WORKLIST ENTRIES (1):
PQVDCCALPHA1 View alignment P/Q-type voltage-dependent calcium channel alpha-1 subunit signature
Type of fingerprint: COMPOUND with 5 elements
Links:
PRINTS; PR00167 CACHANNEL; PR01629 TVDCCALPHA1; PR01630 LVDCCALPHA1
PRINTS; PR01631 NVDCCALPHA1; PR01633 RVDCCALPHA1
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. DIRIONG, S., LORY, P., WILLIAMS, M.E., ELLIS, S.B., HARPOLD, M.M. AND
TAVIAUX, S.
Chromosomal localization of the human genes for alpha 1A, alpha 1B, and
alpha 1E voltage-dependent Ca2+ channel subunits.
GENOMICS 30 605-609 (1995).
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]. P- and Q-type channels are
formed from alpha-1A subunits and function in transmitter release [5].
P-type channels are prevalent in cerebellar Purkinje cells, but are also
expressed in many central and peripheral neurons, such as the spinal cord
and visual cortex. By contrast, Q-type channels are found in cerebellar
granule neurones and the hippocampus. Different mutations in the alpha-1A
subunit produce 3 human diseases: (1) episodic ataxia type-2; (2) familial
hemiplegic migraine; and (3) spinocerebellar ataxia type-6. All 3 diseases
result in cerebellar atrophy, but they differ in the extent and rate of
progression of neuronal degeneration [3].
PQVDCCALPHA1 is a 5-element fingerprint that provides a signature for the
P/Q-type voltage-dependent calcium channel alpha-1 subunits. The fingerprint
was derived from an initial alignment of 4 sequences: the motifs were drawn
from conserved regions spanning the central portion of the alignment: motifs
1-4 lie in the cytoplasmic region between repeats I and II; and motif 5
encodes part of the extracellular region between TM domains 5 and 6 of
repeat IV. Two iterations on SPTR40_18f were required to reach convergence,
at which point a true set comprising 5 sequences was identified.
SUMMARY INFORMATION
5 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
5| 5 5 5 5 5
4| 0 0 0 0 0
3| 0 0 0 0 0
2| 0 0 0 0 0
--+--------------------------
| 1 2 3 4 5
True positives..
CCAA_MOUSE CCAA_RAT CCAA_HUMAN CCAA_RABIT
Q9NS88
PROTEIN TITLES
CCAA_MOUSE Voltage-dependent P/Q-type calcium channel alpha-1A subunit
CCAA_RAT Voltage-dependent P/Q-type calcium channel alpha-1A subunit
CCAA_HUMAN Voltage-dependent P/Q-type calcium channel alpha-1A subunit
CCAA_RABIT Voltage-dependent P/Q-type calcium channel alpha-1A subunit
Q9NS88 ALPHA1A-VOLTAGE-DEPENDENT CALCIUM CHANNEL - Homo sapiens (Hu
SCAN HISTORY
SPTR40_18f 2 200 NSINGLE
INITIAL MOTIF SETS
PQVDCCALPHA11 Length of motif = 21 Motif number = 1
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif I - 1
PCODE ST INT
DARRPWAGSQEAELSREGPYG CCAA_HUMAN 879 879
DARRAWPGSPERAPGREGPYG CCAA_MOUSE 811 811
DARRPWAGSQEAELSREGPYG CCAA_RABIT 881 881
DARRAWPSSPERAPGREGPYG CCAA_RAT 859 859
PQVDCCALPHA12 Length of motif = 19 Motif number = 2
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif II - 1
PCODE ST INT
EGEAERGKAGDPHRRHVHR CCAA_HUMAN 918 18
DADTERAKAGDAPRRHTHR CCAA_MOUSE 851 19
EGEAERGKAGDPHRRHAHR CCAA_RABIT 920 18
DADPERAKAGDAPRRHTHR CCAA_RAT 899 19
PQVDCCALPHA13 Length of motif = 15 Motif number = 3
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif III - 1
PCODE ST INT
KERRHRRRKENQGSG CCAA_HUMAN 1023 86
RERRHRRRKENQGSG CCAA_MOUSE 932 62
RERRHRRRKDTQGSG CCAA_RABIT 1033 94
RERRHRRRKESQGSG CCAA_RAT 980 62
PQVDCCALPHA14 Length of motif = 22 Motif number = 4
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif IV - 1
PCODE ST INT
PDPLPKKEEEKKEEEEDDRGED CCAA_HUMAN 1192 154
PDPLPKKEEEKKEEEEADPGED CCAA_MOUSE 1095 148
PDPLPKKEDEKKEEVDEGPGED CCAA_RABIT 1201 153
PDPLPKKEEEKKEEEEADPGED CCAA_RAT 1143 148
PQVDCCALPHA15 Length of motif = 15 Motif number = 5
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif V - 1
PCODE ST INT
GIDVEDEDSDEDEFQ CCAA_HUMAN 1718 504
GIDGEDEDSDEDEFQ CCAA_MOUSE 1621 504
GIDMEDEDSDEDEFQ CCAA_RABIT 1727 504
GIDGEDEDSDEDEFQ CCAA_RAT 1669 504
FINAL MOTIF SETS
PQVDCCALPHA11 Length of motif = 21 Motif number = 1
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif I - 2
PCODE ST INT
DARRAWPGSPERAPGREGPYG CCAA_MOUSE 811 811
DARRAWPSSPERAPGREGPYG CCAA_RAT 859 859
DARRPWAGSQEAELSREGPYG CCAA_HUMAN 879 879
DARRPWAGSQEAELSREGPYG CCAA_RABIT 881 881
DARRPWAGSQEAELSREDPYG Q9NS88 878 878
PQVDCCALPHA12 Length of motif = 19 Motif number = 2
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif II - 2
PCODE ST INT
DADTERAKAGDAPRRHTHR CCAA_MOUSE 851 19
DADPERAKAGDAPRRHTHR CCAA_RAT 899 19
EGEAERGKAGDPHRRHVHR CCAA_HUMAN 918 18
EGEAERGKAGDPHRRHAHR CCAA_RABIT 920 18
EGEAERGKAGDPHRRHVHR Q9NS88 917 18
PQVDCCALPHA13 Length of motif = 15 Motif number = 3
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif III - 2
PCODE ST INT
RERRHRRRKENQGSG CCAA_MOUSE 932 62
RERRHRRRKESQGSG CCAA_RAT 980 62
KERRHRRRKENQGSG CCAA_HUMAN 1023 86
RERRHRRRKDTQGSG CCAA_RABIT 1033 94
KERRHRRRKENQGSG Q9NS88 1022 86
PQVDCCALPHA14 Length of motif = 22 Motif number = 4
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif IV - 2
PCODE ST INT
PDPLPKKEEEKKEEEEADPGED CCAA_MOUSE 1095 148
PDPLPKKEEEKKEEEEADPGED CCAA_RAT 1143 148
PDPLPKKEEEKKEEEEDDRGED CCAA_HUMAN 1192 154
PDPLPKKEDEKKEEVDEGPGED CCAA_RABIT 1201 153
PDPLPKKEEEKKEEEEDDRGED Q9NS88 1191 154
PQVDCCALPHA15 Length of motif = 15 Motif number = 5
P/Q-type voltage-dependent calcium channel alpha-1 subunit motif V - 2
PCODE ST INT
GIDGEDEDSDEDEFQ CCAA_MOUSE 1621 504
GIDGEDEDSDEDEFQ CCAA_RAT 1669 504
GIDVEDEDSDEDEFQ CCAA_HUMAN 1718 504
GIDMEDEDSDEDEFQ CCAA_RABIT 1727 504
GIDVEDEDSDEDEFQ Q9NS88 1717 504
User query: Display/Full Code "PQVDCCALPHA1"