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PR00817

Identifier
CALCITONINB  [View Relations]  [View Alignment]  
Accession
PR00817
No. of Motifs
4
Creation Date
08-MAR-1998  (UPDATE 06-JUN-1999)
Title
Beta-type calcitonin signature
Database References

PROSITE; PS00258 CALCITONIN
BLOCKS; BL00258
PFAM; PF00214 Calc_CGRP_IAPP
INTERPRO; IPR002163
Literature References
1. STEENBERGH, P.H., HOPPENER, J.W., ZANDBERG, J., LIPS, C.J. AND JANSZ, H.S.
A second human calcitonin/CGRP gene. 
FEBS LETT. 183 403-407 (1985). 
 
2. BREEZE, A.L., HARVEY, T.S., BAZZO, R. AND CAMPBELL, I.D.
Solution structure of human calcitonin gene-related peptide by 1H NMR and
distance geometry with restrained molecular dynamics. 
BIOCHEMISTRY 30 575-582 (1991). 

Documentation
The calcitonin (CT) gene is alternatively expressed in a tissue-specific
manner, producing either the calcium regulatory hormone CT in the thyroid,
or the neuropeptide calcitonin gene related peptide (CGRP) in the brain [1].
In medullary carcinoma of the thyroid, both peptides are produced [1]. 
 
CGRP is a 37-residue peptide produced by alternative splicing of the CT 
gene. CGRP induces vasodilation in various vessels, including those of the
coronary, cerebral and systemic vasculature. A neurotransmitter or neuro-
modulator role is suggested by its abundance in the CNS [1]. The structure
of human CGRP has been determined by 1H NMR [2]. The main conformational
feature of the hormone is an N-terminal disulphide-bonded loop (residues
2-7), leading into a well-defined alpha-helix between residues 8 and 18;
thereafter, the structure is predominantly disordered, although there are
indications of a preference for a turn-type conformation between residues
19 and 21 [2]. 
 
CALCITONINB is a 4-element fingerprint that provides a signature for beta-
type calcitonin and calcitonin gene-related peptides. The fingerprint was
derived from an initial alignment of 12 sequences: the motifs span the full
length of the peptide - motifs 1 and 2 encode the alpha-helix, motif 1 also
including the two Cys residues known to be involved in disulphide bond
formation [2] (these motifs also include the region encoded by PROSITE
pattern CALCITONIN (PS00258)); and motifs 3 and 4 span the structurally-
disordered C-terminal region. A single iteration on OWL30.0 was required
to reach convergence, no further sequences being identified beyond the 
starting set. A single partial match was found, A56855, a closely related 
chicken islet amyloid peptide that makes significant matches with motifs
1 and 2. 
 
An update on SPTR37_9f identified a true set of 8 sequences.
Summary Information
8 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
48888
30000
20000
1234
True Positives
CAL1_HUMAN    CAL1_RAT      CAL2_HUMAN    CAL2_RAT      
CALR_CHICK CGRP_PIG CGRP_RANRI CGRP_SHEEP
Sequence Titles
CAL1_HUMAN  CALCITONIN GENE-RELATED PEPTIDE I PRECURSOR (CGRP-I) (ALPHA-TYPE CGRP) - HOMO SAPIENS (HUMAN). 
CAL1_RAT CALCITONIN GENE-RELATED PEPTIDE I PRECURSOR (CGRP-I) (ALPHA-TYPE CGRP) - RATTUS NORVEGICUS (RAT).
CAL2_HUMAN CALCITONIN GENE-RELATED PEPTIDE II PRECURSOR (CGRP-II) (BETA-TYPE CGRP) - HOMO SAPIENS (HUMAN).
CAL2_RAT CALCITONIN GENE-RELATED PEPTIDE II PRECURSOR (CGRP-II) (BETA-TYPE CGRP) - RATTUS NORVEGICUS (RAT).
CALR_CHICK CALCITONIN GENE-RELATED PEPTIDE PRECURSOR (CGRP) - GALLUS GALLUS (CHICKEN).
CGRP_PIG CALCITONIN GENE-RELATED PEPTIDE (CGRP) - SUS SCROFA (PIG).
CGRP_RANRI CALCITONIN GENE-RELATED PEPTIDE (CGRP) - RANA RIDIBUNDA (LAUGHING FROG) (MARSH FROG).
CGRP_SHEEP CALCITONIN GENE-RELATED PEPTIDE (CGRP) - OVIS ARIES (SHEEP).
Scan History
OWL30_0    1  50   NSINGLE    
SPTR37_9f 2 9 NSINGLE
Initial Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
ACDTATCVTH CAL1_HUMAN 83 83 -
SCNTATCVTH CAL1_RAT 83 83 -
SCNTATCVTH CGRP_SHEEP 1 1 -
ACNTATCVTH CAL2_HUMAN 82 82 -
ACNTATCVTH OGU71287 7 7 -
ACNTATCVTH S40496S2 7 7 -
SCNTATCVTH B44173 83 83 -
SCNTATCVTH RATCAL5 83 83 -
ACNTATCVTH CGRP_RANRI 1 1 -
ACNTATCVTH CALR_CHICK 80 80 -
SCNTATCVTH CGRP_PIG 1 1 -
SCNTATCVTH CAL2_RAT 89 89 -

Motif 2 width=11
Element Seqn Id St Int Rpt
HRLADFLNRSG S40496S2 16 -1 -
HRLAGLLRRSG B44173 92 -1 -
HRLADFLSRSG OGU71287 16 -1 -
HRLAGLLSRSG RATCAL5 92 -1 -
HRLAGLLSRSG CAL2_HUMAN 91 -1 -
HRLAGLLSRSG CGRP_SHEEP 10 -1 -
HRLAGLLSRSG CAL1_RAT 92 -1 -
HRLAGLLSRSG CAL1_HUMAN 92 -1 -
HRLAGLLRRSG CAL2_RAT 98 -1 -
HRLAGLLSRSG CGRP_PIG 10 -1 -
HRLADFLSRSG CALR_CHICK 89 -1 -
HRLADFLSRSG CGRP_RANRI 10 -1 -

Motif 3 width=9
Element Seqn Id St Int Rpt
GGVVKDNFV B44173 102 -1 -
GGMVKSNFV CAL2_HUMAN 101 -1 -
GGVVKSNFV CGRP_SHEEP 20 -1 -
GGVVKDNFV CAL1_RAT 102 -1 -
GGVVKNNFV CAL1_HUMAN 102 -1 -
GGVVKDNFV CAL2_RAT 108 -1 -
GGMVKSNFV CGRP_PIG 20 -1 -
GGVGKNNFV CALR_CHICK 99 -1 -
GGMAKNNFV CGRP_RANRI 20 -1 -
GGVVKDNFV RATCAL5 102 -1 -
GGMGNSNFV S40496S2 26 -1 -
GGMGNSNFV OGU71287 26 -1 -

Motif 4 width=9
Element Seqn Id St Int Rpt
VPTNVGAKA S40496S2 34 -1 -
VPTNVGSQA CGRP_SHEEP 28 -1 -
VPTNVGSEA CAL1_RAT 110 -1 -
VPTNVGSKA CAL1_HUMAN 110 -1 -
VPTNVGSKA CAL2_RAT 116 -1 -
VPTDVGSEA CGRP_PIG 28 -1 -
VPTNVGSKA CALR_CHICK 107 -1 -
VPTNVGSKA CGRP_RANRI 28 -1 -
VPTNVGAKA OGU71287 34 -1 -
VPTNVGSEA B44173 110 -1 -
VPTNVGSKA CAL2_HUMAN 109 -1 -
VPTNVGSEA RATCAL5 110 -1 -
Final Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
ACNTATCVTH CAL2_HUMAN 82 82 -
SCNTATCVTH CGRP_SHEEP 1 1 -
SCNTATCVTH CAL1_RAT 83 83 -
ACDTATCVTH CAL1_HUMAN 83 83 -
SCNTATCVTH CAL2_RAT 89 89 -
SCNTATCVTH CGRP_PIG 1 1 -
ACNTATCVTH CALR_CHICK 80 80 -
ACNTATCVTH CGRP_RANRI 1 1 -

Motif 2 width=11
Element Seqn Id St Int Rpt
HRLAGLLSRSG CAL2_HUMAN 91 -1 -
HRLAGLLSRSG CGRP_SHEEP 10 -1 -
HRLAGLLSRSG CAL1_RAT 92 -1 -
HRLAGLLSRSG CAL1_HUMAN 92 -1 -
HRLAGLLRRSG CAL2_RAT 98 -1 -
HRLAGLLSRSG CGRP_PIG 10 -1 -
HRLADFLSRSG CALR_CHICK 89 -1 -
HRLADFLSRSG CGRP_RANRI 10 -1 -

Motif 3 width=9
Element Seqn Id St Int Rpt
GGMVKSNFV CAL2_HUMAN 101 -1 -
GGVVKSNFV CGRP_SHEEP 20 -1 -
GGVVKDNFV CAL1_RAT 102 -1 -
GGVVKNNFV CAL1_HUMAN 102 -1 -
GGVVKDNFV CAL2_RAT 108 -1 -
GGMVKSNFV CGRP_PIG 20 -1 -
GGVGKNNFV CALR_CHICK 99 -1 -
GGMAKNNFV CGRP_RANRI 20 -1 -

Motif 4 width=9
Element Seqn Id St Int Rpt
VPTNVGSKA CAL2_HUMAN 109 -1 -
VPTNVGSQA CGRP_SHEEP 28 -1 -
VPTNVGSEA CAL1_RAT 110 -1 -
VPTNVGSKA CAL1_HUMAN 110 -1 -
VPTNVGSKA CAL2_RAT 116 -1 -
VPTDVGSEA CGRP_PIG 28 -1 -
VPTNVGSKA CALR_CHICK 107 -1 -
VPTNVGSKA CGRP_RANRI 28 -1 -