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PR00863

Identifier
NODAVIRPTASE  [View Relations]  [View Alignment]  
Accession
PR00863
No. of Motifs
7
Creation Date
06-MAR-1998  (UPDATE 07-JUN-1999)
Title
Nodavirus coat precursor endopeptidase (A6) aspartic protease signature
Database References

INTERPRO; IPR000696
PDB; 2BBV; 1NOV
SCOP; 2BBV;
CATH; 2BBV;
Literature References
1. RAWLINGS, N.D. AND BARRETT A.J.
Families of aspartic peptidases, and those of unkown catalytic mechanism.
METHODS ENZYMOL. 248 183-228 (1995).
 
2. RAWLINGS, N.D. AND BARRETT, A.J.
Evolutionary families of peptidases.
BIOCHEM.J. 290 205-218 (1993).
 
3. BAIROCH, A. AND RAWLINGS, N.
Classification of peptidase families and index of peptidase entries in
SWISS-PROT.
http://expasy.hcuge.ch/cgi-bin/lists?peptidas.txt
 
4. KAESBERG P., DASGUPTA R., SGRO, J.Y., SELLING, B.H., HOSUR, M.V.
AND JOHNSON, J.E.
Structural homology among four nodaviruses as deduced by sequencing
and X-ray crystallography.
J.MOL.BIOL. 214(2) 423-435 (1990).

Documentation
Aspartic proteases have a catalytic aspartate residue at their active site.
More than 8 families (denoted A1-A9) have been identified, three of which 
(pepsin, retropepsin and cauliflower mosaic virus peptidase) have been 
grouped into a single clan (AA), as they are all thought to have a common 
ancestry. The remaining five families have not yet been assigned to clans 
[1-3].
 
Nodavirus coat precusor endopeptidases belong to the A6 family of aspartic
proteases [4]. At the moment, it is not clear whether they share a common 
ancestry with other aspartic proteases. Nodaviruses are small, icosahedral
viruses, pathogenic to insects and mammals. A virus particle consists of a 
single virion, within which is packaged two RNA stands, RNA1 and RNA2. 
Nodavirus coat precursor endopeptidase (also known as protein alpha) is the 
only protein encoded by RNA2. During the process of virion assembly, this 
precursor is cleaved into coat proteins beta and gamma. RNA1 encodes two
proteins, at least one of which is involved in RNA replication. The 
relatively uncomplicated nature of their structural protein and RNA 
constituents make the nodaviruses a good virus model [4].
 
The 3D structure of the capsid protein has been determined by X-ray
crystallography to 2.8A resolution [4]. The structure contains a beta-barrel
domain, with a prominent protrusion composed largely of beta-sheet. This 
protrusion, together with similar protrusions from neighbouring subunits,
forms a prominent trigonal pyramid with quasi-3-fold symmetry [4]. Two
alpha-helices extend toward the interior of the particle [4].
 
NODAVIRPTASE is a 7-element fingerprint that provides a signature for
nodavirus coat 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 first two
alpha-helices; motif 2 spans the C-terminus of the second beta-strand,
leading into the third strand; motif 3 includes helix 3; motif 4 spans
strands 5-7; motif 5 encompasses strands 10 and 11, and helix 5, which
lies between them; motif 6 includes strand 16; and motif 7 lies at the
C-terminus. A single iteration on OWL30.0 was required to reach convergence,
no further sequences being identified beyond the starting set of 4.
 
An update on SPTR37_9f identified a true set of 4 sequences.
Summary Information
4 codes involving  7 elements
0 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 Feature Index
74444444
60000000
50000000
40000000
30000000
20000000
1234567
True Positives
COAT_BBV      COAT_BOOLV    COAT_FHV      COAT_NODAV    
Sequence Titles
COAT_BBV    COAT PROTEIN PRECURSOR - BLACK BEETLE VIRUS (BBV). 
COAT_BOOLV COAT PROTEIN PRECURSOR - BOOLARRA VIRUS.
COAT_FHV COAT PROTEIN PRECURSOR - FLOCK HOUSE VIRUS.
COAT_NODAV COAT PROTEIN PRECURSOR - NODAMURA VIRUS (NOV).
Scan History
OWL30_0    1  50   NSINGLE    
SPTR37_9f 2 5 NSINGLE
Initial Motifs
Motif 1  width=29
Element Seqn Id St Int Rpt
PGLAFLKCAFAPPDFNTDPGKGIPDRFEG COAT_FHV 62 62 -
PGLAFLKCAFAPPDFNTDPGKGIPDRFEG COAT_BBV 62 62 -
PGLSFLKCAFASPDSNTDPGKGIPDNFEG COAT_BOOLV 48 48 -
PGLDFLKCAFASPDFSTDPGKGIPDKFQG COAT_NODAV 54 54 -

Motif 2 width=12
Element Seqn Id St Int Rpt
ILIAPTPGVAYW COAT_FHV 113 22 -
ILIAPTPGVAYW COAT_BBV 113 22 -
IIVLPTPGVAFW COAT_BOOLV 104 27 -
LLVAPIPGIACL COAT_NODAV 105 22 -

Motif 3 width=10
Element Seqn Id St Int Rpt
YPGFTSMFGT COAT_FHV 145 20 -
FPGFNSMFGN COAT_BBV 145 20 -
FPDFTSLFGT COAT_BOOLV 141 25 -
FPGFDQLFGT COAT_NODAV 136 19 -

Motif 4 width=27
Element Seqn Id St Int Rpt
FRYASMNVGIYPTSNLMQFAGSITVWK COAT_FHV 166 11 -
FRYASMNVGIYPTSNLMQFAGSITVWK COAT_BBV 166 11 -
FRYASMNFGLYPTCNSTQYNGGISVWK COAT_BOOLV 162 11 -
FRYASMAAGVYPTSNLMQFAGSIQVYK COAT_NODAV 157 11 -

Motif 5 width=17
Element Seqn Id St Int Rpt
GPDNFSESFIKGVFSQS COAT_FHV 227 34 -
GPDNFSESFIKGVFSQS COAT_BBV 227 34 -
GDENYSESFIDGVFTQS COAT_BOOLV 223 34 -
PNNNYSGSFIEGCYSQS COAT_NODAV 222 38 -

Motif 6 width=19
Element Seqn Id St Int Rpt
GAVNSAILKAWSCIEYRPN COAT_FHV 306 62 -
GAVNSAILKTWACLEYRPN COAT_BBV 306 62 -
GSVNTATIKTWACIEYRPN COAT_BOOLV 302 62 -
GAVNTAVLKVWACVEYRPN COAT_NODAV 298 59 -

Motif 7 width=15
Element Seqn Id St Int Rpt
ASNIPGPIGVAASGI COAT_FHV 381 56 -
ASNVPGPIGIAASGL COAT_BBV 381 56 -
ASYVPGPVGGIATGV COAT_BOOLV 377 56 -
ASTIPGPVGVAATGI COAT_NODAV 373 56 -
Final Motifs
Motif 1  width=29
Element Seqn Id St Int Rpt
PGLAFLKCAFAPPDFNTDPGKGIPDRFEG COAT_FHV 62 62 -
PGLAFLKCAFAPPDFNTDPGKGIPDRFEG COAT_BBV 62 62 -
PGLSFLKCAFASPDSNTDPGKGIPDNFEG COAT_BOOLV 48 48 -
PGLDFLKCAFASPDFSTDPGKGIPDKFQG COAT_NODAV 54 54 -

Motif 2 width=12
Element Seqn Id St Int Rpt
ILIAPTPGVAYW COAT_FHV 113 22 -
ILIAPTPGVAYW COAT_BBV 113 22 -
IIVLPTPGVAFW COAT_BOOLV 104 27 -
LLVAPIPGIACL COAT_NODAV 105 22 -

Motif 3 width=10
Element Seqn Id St Int Rpt
YPGFTSMFGT COAT_FHV 145 20 -
FPGFNSMFGN COAT_BBV 145 20 -
FPDFTSLFGT COAT_BOOLV 141 25 -
FPGFDQLFGT COAT_NODAV 136 19 -

Motif 4 width=27
Element Seqn Id St Int Rpt
FRYASMNVGIYPTSNLMQFAGSITVWK COAT_FHV 166 11 -
FRYASMNVGIYPTSNLMQFAGSITVWK COAT_BBV 166 11 -
FRYASMNFGLYPTCNSTQYNGGISVWK COAT_BOOLV 162 11 -
FRYASMAAGVYPTSNLMQFAGSIQVYK COAT_NODAV 157 11 -

Motif 5 width=17
Element Seqn Id St Int Rpt
GPDNFSESFIKGVFSQS COAT_FHV 227 34 -
GPDNFSESFIKGVFSQS COAT_BBV 227 34 -
GDENYSESFIDGVFTQS COAT_BOOLV 223 34 -
PNNNYSGSFIEGCYSQS COAT_NODAV 222 38 -

Motif 6 width=19
Element Seqn Id St Int Rpt
GAVNSAILKAWSCIEYRPN COAT_FHV 306 62 -
GAVNSAILKTWACLEYRPN COAT_BBV 306 62 -
GSVNTATIKTWACIEYRPN COAT_BOOLV 302 62 -
GAVNTAVLKVWACVEYRPN COAT_NODAV 298 59 -

Motif 7 width=15
Element Seqn Id St Int Rpt
ASNIPGPIGVAASGI COAT_FHV 381 56 -
ASNVPGPIGIAASGL COAT_BBV 381 56 -
ASYVPGPVGGIATGV COAT_BOOLV 377 56 -
ASTIPGPVGVAATGI COAT_NODAV 373 56 -