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PR01273

Identifier
INVTBRTCOLOR  [View Relations]  [View Alignment]  
Accession
PR01273
No. of Motifs
6
Creation Date
10-JAN-2000
Title
Invertebrate colouration protein signature
Database References
PRINTS; PR00179 LIPOCALIN
PDB; 1BBP
SCOP; 1BBP
CATH; 1BBP
Literature References
1. PERVAIS, S. AND BREW, K. 
Homology of beta-lactoglobulin, serum retinol-binding protein and 
protein HC.
SCIENCE 228 335-337 (1985).
 
2. FLOWER, D.R.
The lipocalin protein family: structure and function.
BIOCHEM.J. 318 1-14 (1996).
 
3. FLOWER, D.R., NORTH, A.C.T. AND ATTWOOD, T.K.
Structural and sequence relationships in the lipocalins and related
proteins.
PROTEIN SCI. 2 753-761 (1993). 
 
4. FLOWER, D.R.
Multiple molecular recognition properties of the lipocalin protein family.
J.MOL.REC. 8 185-195 (1995).
 
5. ZAGALSKY, P.F., ELIOPOULOS, E.E. AND FINDLAY, J.B.C.
The architecture of invertebrate carotenoproteins.
COMP.BIOCHEM.PHYSIOL. 97 1-18 (1990).
 
6. HUBER, R., SCHNEIDER, M., MAYR, I., MULLER, R., DEUTZMANN, R., SUTER, F.,  
ZUBER, H., FALK, H. AND KAYSER, H. 
Molecular structure of the bilin binding protein (BBP) from Pieris brassicae 
after refinement at 2.0A resolution.
J.MOL.BIOL. 198 499-513 (1987). 

Documentation
The lipocalins are a diverse, interesting, yet poorly understood family of 
proteins composed, in the main, of extracellular ligand-binding proteins
displaying high specificity for small hydrophobic molecules [1,2]. Functions
of these proteins include transport of nutrients, control of cell regula-
tion, pheromone transport, cryptic colouration and the enzymatic synthesis
of prostaglandins.
   
The crystal structures of several lipocalins have been solved and show a 
novel 8-stranded anti-parallel beta-barrel fold well conserved within the
family. Sequence similarity within the family is at a much lower level and
would seem to be restricted to conserved disulphides and 3 motifs, which
form a juxtaposed cluster that may act as a common cell surface receptor
site [2]. By contrast, at the more variable end of the fold are found an 
internal ligand binding site and a putative surface for the formation of 
macromolecular complexes [4]. The anti-parallel beta-barrel fold is also
exploited by the fatty acid-binding proteins (which function similarly by
binding small hydrophobic molecules), by avidin and the closely related
metalloprotease inhibitors, and by triabin. Similarity at the sequence 
level, however, is less obvious, being confined to a single short 
N-terminal motif.
 
The lipocalin family can be subdivided into kernal and outlier sets. The
kernal lipocalins form the largest self-consistent group (see LIPOCALIN
signature). The outlier lipocalins form several smaller distinct subgroups: 
the OBPs, the von Ebner's gland proteins, alpha-1-acid glycoproteins, 
tick histamine binding proteins and the nitrophorins.
 
A number of lipocalins act in invertebrate colouration: bilin binding
protein from the cabbage white butterfly (Pieris brassicae), the closely
related protein insecticyanin from Manduca sexta (tobacco hornworm) and the
lobster protein crustacyanin. Like other members of the family, they bind 
small molecules, and gain their colourant properties from interaction with
their ligands.
 
Crustacyanin (meaning `shell blue') is the general name given to the 
carotenoprotein complex found in the epicuticle, or calcified outer layer,
of the lobster carapace [5]. It acts as the dominant pigment of the lobster 
shell, giving rise to its characteristic blue colour. In solution, 
crustacyanin exists as an equilibrium mixture between several distinct
forms, differing in their physical and spectral properties [5]. The native, 
blue form (alpha-crustacyanin), which predominates in vivo, will, at low 
ionic strength, form alpha'-crustacyanin; this in turn changes to purple
beta-crustacyanin on standing. The alpha to alpha' transition is favoured
by low ionic strength and is reversible, while conversion into beta-
crustacyanin is irreversible. Native alpha-crustacyanin is an octamer of
heterodimers, totalling 16 separate polypeptide chains, each dimer binding 
two molecules of astaxanthin, beta-crustacyanin corresponding to the free 
heterodimer.
 
A variety of different bilin pigments, derived from haem-breakdown products,
are distributed widely in insects. Biliverdin IXy is amongst the most common,
especially in butterfiies and moths. These pigments are usually associated
with proteins, and they contribute significantly to colouration in the
epidermis or inter-lamellar space of the wing. Two insect bilin-binding 
lipocalins have been studied in great detail: insecticyanin from the tobacco
hornworm and bilin-binding protein (BBP) from Pieris brassicae [6]. Both are
blue pigment proteins forming complexes with biliverdin IXy. The precise 
function of these proteins is unclear; apart from their role as pigments, 
it has been suggested that they may function in photoreception and 
protection from photo-induced free radicals. Many of these pigment
complexes are remarkably stable, and persist, during insect development,
from their synthesis during the larval stage, through the pupal stage 
into adulthood.
 
INVTBRTCOLOR is a 6-element fingerprint that provides a signature for 
invertebrate colouration proteins. The fingerprint was derived from an 
initial alignment of 4 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length - motif 1 spans the
conserved N-terminal 310 helix and the first strand (this includes the 
region encoded by PROSITE pattern LIPOCALIN (PS00213) and corresponds to 
the first LIPOCALIN fingerprint motif); motif 2 encodes loop L1 and the
anterior part of the second strand; motif 3 spans the posterior half
of the second strand, loop L2 and the anterior part of the third strand; 
motif 4 encodes the fifth and sixth strands and corresponds to the second
LIPOCALIN motif; motif 5, which corresponds to strand 8 and the loop
connecting it to the main C-terminal alpha-helix, is similar to the third
LIPOCALIN motif; and motif 6 spans the short strand I and flanking regions.
Two iterations on SPRT37_10f were required to reach convergence, at which 
point a true set comprising 7 sequences was identified. Several partial
matches were also found, all of which are related lipocalins that match
motifs 1, 4 and 5, the characteristic motifs of the lipocalin signature. 
Summary Information
   7 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
2 codes involving 3 elements
5 codes involving 2 elements
Composite Feature Index
6777777
5000000
4000000
3200220
2300520
123456
True Positives
BBP_PIEBR     CRA2_HOMGA    CRC1_HOMGA    ICYA_MANSE    
ICYB_MANSE Q00629 Q24996
True Positive Partials
Codes involving 3 elements
APD_CAVPO APD_HUMAN
Codes involving 2 elements
APD_MOUSE APD_RABIT LAZA_SCHAM RET1_ONCMY
RET2_ONCMY
Sequence Titles
BBP_PIEBR   BILIN-BINDING PROTEIN PRECURSOR (BBP) - PIERIS BRASSICAE (WHITE BUTTERFLY). 
CRA2_HOMGA CRUSTACYANIN A2 SUBUNIT - HOMARUS GAMMARUS (EUROPEAN LOBSTER) (HOMARUS VULGARIS).
CRC1_HOMGA CRUSTACYANIN C1 SUBUNIT - HOMARUS GAMMARUS (EUROPEAN LOBSTER) (HOMARUS VULGARIS).
ICYA_MANSE INSECTICYANIN A FORM (BLUE BILIPROTEIN) (INS-A) - MANDUCA SEXTA (TOBACCO HAWKMOTH) (TOBACCO HORNWORM).
ICYB_MANSE INSECTICYANIN B FORM PRECURSOR (BLUE BILIPROTEIN) (INS-B) - MANDUCA SEXTA (TOBACCO HAWKMOTH) (TOBACCO HORNWORM).
Q00629 INSECTICYANIN A FORM (BLUE BILIPROTEIN) - MANDUCA SEXTA (TOBACCO HAWKMOTH) (TOBACCO HORNWORM).
Q24996 GALLERIN - GALLERIA MELLONELLA (WAX MOTH).

APD_CAVPO APOLIPOPROTEIN D PRECURSOR - CAVIA PORCELLUS (GUINEA PIG).
APD_HUMAN APOLIPOPROTEIN D PRECURSOR - HOMO SAPIENS (HUMAN).

APD_MOUSE APOLIPOPROTEIN D PRECURSOR - MUS MUSCULUS (MOUSE).
APD_RABIT APOLIPOPROTEIN D PRECURSOR - ORYCTOLAGUS CUNICULUS (RABBIT).
LAZA_SCHAM LAZARILLO PROTEIN PRECURSOR - SCHISTOCERCA AMERICANA (AMERICAN GRASSHOPPER).
RET1_ONCMY PLASMA RETINOL-BINDING PROTEIN I (PRBP-I) - ONCORHYNCHUS MYKISS (RAINBOW TROUT) (SALMO GAIRDNERI).
RET2_ONCMY PLASMA RETINOL-BINDING PROTEIN II (PRBP-II) - ONCORHYNCHUS MYKISS (RAINBOW TROUT) (SALMO GAIRDNERI).
Scan History
SPTR37_10f 2  17   NSINGLE    
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
NDFDLSAFAGAWHEIAK ICYA_MANSE 16 16 -
DNFDWSNYHGKWWEVAK BBP_PIEBR 30 30 -
QTPNRNSYAGVWYQFAL CRC1_HOMGA 24 24 -
DNFDLRRYAGRWYQTHI CRA2_HOMGA 19 19 -

Motif 2 width=13
Element Seqn Id St Int Rpt
PLENENQGKCTIA ICYA_MANSE 34 1 -
PNSVEKYGKCGWA BBP_PIEBR 48 1 -
NNPYQLIEKCVRN CRC1_HOMGA 42 1 -
ENAYQPVTRCIHS CRA2_HOMGA 37 1 -

Motif 3 width=13
Element Seqn Id St Int Rpt
EYSTNDYGFKVTT CRA2_HOMGA 52 2 -
EYKYDGKKASVYN ICYA_MANSE 47 0 -
EYSFDGKQFVIKS CRC1_HOMGA 55 0 -
EYTPEGKSVKVSN BBP_PIEBR 61 0 -

Motif 4 width=15
Element Seqn Id St Int Rpt
VIETDYETYSCVYSC CRA2_HOMGA 105 40 -
ILETDYSNYACLYSC CRC1_HOMGA 107 39 -
VLSTDNKNYIIGYYC BBP_PIEBR 116 42 -
VLATDYKNYAINYNC ICYA_MANSE 105 45 -

Motif 5 width=14
Element Seqn Id St Int Rpt
HSIHAWILSKSKVL ICYA_MANSE 128 8 -
HQDFVWVLSRSKVL BBP_PIEBR 139 8 -
HSDFSFIFSRSANL CRC1_HOMGA 129 7 -
KSEFAFVFSRTPQT CRA2_HOMGA 126 6 -

Motif 6 width=13
Element Seqn Id St Int Rpt
VEFSKFVPVSHTA CRA2_HOMGA 156 16 -
VDTTRFVKTVQGS CRC1_HOMGA 159 16 -
VDSQKLVYSDFSE BBP_PIEBR 170 17 -
IDASKFISNDFSE ICYA_MANSE 160 18 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
DDFDLSAFAGAWHEIAK ICYB_MANSE 33 33 -
QTPNRNSYAGVWYQFAL CRC1_HOMGA 24 24 -
DNFDLRRYAGRWYQTHI CRA2_HOMGA 19 19 -
NDFDLSAFAGAWHEIAK ICYA_MANSE 16 16 -
DDFDLSAFAGAWHEIAK Q00629 33 33 -
DNFNLTAYQGVWYEISK Q24996 30 30 -
DNFDWSNYHGKWWEVAK BBP_PIEBR 30 30 -

Motif 2 width=13
Element Seqn Id St Int Rpt
PLENENQGKCTIA ICYB_MANSE 51 1 -
PLENENQGKCTIA ICYA_MANSE 34 1 -
PLENENEGKCTVA Q00629 51 1 -
PNDAEKNGKCGQA Q24996 48 1 -
PNSVEKYGKCGWA BBP_PIEBR 48 1 -
NNPYQLIEKCVRN CRC1_HOMGA 42 1 -
ENAYQPVTRCIHS CRA2_HOMGA 37 1 -

Motif 3 width=13
Element Seqn Id St Int Rpt
EYKYDGKKASVYN ICYB_MANSE 64 0 -
EYKYDGKKASVYN Q00629 64 0 -
EYKLEGEVVKVKN Q24996 61 0 -
EYSTNDYGFKVTT CRA2_HOMGA 52 2 -
EYTPEGKSVKVSN BBP_PIEBR 61 0 -
EYSFDGKQFVIKS CRC1_HOMGA 55 0 -
EYKYDGKKASVYN ICYA_MANSE 47 0 -

Motif 4 width=15
Element Seqn Id St Int Rpt
VLSTDNKNYIIGYYC BBP_PIEBR 116 42 -
VLATDYKNYAINYNC ICYB_MANSE 122 45 -
VLATDYKNYAINYNC ICYA_MANSE 105 45 -
VLATDYKNYAINYNC Q00629 122 45 -
VIATDYQNYAIAYTC Q24996 117 43 -
ILETDYSNYACLYSC CRC1_HOMGA 107 39 -
VIETDYETYSCVYSC CRA2_HOMGA 105 40 -

Motif 5 width=14
Element Seqn Id St Int Rpt
HQDFVWVLSRSKVL BBP_PIEBR 139 8 -
HSDFSFIFSRSANL CRC1_HOMGA 129 7 -
KSEFAFVFSRTPQT CRA2_HOMGA 126 6 -
HNDSIWILSRAKKL Q24996 140 8 -
HSIHAWVLSRNKVL Q00629 145 8 -
HSIHAWILSKSKVL ICYA_MANSE 128 8 -
HSIHAWILSKSKVL ICYB_MANSE 145 8 -

Motif 6 width=13
Element Seqn Id St Int Rpt
VDSQKLVYSDFSE BBP_PIEBR 170 17 -
VDTTRFVKTVQGS CRC1_HOMGA 159 16 -
VEFSKFVPVSHTA CRA2_HOMGA 156 16 -
IDASKFISNDFSE ICYB_MANSE 177 18 -
IDASKFISNDFSE ICYA_MANSE 160 18 -
IDASKFMSNEFSE Q00629 177 18 -
IDASKLVQTDFSE Q24996 172 18 -