WORKLIST ENTRIES (1):
SKCHANNEL View alignment Calcium-activated SK potassium channel signature
Type of fingerprint: COMPOUND with 2 elements
Links:
PRINTS; PR00169 KCHANNEL; PR01449 BKCHANNELA; PR01450 BKCHANNELB
Creation date 05-DEC-2000
1. MILLER, C.
An overview of the potassium channel family.
GENOME BIOL. 1(4) 1-5 (2000).
2. ASHCROFT, F.M.
Ca2+-activated K+ channels.
IN ION CHANNELS AND DISEASE, ACADEMIC PRESS, 2000, PP.125-133.
3. VERGARA, C., LATORRE, R., MARRION, N.V. AND ADELMAN, J.P.
Calcium-activated potassium channels.
CURR.OPIN.NEUROBIOL. 8(3) 321-329 (1998).
4. ISHII, T.M., MAYLIE, J. AND ADELMAN, J.P.
Determinants of apamin and d-tubocurarine block in SK potassium channels.
J.BIOL.CHEM. 272(37) 23195-23200 (1997).
5. BOND, C.T., MAYLIE, J. AND ADELMAN, J.P.
Small-conductance calcium-activated potassium channels.
ANN.N.Y.ACAD.SCI. 868 370-378 (1999).
6. CASTLE, N.A.
Recent advances in the biology of small-conductance calcium-activated
potassium channels.
PERSPECTIVES DRUG DISCOVERY DESIGN 16 131-154 (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 [1].
Structurally, calcium (Ca2+) activated 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+ channel (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].
Ca2+-activated K+ channels are a diverse group of channels that are
activated by an increase in intracellular Ca2+ concentration. They are
found in the majority of nerve cells, where they modulate cell excitability
and action potential. Three types of Ca2+-activated K+ channel have been
characterised, termed small-conductance (SK), intermediate conductance (IK)
and large conductance (BK) respectively [2-3].
SK channels are thought to play an important role in the functioning of
all excitable tissues. To date, 3 subtypes (designated SK1-SK3) have been
cloned, each of which possesses a different tissue expression profile: SK1
channels are expressed in the heart; SK2 channels are found in the adrenal
gland; and SK3 channels are known to be present in skeletal muscle.
Although SK channels have been classified as belonging to the 6TM domain
voltage-gated K+ channel family, they show little or no sequence similarity
to other family members. The fourth TM domain resembles the S4 voltage
sensor domain of Kv channels, since it contains 3 positively charged
residues. However, despite similarity to the Kv voltage-sensory motif, SK
channel activation is not voltage sensitive.
SKCHANNEL is a 2-element fingerprint that provides a signature for the
calcium-activated SK potassium channels. The fingerprint was derived from
an initial alignment of 2 sequences: the motifs were drawn from conserved
regions within the N-terminal portion of the alignment, focusing on those
sections that characterise the SK potassium channels but distinguish them
from other members of the K+ channel superfamily. Three iterations on
SPTR39_14f were required to reach convergence, at which point a true set
comprising 7 sequences was identified.
SUMMARY INFORMATION
7 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
2| 7 7
--+-----------
| 1 2
True positives..
P70605 Q9UGI6 P70604 Q9PTS9
O43517 P70606 Q92952
PROTEIN TITLES
P70605 CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK3 - Rattus norvegicus
Q9UGI6 SK3 PROTEIN - Homo sapiens (Human).
P70604 CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK2 - Rattus norvegicus
Q9PTS9 SMALL-CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL - Gall
O43517 CALCIUM-ACTIVATED POTASSIUM CHANNEL - Homo sapiens (Human).
P70606 CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK1 - Rattus norvegicus
Q92952 CALCIUM-ACTIVATED POTASSIUM CHANNEL HSK1 - Homo sapiens (Hum
SCAN HISTORY
SPTR39_14f 3 100 NSINGLE
INITIAL MOTIF SETS
SKCHANNEL1 Length of motif = 21 Motif number = 1
Calcium-activated SK potassium channel motif I - 1
PCODE ST INT
RLGHRRALFEKRKRLSDYALI P70606 88 88
KLGHRRALFEKRKRLSDYALI P70604 121 121
SKCHANNEL2 Length of motif = 19 Motif number = 2
Calcium-activated SK potassium channel motif II - 1
PCODE ST INT
ELAVCAIHPVPGHYRFTWT P70606 188 79
EILVCAIHPIPGNYTFTWT P70604 221 79
FINAL MOTIF SETS
SKCHANNEL1 Length of motif = 21 Motif number = 1
Calcium-activated SK potassium channel motif I - 3
PCODE ST INT
KLGHRRALFEKRKRLSDYALI P70605 270 270
KLGHRRALFEKRKRLSDYALI Q9UGI6 274 274
KLGHRRALFEKRKRLSDYALI P70604 121 121
KLGHRRALFEKRKRLSDYALI Q9PTS9 94 94
KLGHRRAPFEKRKRLSDYALI O43517 269 269
RLGHRRALFEKRKRLSDYALI P70606 88 88
RLGHRRALFEKRKRLSDYALI Q92952 110 110
SKCHANNEL2 Length of motif = 19 Motif number = 2
Calcium-activated SK potassium channel motif II - 3
PCODE ST INT
EMLVCAIHPIPGEYKFFWT P70605 370 79
EMLVCAIHPIPGEYKFFWT Q9UGI6 374 79
EILVCAIHPIPGNYTFTWT P70604 221 79
EILVCAIHPIPGNYTFTWT Q9PTS9 194 79
EMLVCAIHPIPGEYKFFWT O43517 369 79
ELAVCAIHPVPGHYRFTWT P70606 188 79
ELAVCAIHPVPGHYRFTWT Q92952 210 79
User query: Display/Full Code "SKCHANNEL"