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PR01627

Identifier
LCACHANNELB1  [View Relations]  [View Alignment]  
Accession
PR01627
No. of Motifs
4
Creation Date
21-DEC-2001
Title
L-type calcium channel beta-1 subunit signature
Database References
PRINTS; PR00167 CACHANNEL; PR01626 LCACHANNELB
Literature References
1. PICHLER, M., CASSIDY, T.N., REIMER, D., HAASE, H., KRAUS, R., OSTLER, D.
AND STRIESSNIG, J.
Beta subunit heterogeneity in neuronal L-type calcium channels.
J.BIOL.CHEM. 272(21) 13877-13882 (1997).
 
2. BRAMMAR, W.J.
VLG Ca.
IN THE ION CHANNEL FACTSBOOK, VOLUME IV, ACADEMIC PRESS, 1999, PP.22-153.
 
3. NEUHUBER, B., GERSTER, U., DORING, F., GLOSSMANN, H., TANABE, T. AND
FLUCHER, B.E.
Association of calcium channel alpha-1s and beta-1a subunits is required for
the targetting of beta-1a but not of alpha-1s into skeletal muscle triads.
PROC.NATL.ACAD.SCI.U.S.A. 95 5015-5020 (1998).

Documentation
Calcium channels are generally discriminated by their biophysical and/or
pharmacological sensitivity. L-type calcium channels are distinguished by
their modulation by compounds such as dihydropyridines. These channels
tend to be localised mainly around the neuronal cell body, where they
influence calcium-dependent modulation and excitation-transcription coupling,
but are also found in skeletal and cardiac muscle, where they play a role in
excitation-contraction coupling and action potential shaping, respectively.
 
L-type calcium channnels are formed from different alpha-1 subunit isoforms
that determine the pharmacological properties of the channel, since they
form the drug binding domain. Other properties, such as gating voltage-
dependence, G protein modulation and kinase susceptibility, are influenced 
by alpha-2, delta and beta subunits [1].
 
Co-expression of beta subunit mRNA with alpha-1 subunit mRNA in xenopus
oocytes produces increased calcium currents, which are accompanied by a
shift in the voltage-dependence of activation to more negative membrane
potentials. Conversely, microinjection of antisense oligonucleotides to 
beta subunit mRNA produces decreased calcium currents and shifts voltage-
dependent activation to more positive membrane potentials. There are
four distinct beta subunits: beta-1, beta-2, beta-3 and beta-4; and the
magnitude of these effects varies with the particular subtype [2].
 
There are 3 splice variants of the beta-1 subunit: beta-1a, beta-1b and beta
1c. Beta-1a is the most extensively studied of these and is known to be 
expressed in skeletal muscle and brain, but not in smooth muscle or heart.
Beta-1a appears to be important for the functional expression of the alpha-1
subunit in skeletal muscle. It is a 524-residue peripheral membrane protein 
that associates with a conserved 9-residue motif between repeats I and II 
of the alpha-1 subunit [3]. Beta-1b was identified by cloning in rat brain, 
heart and hippocampus, and differs from beta-1a by having a deletion of ~50
amino acids at residue 209, and having a 120-residue C-terminal elongation.
Beta-1c was cloned from human heart and hippocampus and has the same
deletion as beta-1b, but lacks the C-terminal extension.
 
LCACHANNELB1 is a 4-element fingerprint that provides a signature for the
L-type calcium channel beta-1 subunits. 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, focusing on those
sections that characterise the beta-1 subunits but distinguish them from 
the rest of the L-type calcium channel beta subunits. Two iterations on
SPTR40_18f were required to reach convergence, at which point a true set
comprising 10 sequences was identified.
Summary Information
10 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
410101010
30000
20000
1234
True Positives
CCBA_HUMAN    CCBA_RAT      CCBB_HUMAN    CCBC_HUMAN    
CCBC_RABIT O15331 Q9C085 Q9EPT9
Q9MZL6 Q9MZL7
Sequence Titles
CCBA_HUMAN  Dihydropyridine-sensitive L-type, channel beta-1-B2 subunit (Beta-1 isoform A) - Homo sapiens (Human). 
CCBA_RAT Dihydropyridine-sensitive L-type, channel beta-1-B2 subunit (Beta-1 isoform A) - Rattus norvegicus (Rat).
CCBB_HUMAN Dihydropyridine-sensitive L-type, calcium channel beta-1-B1 subunit (Beta-1 isoform B) (Beta-2) (Beta-1C) - Homo sapiens (Human).
CCBC_HUMAN Dihydropyridine-sensitive L-type, calcium channel beta-1M subunit (Beta-1 isoform C) (Beta-1A) - Homo sapiens (Human).
CCBC_RABIT Dihydropyridine-sensitive L-type, calcium channel beta-1M subunit (Beta-1 isoform C) - Oryctolagus cuniculus (Rabbit).
O15331 DIHYDROPYRIDINE-SENSITIVE L-TYPE, CALCIUM CHANNEL BETA-1B SUBUNIT - Homo sapiens (Human).
Q9C085 VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA-1B SUBUNIT - Homo sapiens (Human).
Q9EPT9 L-TYPE CALCIUM CHANNEL BETA 1A SUBUNIT - Mus musculus (Mouse).
Q9MZL6 VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA1C SUBUNIT - Bos taurus (Bovine).
Q9MZL7 VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA1B SUBUNIT - Bos taurus (Bovine).
Scan History
SPTR40_18f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
MVQKTSMSRGPYPPSQ CCBA_HUMAN 1 1 -
MVQKTSMSRGPYPPSQ CCBB_HUMAN 1 1 -
MVQKTSMSRGPYPSSQ Q9MZL7 1 1 -
MVQKTSMSRGPYPPSQ CCBC_RABIT 1 1 -
MVQKSGMSRGPYPPSQ Q9EPT9 1 1 -

Motif 2 width=16
Element Seqn Id St Int Rpt
EIPMEVFDPSPQGKYS CCBA_HUMAN 17 0 -
EIPMEVFDPSPQGKYS CCBB_HUMAN 17 0 -
EIPMEVFDPSPQGKYS Q9MZL7 17 0 -
EIPMEVFDPSPQGKYS CCBC_RABIT 17 0 -
EIPMEVFDPSPQGKYS Q9EPT9 17 0 -

Motif 3 width=14
Element Seqn Id St Int Rpt
GYNPSPGDEVPVQG CCBA_HUMAN 110 77 -
GYNPSPGDEVPVQG CCBB_HUMAN 110 77 -
GYNPSPGDEVPVQG Q9MZL7 110 77 -
GYNPSPGDEVPVEG CCBC_RABIT 110 77 -
GYNPSPGDEVPVQG Q9EPT9 110 77 -

Motif 4 width=18
Element Seqn Id St Int Rpt
LQEQKLRQNRLGSSKSGD CCBA_HUMAN 171 47 -
LQEQKLRQNRLGSSKSGD CCBB_HUMAN 171 47 -
LQEQKLRQNRLSSSKSGD Q9MZL7 171 47 -
LQEQKLRQSRLSSSKSGD CCBC_RABIT 171 47 -
LQEQTLRQNRLSSSKSGD Q9EPT9 171 47 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
MVQKTSMSRGPYPPSQ CCBA_HUMAN 1 1 -
MVQKTSMSRGPYPPSQ Q9C085 1 1 -
MVQKTSMSRGPYPPSQ O15331 1 1 -
MVQKTSMSRGPYPPSQ CCBC_HUMAN 1 1 -
MVQKTSMSRGPYPPSQ CCBB_HUMAN 1 1 -
MVQKTSMSRGPYPSSQ Q9MZL6 1 1 -
MVQKTSMSRGPYPSSQ Q9MZL7 1 1 -
MVQKTSMSRGPYPPSQ CCBC_RABIT 1 1 -
MVQKSGMSRGPYPPSQ CCBA_RAT 1 1 -
MVQKSGMSRGPYPPSQ Q9EPT9 1 1 -

Motif 2 width=16
Element Seqn Id St Int Rpt
EIPMEVFDPSPQGKYS CCBA_HUMAN 17 0 -
EIPMEVFDPSPQGKYS Q9C085 17 0 -
EIPMEVFDPSPQGKYS O15331 17 0 -
EIPMEVFDPSPQGKYS CCBC_HUMAN 17 0 -
EIPMEVFDPSPQGKYS CCBB_HUMAN 17 0 -
EIPMEVFDPSPQGKYS Q9MZL6 17 0 -
EIPMEVFDPSPQGKYS Q9MZL7 17 0 -
EIPMEVFDPSPQGKYS CCBC_RABIT 17 0 -
EIPMEVFDPSPQGKYS CCBA_RAT 17 0 -
EIPMEVFDPSPQGKYS Q9EPT9 17 0 -

Motif 3 width=14
Element Seqn Id St Int Rpt
GYNPSPGDEVPVQG CCBA_HUMAN 110 77 -
GYNPSPGDEVPVQG Q9C085 110 77 -
GYNPSPGDEVPVQG O15331 110 77 -
GYNPSPGDEVPVQG CCBC_HUMAN 110 77 -
GYNPSPGDEVPVQG CCBB_HUMAN 110 77 -
GYNPSPGDEVPVQG Q9MZL6 110 77 -
GYNPSPGDEVPVQG Q9MZL7 110 77 -
GYNPSPGDEVPVEG CCBC_RABIT 110 77 -
GYNPSPGDEVPVQG CCBA_RAT 110 77 -
GYNPSPGDEVPVQG Q9EPT9 110 77 -

Motif 4 width=18
Element Seqn Id St Int Rpt
LQEQKLRQNRLGSSKSGD CCBA_HUMAN 171 47 -
LQEQKLRQNRLGSSKSGD Q9C085 171 47 -
LQEQKLRQNRLGSSKSGD O15331 171 47 -
LQEQKLRQNRLGSSKSGD CCBC_HUMAN 171 47 -
LQEQKLRQNRLGSSKSGD CCBB_HUMAN 171 47 -
LQEQKLRQNRLSSSKSGD Q9MZL6 171 47 -
LQEQKLRQNRLSSSKSGD Q9MZL7 171 47 -
LQEQKLRQSRLSSSKSGD CCBC_RABIT 171 47 -
LQEQTLRQNRLSSSKSGD CCBA_RAT 171 47 -
LQEQTLRQNRLSSSKSGD Q9EPT9 171 47 -