E2 motif I - 1 PCODE ST INT TQTLEDVFRRIFITY MIR1_HUMAN 8 8 TQTLEDAFKKVFITY MIR1_RAT 8 8 KCNE2CHANNEL2 Length of motif = 14 Motif number = 2 KCNE voltage-gated K+ channel subfamily E2 motif II - 1 PCODE ST INT MDNWRQNTTAEQEA MIR1_HUMAN 23 0 MDSWRRNTTAEQQA MIR1_RAT 23 0 KCNE2CHANNEL3 Length of motif = 12 Motif number = 3 KCNE voltage-gated K+ channel subfamily E2 motif III - 1 PCODE ST INT LQAKVDAENFYY MIR1_HUMAN 37 0 LQARVDAENFYY MIR1_RAT 37 0 KCNE2CHANNEL4 Length of motif = 13 Motif number = 4 KCNE voltage-gated K+ channel subfamily E2 motif IV - 1 PCODE ST INT SQILNLEESKATI MIR1_HUMAN 98 49 SQILHLEDSKATI MIR1_RAT 98 49 FINAL MOTIF SETS KCNE2CHANNEL1 Length of motif = 15 Motif number = 1 KCNE voltage-gated K+ channel subfamily E2 motif I - 2 PCODE ST INT TQTLEDAFKKVFITY MIR1_RAT 8 8 TQTLEDAFKKIFITY Q9D808 8 8 TQTLEDVFRRIFITY MIR1_HUMAN 8 8 KCNE2CHANNEL2 Length of motif = 14 Motif number = 2 KCNE voltage-gated K+ channel subfamily E2 motif II - 2 PCODE ST INT MDSWRRNTTAEQQA MIR1_RAT 23 0 MDSWRRNTTAEEQA Q9D808 23 0 MDNWRQNTTAEQEA MIR1_HUMAN 23 0 KCNE2CHANNEL3 Length of motif = 12 Motif number = 3 KCNE voltage-gated K+ channel subfamily E2 motif III - 2 PCODE ST INT LQARVDAENFYY MIR1_RAT 37 0 LQARVDAENFYY Q9D808 37 0 LQAKVDAENFYY MIR1_HUMAN 37 0 KCNE2CHANNEL4 Length of motif = 13 Motif number = 4 KCNE voltage-gated K+ channel subfamily E2 motif IV - 2 PCODE ST INT SQILHLEDSKATI MIR1_RAT 98 49 SQILHLEDSKATI Q9D808 98 49 SQILNLEESKATI MIR1_HUMAN 98 49
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