WORKLIST ENTRIES (1):
RVDCCALPHA1 View alignment R-type voltage-dependent calcium channel alpha-1 subunit signature
Type of fingerprint: COMPOUND with 6 elements
Links:
PRINTS; PR00167 CACHANNEL; PR01629 TVDCCALPHA1; PR01630 LVDCCALPHA1
PRINTS; PR01631 NVDCCALPHA1; PR01632 PQVDCCALPHA1
Creation date 11-DEC-2001
1. WILLIAMS, M.E., BRUST, P.F., FELDMAN, D.H., PATTHI, S., SIMERSON, S.,
MAROUFI, A., MCCUE, A.F., VELICELBI, G., ELLIS, S.B. AND HARPOLD, M.M.
Structure and functional expression of an omega-conotoxin sensitive human
N-type calcium channel.
SCIENCE 257 389-395 (1992).
2. MORI, Y., FRIEDRICH, T., KIM, MS., MIKAMI, A., NAKAI, J., RUTH, P.,
BOSSE, E., HOFMANN, F., FLOCKERZI, V., FURUICHI, T., MIKOSHIBA, K.,
IMOTO, K., TANABE, T. AND NUMA, S.
Primary structure and functional expression from complementary DNA of a
brain calcium channel.
NATURE 350 398-402 (1991).
3. ASHCROFT, F.M.
Voltage-gated Ca2+ channels.
IN ION CHANNELS AND DISEASE, ACADEMIC PRESS, 2000, PP.161-183.
4. KOCH, W.J., ELLINOR, P.T. AND SCHWARTZ, A.
cDNA cloning of a dihydropyridine-sensitive calcium channel from rat aorta -
evidence for the existence of alternatively spliced forms.
J.BIOL.CHEM. 265(29) 17786-17791 (1990).
5. RANDALL, A.D. AND TSIEN, R.W.
Contrasting biophysical and pharmacological properties of T-type and R-type
calcium channels.
NEUROPHARMACOLOGY 36(7) 879-893 (1997).
6. FOEHRING, R.C., MERMELSTEIN, P.G., SONG, W., ULRICH, S. AND SURMEIER, D.J.
Unique properties of R-type calcium currents in neocortical and neostriatal
neurons.
J.NEUROPHYSIOL. 84(5) 2225-2236 (2000).
7. GASPARINI, S., KASYANOV, A.M., PIETROBON, D., VORONIN, L.L. AND
CHERUBINI, E.
Presynaptic R-type calcium channels contribute to fast excitatory synaptic
transmission in the rat hippocampus.
J.NEUROSCI. 21(22) 8715-8721 (2001).
Calcium channel proteins are involved in the control of neurotransmitter
release from neurons [1], and play an important role in the regulation of a
variety of cellular functions, including membrane excitability, muscle
contraction and synaptic transmission [2]. Voltage-gated calcium channels
are classified as T, L, N, P, Q and R, and are distinguished by their
sensitivity to pharmacological blocks, single-channel conductance kinetics,
and voltage-dependence. On the basis of their voltage activation
properties, the voltage-gated calcium classes can be further divided into
two broad groups: the low (T-type) and high (L, N, P, Q and R-type)
threshold-activated channels [3].
Generally, the channel proteins are composed of 4 tightly-coupled subunits
(alpha-1, alpha-2, beta and gamma), the alpha-1 subunit from each creating
the pore for the import of extracellular calcium ions. The alpha-1 subunit
shares sequence characteristics with all voltage-dependent cation channels,
and exploits the same 6-helix bundle structural motif - in both sodium and
calcium channels, this motif is repeated 4 times within the sequence to give
a 24-helix bundle. Within each of these repeats, 5 of the transmembrane (TM)
segments (S1, S2, S3, S5, S6) are hydrophobic and one is positively charged
(S4) - the latter is characterised by charged amino acids at very third
position, and probably represents the voltage-sensor.
Several genes encoding alpha-1 subunits have been identified, each forming
a distinct electrophysiological channel [4]. R-type calcium channels are
composed of alpha-1E subunits and are found in a variety of neuronal
populations, such as cerebellar granule neurons and dendrites of hippocampal
pyrimidal neurons [5]. They are believed to play an important role in the
body's natural communication network, where they contribute to the
regulation of brain function by synaptic integration [6]. Their hypolarised
inactivation range and rapid kinetics of inactivation make R-type channels
more suited to providing a transient surge of Ca2+ influx [6,7].
RVDCCALPHA1 is a 6-element fingerprint that provides a signature for the
R-type voltage-dependent calcium channel alpha-1 subunit. The fingerprint
was derived from an initial alignment of 5 sequences: the motifs were drawn
from conserved regions spanning the N-terminal half of the alignment: motifs
1 and 2 lie in the extracellular region between TM domains 5 and 6 of repeat
I; motif 3 resides in the cytoplasmic region between TM domain 6 of repeat I
and TM domain 1 of repeat II; and motifs 4-6 span the cytoplasmic region
between TM domain 6 of repeat II and TM domain 1 of repeat III. A single
iteration on SPTR40_18f was required to reach convergence, no further
sequences being identified beyond the starting set.
SUMMARY INFORMATION
5 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
6| 5 5 5 5 5 5
5| 0 0 0 0 0 0
4| 0 0 0 0 0 0
3| 0 0 0 0 0 0
2| 0 0 0 0 0 0
--+-------------------------------
| 1 2 3 4 5 6
True positives..
CCAE_RAT CCAE_HUMAN CCAE_MOUSE CCAE_RABIT
CCAE_DISOM
PROTEIN TITLES
CCAE_RAT Voltage-dependent R-type calcium channel alpha-1E subunit (C
CCAE_HUMAN Voltage-dependent R-type calcium channel alpha-1E subunit (C
CCAE_MOUSE Voltage-dependent R-type calcium channel alpha-1E subunit (C
CCAE_RABIT Voltage-dependent R-type calcium channel alpha-1E subunit (C
CCAE_DISOM Probable voltage-dependent R-type calcium channel alpha-1E s
SCAN HISTORY
SPTR40_18f 1 170 NSINGLE
INITIAL MOTIF SETS
RVDCCALPHA11 Length of motif = 15 Motif number = 1
R-type voltage-dependent calcium channel alpha-1 subunit motif I - 1
PCODE ST INT
AAEELDLQFPCGTQE CCAE_DISOM 266 266
ILEGFDPPHPCGVQG CCAE_HUMAN 258 258
ILEGFDPPHPCGVQG CCAE_MOUSE 259 259
VLEGFDPPHPCGVQG CCAE_RABIT 258 258
ILEGFDPPHPCGVQG CCAE_RAT 209 209
RVDCCALPHA12 Length of motif = 12 Motif number = 2
R-type voltage-dependent calcium channel alpha-1 subunit motif II - 1
PCODE ST INT
CPNGTVCSYWIG CCAE_DISOM 285 4
CPAGYECKDWIG CCAE_HUMAN 273 0
CPAGYECKDWIG CCAE_MOUSE 274 0
CPAGYECKDWIG CCAE_RABIT 273 0
CPAGYECKDWIG CCAE_RAT 224 0
RVDCCALPHA13 Length of motif = 13 Motif number = 3
R-type voltage-dependent calcium channel alpha-1 subunit motif III - 1
PCODE ST INT
RRKERMLRISIRH CCAE_DISOM 473 176
RHKERLLRISIRH CCAE_HUMAN 459 174
RHKERLLRISIRH CCAE_MOUSE 460 174
RHKERLLRISVRH CCAE_RABIT 459 174
RHKERLLRISIRH CCAE_RAT 410 174
RVDCCALPHA14 Length of motif = 14 Motif number = 4
R-type voltage-dependent calcium channel alpha-1 subunit motif IV - 1
PCODE ST INT
GEQGRALGRSVEAG CCAE_DISOM 866 380
PCHGNCDPTQQEAG CCAE_HUMAN 886 414
SCHGNCDPIQQEAG CCAE_MOUSE 888 415
PCHGNCEPALQETA CCAE_RABIT 878 406
SCHGNCDPTQQETG CCAE_RAT 838 415
RVDCCALPHA15 Length of motif = 11 Motif number = 5
R-type voltage-dependent calcium channel alpha-1 subunit motif V - 1
PCODE ST INT
LEESAETSLSR CCAE_DISOM 905 25
GKESSSASRSR CCAE_HUMAN 929 29
GKDSASASRSR CCAE_MOUSE 931 29
AKESSSASRSR CCAE_RABIT 921 29
GKESASASRSR CCAE_RAT 881 29
RVDCCALPHA16 Length of motif = 20 Motif number = 6
R-type voltage-dependent calcium channel alpha-1 subunit motif VI - 1
PCODE ST INT
TQEQTEIDVDCENTETPMDS CCAE_DISOM 1036 120
TTESTSVTVAIPDVDPLVDS CCAE_HUMAN 1063 123
TTESTSVTVAIPDVDPLVDS CCAE_MOUSE 1066 124
TTESTDVTVAIPDAEPLVDS CCAE_RABIT 1055 123
TTESTSVTVAIPDVDPLVDS CCAE_RAT 1016 124
FINAL MOTIF SETS
RVDCCALPHA11 Length of motif = 15 Motif number = 1
R-type voltage-dependent calcium channel alpha-1 subunit motif I - 1
PCODE ST INT
ILEGFDPPHPCGVQG CCAE_RAT 209 209
ILEGFDPPHPCGVQG CCAE_HUMAN 258 258
ILEGFDPPHPCGVQG CCAE_MOUSE 259 259
VLEGFDPPHPCGVQG CCAE_RABIT 258 258
AAEELDLQFPCGTQE CCAE_DISOM 266 266
RVDCCALPHA12 Length of motif = 12 Motif number = 2
R-type voltage-dependent calcium channel alpha-1 subunit motif II - 1
PCODE ST INT
CPAGYECKDWIG CCAE_RAT 224 0
CPAGYECKDWIG CCAE_HUMAN 273 0
CPAGYECKDWIG CCAE_MOUSE 274 0
CPAGYECKDWIG CCAE_RABIT 273 0
CPNGTVCSYWIG CCAE_DISOM 285 4
RVDCCALPHA13 Length of motif = 13 Motif number = 3
R-type voltage-dependent calcium channel alpha-1 subunit motif III - 1
PCODE ST INT
RHKERLLRISIRH CCAE_RAT 410 174
RHKERLLRISIRH CCAE_HUMAN 459 174
RHKERLLRISIRH CCAE_MOUSE 460 174
RHKERLLRISVRH CCAE_RABIT 459 174
RRKERMLRISIRH CCAE_DISOM 473 176
RVDCCALPHA14 Length of motif = 14 Motif number = 4
R-type voltage-dependent calcium channel alpha-1 subunit motif IV - 1
PCODE ST INT
SCHGNCDPTQQETG CCAE_RAT 838 415
PCHGNCDPTQQEAG CCAE_HUMAN 886 414
SCHGNCDPIQQEAG CCAE_MOUSE 888 415
PCHGNCEPALQETA CCAE_RABIT 878 406
GEQGRALGRSVEAG CCAE_DISOM 866 380
RVDCCALPHA15 Length of motif = 11 Motif number = 5
R-type voltage-dependent calcium channel alpha-1 subunit motif V - 1
PCODE ST INT
GKESASASRSR CCAE_RAT 881 29
GKESSSASRSR CCAE_HUMAN 929 29
GKDSASASRSR CCAE_MOUSE 931 29
AKESSSASRSR CCAE_RABIT 921 29
LEESAETSLSR CCAE_DISOM 905 25
RVDCCALPHA16 Length of motif = 20 Motif number = 6
R-type voltage-dependent calcium channel alpha-1 subunit motif VI - 1
PCODE ST INT
TTESTSVTVAIPDVDPLVDS CCAE_RAT 1016 124
TTESTSVTVAIPDVDPLVDS CCAE_HUMAN 1063 123
TTESTSVTVAIPDVDPLVDS CCAE_MOUSE 1066 124
TTESTDVTVAIPDAEPLVDS CCAE_RABIT 1055 123
TQEQTEIDVDCENTETPMDS CCAE_DISOM 1036 120
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