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PR01517

Identifier
KV42CHANNEL  [View Relations]  [View Alignment]  
Accession
PR01517
No. of Motifs
5
Creation Date
19-JUN-2001
Title
Kv4.2 voltage-gated K+ channel signature
Database References
PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL; PR01497 SHALCHANNEL
Literature References
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 BRAMMER, W.J.
Shal.
IN THE ION CHANNEL FACTSBOOK, VOLUME IV, ACADEMIC PRESS, 1999, PP.617-646.
 
5. TKATCH, T., BARANAUSKAS, G. AND SURMEIER, J.
K+ Current amplitude are linearly related in basal ganglia and basal
forebrain neurons.
J.NEUROSCIENCE 20(2) 579-588 (2000).
 
6. ADAMS, J.P., ANDERSON, A.E., VARGA, A.W., DINELEY, K.T., COOK, R.G.,
PFAFFINGER, P.J. AND SWEATT, J.D.
The A-type potassium channel Kv4.2 is a substrate for the mitogen-activated
protein kinase ERK.
J.NEUROCHEM. 75(6) 2277-87 (2000).

Documentation
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 [1].
      
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) [2]. 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 [3].
     
The first Shal (Kv4) sequence was found in Drosophila. Several vertebrate
K+ channels with similar amino acid sequences were subsequently found and,
together with the Drosophila Shal channel, now constitute the Shal (Kv4)
family. These channels support outward K+-selective currents and are
inhibited by free fatty acids [4]. The Shal family can be further divided 
into 3 families, designated Kv4.1, Kv4.2 and Kv4.3.
 
Kv4.2 channels are the major contributors to somatodendritic A-type K+
channels in the basal ganglia and basal forebrain neurons [5]. They are also
expressed in the heart and CNS. In rodents, they are an important
constituent of the cardiac transient outward current, Ito. In addition, they
have a predicted role in regulating neuronal transmission at post-synaptic 
loci in defined brain regions [4-5]. Kv4.2 channels contain a number of
conserved sites for mitogen-activated protein kinase ERK phosphorylation, 
suggesting that ERK may regulate potassium channel function by direct
phosphorylation [6].
 
KV42CHANNEL is a 5-element fingerprint that provides a signature for the
Kv4.2 voltage-gated K+ channel. The fingerprint was derived from an initial
alignment of 4 sequences: the motifs were drawn from conserved regions 
spanning virtually the full alignment length, focusing on those sections 
that characterise the Kv4.2 channels but distinguish them from other 
members of the Shal family - motifs 1 and 2 reside at the N-terminus; and
motifs 3-5 span the C-terminus. Two iterations on SPTR39_15f were required
to reach convergence, at which point a true set comprising 5 sequences was
identified. Two partial matches were also found, Q99249 and Q9JJ60, both of
which are closely related K+ channel proteins that match motifs 1-3.
Summary Information
   5 codes involving  5 elements
0 codes involving 4 elements
2 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
555555
400000
322200
200000
12345
True Positives
Q63881        Q9NZV8        Q9UBY7        Q9UNH9        
Q9Z0V2
True Positive Partials
Codes involving 3 elements
Q99249 Q9JJ60
Sequence Titles
Q63881      SHAL1 - Rattus norvegicus (Rat).              
Q9NZV8 VOLTAGE-GATED POTASSIUM CHANNEL KV4.2 - Homo sapiens (Human).
Q9UBY7 POTASSIUM CHANNEL KV4.2 - Homo sapiens (Human).
Q9UNH9 POTASSIUM CHANNEL KV4.2 - Homo sapiens (Human).
Q9Z0V2 POTASSIUM CHANNEL KV4.2 - Mus musculus (Mouse).

Q99249 POTASSIUM CHANNEL PROTEIN RK5 - Rattus norvegicus (Rat).
Q9JJ60 BRAIN CDNA, CLONE MNCB-7013, SIMILAR TO MUS MUSCULUS POTASSIUM CHANNEL KV4.2 MRNA - Mus musculus (Mouse).
Scan History
SPTR39_15f 2  80   NSINGLE    
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
PPRQERKRTQDAL Q9NZV8 30 30 -
PPRQERKRTQDAL Q9UNH9 30 30 -
PPRQERKRTQDAL Q9UBY7 30 30 -
PPRQERKRTQDAL Q9Z0V2 30 30 -

Motif 2 width=17
Element Seqn Id St Int Rpt
LQDDADTDTAGESALPT Q9NZV8 148 105 -
LQDDADTDTAGESALPT Q9UNH9 148 105 -
LQDDADTDTAGESALPT Q9UBY7 148 105 -
LQDDADTDNTGESALPT Q9Z0V2 148 105 -

Motif 3 width=13
Element Seqn Id St Int Rpt
EDEQAFVSKSGSS Q9NZV8 461 296 -
EDEPAFVSKSGSS Q9UNH9 461 296 -
EDEQAFVSKSGSS Q9UBY7 461 296 -
EDEPAFISKSGSS Q9Z0V2 461 296 -

Motif 4 width=14
Element Seqn Id St Int Rpt
QIRCVERTPLSNSR Q9NZV8 560 86 -
QIRCVERTPLSNSR Q9UNH9 560 86 -
QIRCVERTPLSNSR Q9UBY7 560 86 -
QIRCVERTPLSNSR Q9Z0V2 560 86 -

Motif 5 width=13
Element Seqn Id St Int Rpt
MEECVKLNCEQPY Q9NZV8 580 6 -
MEECVKLNCEQPY Q9UNH9 580 6 -
MEECVKLNCEQPY Q9UBY7 580 6 -
MEECVKLNCEQPY Q9Z0V2 580 6 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
PPRQERKRTQDAL Q9NZV8 30 30 -
PPRQERKRTQDAL Q9UNH9 30 30 -
PPRQERKRTQDAL Q9UBY7 30 30 -
PPRQERKRTQDAL Q63881 30 30 -
PPRQERKRTQDAL Q9Z0V2 30 30 -

Motif 2 width=17
Element Seqn Id St Int Rpt
LQDDADTDTAGESALPT Q9NZV8 148 105 -
LQDDADTDTAGESALPT Q9UNH9 148 105 -
LQDDADTDTAGESALPT Q9UBY7 148 105 -
LQDDADTDNTGESALPT Q63881 148 105 -
LQDDADTDNTGESALPT Q9Z0V2 148 105 -

Motif 3 width=13
Element Seqn Id St Int Rpt
EDEQAFVSKSGSS Q9NZV8 461 296 -
EDEPAFVSKSGSS Q9UNH9 461 296 -
EDEQAFVSKSGSS Q9UBY7 461 296 -
EDEPAFVSKSGSS Q63881 461 296 -
EDEPAFISKSGSS Q9Z0V2 461 296 -

Motif 4 width=14
Element Seqn Id St Int Rpt
QIRCVERTPLSNSR Q9NZV8 560 86 -
QIRCVERTPLSNSR Q9UNH9 560 86 -
QIRCVERTPLSNSR Q9UBY7 560 86 -
QIRCVERTPLSNSR Q63881 560 86 -
QIRCVERTPLSNSR Q9Z0V2 560 86 -

Motif 5 width=13
Element Seqn Id St Int Rpt
MEECVKLNCEQPY Q9NZV8 580 6 -
MEECVKLNCEQPY Q9UNH9 580 6 -
MEECVKLNCEQPY Q9UBY7 580 6 -
MEECVKLNCEQPY Q63881 580 6 -
MEECVKLNCEQPY Q9Z0V2 580 6 -