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PR01509

Identifier
KV12CHANNEL  [View Relations]  [View Alignment]  
Accession
PR01509
No. of Motifs
5
Creation Date
19-JUN-2001
Title
Kv1.2 voltage-gated K+ channel signature
Database References
PRINTS; PR00169 KCHANNEL; PR01491 KVCHANNEL; PR01496 SHAKERCHANEL
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. LITTLETON, J.T. AND GANETZKY, B.
Ion Channels and synaptic organisation: analysis of the Drosophila genome.   
NEURON 26 35-43 (2000).
 
5. CONLEY, E.C. AND BRAMMAR, W.J.
Shaker.
IN THE ION CHANNEL FACTSBOOK, VOLUME IV, ACADEMIC PRESS, 1999, PP.559-614.

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 Shaker (Kv1) sequence was found in Drosophila. Several vertebrate
K+ channels with similar amino acid sequences were subsequently found and,
together with the Drosophila Shaker channel, now constitute the Shaker (Kv1) 
family. These channels are mostly expressed in the brain, but can also be
found in non-excitable cells, such as lymphocytes [4,5]. 
 
Kv1.2 channels are uniformly distributed in the heart and brain [5]. They
play diverse functional roles in several neuronal compartments, especially
in the regulation of pre- and post-synaptic membrane excitability [5]. 
Kv1.2 subunits can co-localise with other kv1 subunits. For example, Kv1.2
colocalises with Kv1.1 in the nodes of Ranvier in myelinated axons, and in
the brain, in particular, the axons and nerve terminals; Kv1.2 coassembles
with Kv1.4 subunits. In addition, Kv1.2 assembles with the Kv-beta2 subunit
resulting in the promotion of Kv1.2 transport to the cell surface [5].
 
KV12CHANNEL is a 5-element fingerprint that provides a signature for the Kv
1.2 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 - motifs 1 and 2 span the loop
region between TM domains 1 and 2; motif 3 lies in the loop region between
TM domains 3 and 4; and motifs 4 and 5 reside at the C-terminus. Two
iterations on SPTR39_15f were required to reach convergence, at which point
a true set comprising 5 sequences was identified. A single partial match was
also found, Q9I830, a family member from Rainbow trout that fails to make
significant matches with motifs 1 and 4. 
Summary Information
   5 codes involving  5 elements
0 codes involving 4 elements
1 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
555555
400000
301101
200000
12345
True Positives
CIK2_HUMAN    CIK2_MOUSE    CIK2_XENLA    Q28293        
Q9MYX3
True Positive Partials
Codes involving 3 elements
Q9I830
Sequence Titles
CIK2_HUMAN  VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV1.2 (RBK2) (HBK5) (NGK1) (MK2) (HUKIV) - Homo sapiens (Human). 
CIK2_MOUSE VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV1.2 (RBK2) (RCK5) (NGK1) (MK2) (HUKIV) - Mus musculus (Mouse), and Rattus norvegicus (Rat).
CIK2_XENLA VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV1.2 (XSHA2) - Xenopus laevis (African clawed frog).
Q28293 DELAYED RECTIFIER K+ CHANNEL - Canis familiaris (Dog).
Q9MYX3 POTASSIUM CHANNEL SUBUNIT KV 1.2 - Oryctolagus cuniculus (Rabbit).

Q9I830 SHAKER-RELATED POTASSIUM CHANNEL TSHA1 - Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri).
Scan History
SPTR39_15f 2  250  NSINGLE    
Initial Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
MHGSGVTFHTYSNST CIK2_HUMAN 195 195 -
MHGGGVTFHTYSNST CIK2_MOUSE 195 195 -
MHGSGMTFHTYSNST Q9MYX3 195 195 -
MHGSGGNYYSYPNST CIK2_XENLA 195 195 -

Motif 2 width=13
Element Seqn Id St Int Rpt
GYQQSTSFTDPFF CIK2_HUMAN 211 1 -
GYQQSTSFTDPFF CIK2_MOUSE 211 1 -
GYQQSTSFTDPFF Q9MYX3 211 1 -
RFQKSNTFTDPFF CIK2_XENLA 211 1 -

Motif 3 width=12
Element Seqn Id St Int Rpt
EKPEDAQQGQQA CIK2_HUMAN 276 52 -
EKPEDAQQGQQA CIK2_MOUSE 276 52 -
EKPEDAQQGQQA Q9MYX3 276 52 -
EKTEDGQQGQQA CIK2_XENLA 276 52 -

Motif 4 width=18
Element Seqn Id St Int Rpt
QAQYLQVTSCPKIPSSPD CIK2_HUMAN 426 138 -
QAQYLQVTSCPKIPSSPD CIK2_MOUSE 426 138 -
QAQYLQVTSCPKIPSSPD Q9MYX3 426 138 -
QAQYLQVTSCPKIPSSPD CIK2_XENLA 426 138 -

Motif 5 width=14
Element Seqn Id St Int Rpt
QEGVNNSNEDFREE CIK2_HUMAN 462 18 -
QEGVNNSNEDFREE CIK2_MOUSE 462 18 -
QEGVNNSNEDFREE Q9MYX3 462 18 -
QEGVNHSNEDFREK CIK2_XENLA 462 18 -
Final Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
MHGSGVTFHTYSNST CIK2_HUMAN 195 195 -
MHGGGVTFHTYSNST CIK2_MOUSE 195 195 -
MHGGGVTFHTYSNST Q28293 195 195 -
MHGSGMTFHTYSNST Q9MYX3 195 195 -
MHGSGGNYYSYPNST CIK2_XENLA 195 195 -

Motif 2 width=13
Element Seqn Id St Int Rpt
GYQQSTSFTDPFF CIK2_HUMAN 211 1 -
GYQQSTSFTDPFF CIK2_MOUSE 211 1 -
GYQQSTSFTDPFF Q28293 211 1 -
GYQQSTSFTDPFF Q9MYX3 211 1 -
RFQKSNTFTDPFF CIK2_XENLA 211 1 -

Motif 3 width=12
Element Seqn Id St Int Rpt
EKPEDAQQGQQA CIK2_HUMAN 276 52 -
EKPEDAQQGQQA CIK2_MOUSE 276 52 -
EKPEDAQQGQQA Q28293 276 52 -
EKPEDAQQGQQA Q9MYX3 276 52 -
EKTEDGQQGQQA CIK2_XENLA 276 52 -

Motif 4 width=18
Element Seqn Id St Int Rpt
QAQYLQVTSCPKIPSSPD CIK2_HUMAN 426 138 -
QAQYLQVTSCPKIPSSPD CIK2_MOUSE 426 138 -
QAQYLQVTSCPKIPSSPD Q28293 426 138 -
QAQYLQVTSCPKIPSSPD Q9MYX3 426 138 -
QAQYLQVTSCPKIPSSPD CIK2_XENLA 426 138 -

Motif 5 width=14
Element Seqn Id St Int Rpt
QEGVNNSNEDFREE CIK2_HUMAN 462 18 -
QEGVNNSNEDFREE CIK2_MOUSE 462 18 -
QEGVNNSNEDFREE Q28293 462 18 -
QEGVNNSNEDFREE Q9MYX3 462 18 -
QEGVNHSNEDFREK CIK2_XENLA 462 18 -