POLS_IBDV
ID POLS_IBDV Reviewed; 1012 AA.
AC P61825; Q9Q6Q6;
DT 07-JUN-2004, integrated into UniProtKB/Swiss-Prot.
DT 04-APR-2006, sequence version 2.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=Structural polyprotein;
DE Short=PP;
DE Contains:
DE RecName: Full=Precursor of VP2;
DE Short=Pre-VP2;
DE Contains:
DE RecName: Full=Capsid protein VP2;
DE Contains:
DE RecName: Full=Structural peptide 1;
DE Short=p1;
DE AltName: Full=pep46;
DE Contains:
DE RecName: Full=Structural peptide 2;
DE Short=p2;
DE AltName: Full=pep7a;
DE Contains:
DE RecName: Full=Structural peptide 3;
DE Short=p3;
DE AltName: Full=pep7b;
DE Contains:
DE RecName: Full=Structural peptide 4;
DE Short=p4;
DE AltName: Full=pep11;
DE Contains:
DE RecName: Full=Protease VP4;
DE EC=3.4.21.-;
DE AltName: Full=Non-structural protein VP4;
DE Short=NS;
DE Contains:
DE RecName: Full=Capsid protein VP3;
OS Avian infectious bursal disease virus (IBDV) (Gumboro disease virus).
OC Viruses; Riboviria; Orthornavirae; Birnaviridae; Avibirnavirus.
OX NCBI_TaxID=10995;
OH NCBI_TaxID=9031; Gallus gallus (Chicken).
OH NCBI_TaxID=9103; Meleagris gallopavo (Wild turkey).
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Isolate CEF94;
RX PubMed=10600604; DOI=10.1006/viro.1999.0042;
RA Boot H.J., ter Huurne A.A., Peeters B.P.H., Gielkens A.L.;
RT "Efficient rescue of infectious bursal disease virus from cloned cDNA:
RT evidence for involvement of the 3'-terminal sequence in genome
RT replication.";
RL Virology 265:330-341(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1-453.
RC STRAIN=Isolate Indian;
RA Chauhan S., Rai A., Rai N., Gupta P.K.;
RT "Cloning of VP2 gene of infectious bursal disease virus in a mammalian
RT expression vector for use as DNA vaccine.";
RL Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP INTERACTION OF VP3 WITH VP1, AND RNA-BINDING.
RC STRAIN=Isolate CEF94;
RX PubMed=12388690; DOI=10.1128/jvi.76.22.11301-11311.2002;
RA Tacken M.G., Peeters B.P.H., Thomas A.A.M., Rottier P.J.M., Boot H.J.;
RT "Infectious bursal disease virus capsid protein VP3 interacts both with
RT VP1, the RNA-dependent RNA polymerase, and with viral double-stranded
RT RNA.";
RL J. Virol. 76:11301-11311(2002).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-456.
RX PubMed=16809295; DOI=10.1128/jvi.00368-06;
RA Garriga D., Querol-Audi J., Abaitua F., Saugar I., Pous J., Verdaguer N.,
RA Caston J.R., Rodriguez J.F.;
RT "The 2.6-Angstrom structure of infectious bursal disease virus-derived T=1
RT particles reveals new stabilizing elements of the virus capsid.";
RL J. Virol. 80:6895-6905(2006).
RN [5]
RP STRUCTURE BY NMR OF 442-487.
RX PubMed=17488723; DOI=10.1074/jbc.m701048200;
RA Galloux M., Libersou S., Morellet N., Bouaziz S., Da Costa B., Ouldali M.,
RA Lepault J., Delmas B.;
RT "Infectious bursal disease virus, a non-enveloped virus, possesses a
RT capsid-associated peptide that deforms and perforates biological
RT membranes.";
RL J. Biol. Chem. 282:20774-20784(2007).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 1-452.
RX PubMed=19144647; DOI=10.1074/jbc.m808942200;
RA Irigoyen N., Garriga D., Navarro A., Verdaguer N., Rodriguez J.F.,
RA Caston J.R.;
RT "Autoproteolytic activity derived from the infectious bursal disease virus
RT capsid protein.";
RL J. Biol. Chem. 284:8064-8072(2009).
CC -!- FUNCTION: Capsid protein VP2 self assembles to form an icosahedral
CC capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of
CC 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also
CC involved in attachment and entry into the host cell by interacting with
CC host ITGA4/ITGB1 (By similarity). {ECO:0000250}.
CC -!- FUNCTION: The precursor of VP2 plays an important role in capsid
CC assembly. First, pre-VP2 and VP2 oligomers assemble to form a
CC procapsid. Then, the pre-VP2 intermediates may be processed into VP2
CC proteins by proteolytic cleavage mediated by VP4 to obtain the mature
CC virion. The final capsid is composed of pentamers and hexamers but VP2
CC has a natural tendency to assemble into all-pentameric structures.
CC Therefore pre-VP2 may be required to allow formation of the hexameric
CC structures (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Protease VP4 is a serine protease that cleaves the
CC polyprotein into its final products. Pre-VP2 is first partially
CC cleaved, and may be completely processed by VP4 upon capsid maturation.
CC {ECO:0000255|PROSITE-ProRule:PRU00881}.
CC -!- FUNCTION: Capsid protein VP3 plays a key role in virion assembly by
CC providing a scaffold for the capsid made of VP2. May self-assemble to
CC form a T=4-like icosahedral inner-capsid composed of at least 180
CC trimers. Plays a role in genomic RNA packaging by recruiting VP1 into
CC the capsid and interacting with the dsRNA genome segments to form a
CC ribonucleoprotein complex. Additionally, the interaction of the VP3 C-
CC terminal tail with VP1 removes the inherent structural blockade of the
CC polymerase active site. Thus, VP3 can also function as a
CC transcriptional activator (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Structural peptide 1 is a small peptide derived from pre-VP2
CC C-terminus. It destabilizes and perforates cell membranes, suggesting a
CC role during entry.
CC -!- FUNCTION: Structural peptide 2 is a small peptide derived from pre-VP2
CC C-terminus. It is not essential for the virus viability, but viral
CC growth is affected when missing (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Structural peptide 3 is a small peptide derived from pre-VP2
CC C-terminus. It is not essential for the virus viability, but viral
CC growth is affected when missing (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Structural peptide 4 is a small peptide derived from pVP2 C-
CC terminus. It is essential for the virus viability (By similarity).
CC {ECO:0000250}.
CC -!- SUBUNIT: Capsid protein VP2 is a homotrimer. A central divalent metal
CC stabilizes the VP2 trimer, possibly calcium. Capsid protein VP3 is a
CC homodimer. Capsid protein VP2 interacts with host ITGA4/ITGB1. Capsid
CC protein VP3 interacts (via C-terminus) with VP1 in the cytoplasm.
CC Capsid VP3 interacts with VP2 (By similarity). {ECO:0000250}.
CC -!- INTERACTION:
CC P61825; P61825: -; NbExp=3; IntAct=EBI-15554394, EBI-15554394;
CC -!- SUBCELLULAR LOCATION: [Capsid protein VP2]: Virion {ECO:0000305}. Host
CC cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Capsid protein VP3]: Virion {ECO:0000305}. Host
CC cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Structural peptide 1]: Virion {ECO:0000305}.
CC Host cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Structural peptide 2]: Virion {ECO:0000305}.
CC Host cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Structural peptide 3]: Virion {ECO:0000305}.
CC Host cytoplasm {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Structural peptide 4]: Virion {ECO:0000305}.
CC Host cytoplasm {ECO:0000305}.
CC -!- PTM: Specific enzymatic cleavages yield mature proteins. The capsid
CC assembly seems to be regulated by polyprotein processing. The protease
CC VP4 cleaves itself off the polyprotein, thus releasing pre-VP2 and VP3
CC within the infected cell. During capsid assembly, the C-terminus of
CC pre-VP2 is further processed by VP4, giving rise to VP2, the external
CC capsid protein and three small peptides that all stay closely
CC associated with the capsid (By similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: The sequence shown is that of isolate CEF94.
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DR EMBL; AF194428; AAF16082.1; -; mRNA.
DR EMBL; AJ621158; CAF18300.1; -; Genomic_RNA.
DR PDB; 2GSY; X-ray; 2.60 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T=1-456.
DR PDB; 2IMU; NMR; -; A=442-487.
DR PDB; 3FBM; X-ray; 3.10 A; A=6-452.
DR PDBsum; 2GSY; -.
DR PDBsum; 2IMU; -.
DR PDBsum; 3FBM; -.
DR SMR; P61825; -.
DR DIP; DIP-29594N; -.
DR MEROPS; S50.002; -.
DR TCDB; 1.A.59.1.1; the bursal disease virus pore-forming peptide, pep46 (pep46) family.
DR EvolutionaryTrace; P61825; -.
DR GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0039621; C:T=13 icosahedral viral capsid; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008236; F:serine-type peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR Gene3D; 1.10.150.620; -; 1.
DR Gene3D; 1.10.8.880; -; 1.
DR Gene3D; 2.60.120.20; -; 1.
DR InterPro; IPR002662; Birna_VP2.
DR InterPro; IPR002663; Birna_VP3.
DR InterPro; IPR043048; Birna_VP3_dom1.
DR InterPro; IPR043049; Birna_VP3_dom2.
DR InterPro; IPR025775; Birna_VP4_Prtase_dom.
DR InterPro; IPR029053; Viral_coat.
DR Pfam; PF01766; Birna_VP2; 1.
DR Pfam; PF01767; Birna_VP3; 1.
DR Pfam; PF01768; Birna_VP4; 1.
DR PROSITE; PS51548; BIRNAVIRUS_VP4_PRO; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Capsid protein; Host cytoplasm; Hydrolase; Metal-binding;
KW Protease; Serine protease; T=13 icosahedral capsid protein; Virion.
FT CHAIN 1..1012
FT /note="Structural polyprotein"
FT /id="PRO_0000378356"
FT CHAIN 1..512
FT /note="Precursor of VP2"
FT /id="PRO_0000378357"
FT CHAIN 1..441
FT /note="Capsid protein VP2"
FT /id="PRO_0000036776"
FT PEPTIDE 442..487
FT /note="Structural peptide 1"
FT /evidence="ECO:0000250"
FT /id="PRO_0000227849"
FT PEPTIDE 488..494
FT /note="Structural peptide 2"
FT /evidence="ECO:0000250"
FT /id="PRO_0000227850"
FT PEPTIDE 495..501
FT /note="Structural peptide 3"
FT /evidence="ECO:0000250"
FT /id="PRO_0000227851"
FT PEPTIDE 502..512
FT /note="Structural peptide 4"
FT /evidence="ECO:0000250"
FT /id="PRO_0000227852"
FT CHAIN 513..755
FT /note="Protease VP4"
FT /id="PRO_0000227853"
FT CHAIN 756..1012
FT /note="Capsid protein VP3"
FT /id="PRO_0000227854"
FT DOMAIN 513..755
FT /note="Peptidase S50"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00881"
FT REGION 969..1012
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1003..1012
FT /note="Interaction with VP1 protein"
FT ACT_SITE 652
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00881"
FT ACT_SITE 692
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00881"
FT BINDING 30
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="ligand shared between trimeric partners"
FT /evidence="ECO:0000250"
FT SITE 441..442
FT /note="Cleavage; by protease VP4"
FT /evidence="ECO:0000250"
FT SITE 487..488
FT /note="Cleavage; by protease VP4"
FT /evidence="ECO:0000250"
FT SITE 494..495
FT /note="Cleavage; by protease VP4"
FT /evidence="ECO:0000250"
FT SITE 501..502
FT /note="Cleavage; by protease VP4"
FT /evidence="ECO:0000250"
FT SITE 512..513
FT /note="Cleavage; by protease VP4"
FT /evidence="ECO:0000250"
FT SITE 755..756
FT /note="Cleavage; by protease VP4"
FT /evidence="ECO:0000250"
FT VARIANT 80
FT /note="Y -> L (in strain: Isolate Indian)"
FT VARIANT 253
FT /note="H -> Q (in strain: Isolate Indian)"
FT VARIANT 263
FT /note="L -> F (in strain: Isolate Indian)"
FT VARIANT 270
FT /note="A -> T (in strain: Isolate Indian)"
FT VARIANT 279
FT /note="N -> D (in strain: Isolate Indian)"
FT VARIANT 284
FT /note="T -> A (in strain: Isolate Indian)"
FT VARIANT 290
FT /note="L -> M (in strain: Isolate Indian)"
FT VARIANT 312
FT /note="I -> V (in strain: Isolate Indian)"
FT VARIANT 330
FT /note="R -> S (in strain: Isolate Indian)"
FT VARIANT 409
FT /note="G -> A (in strain: Isolate Indian)"
FT HELIX 13..19
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 21..23
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 36..48
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:3FBM"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 64..74
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 96..110
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 123..131
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 154..159
FT /evidence="ECO:0007829|PDB:2GSY"
FT TURN 160..162
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 204..218
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 225..238
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 240..249
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 255..265
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 270..277
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 288..296
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 298..300
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 305..318
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 325..337
FT /evidence="ECO:0007829|PDB:2GSY"
FT TURN 338..341
FT /evidence="ECO:0007829|PDB:2GSY"
FT TURN 343..345
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 349..356
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 362..375
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 379..381
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 394..403
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 405..408
FT /evidence="ECO:0007829|PDB:2GSY"
FT STRAND 412..415
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 416..425
FT /evidence="ECO:0007829|PDB:2GSY"
FT TURN 434..438
FT /evidence="ECO:0007829|PDB:2GSY"
FT HELIX 444..454
FT /evidence="ECO:0007829|PDB:2IMU"
FT HELIX 456..462
FT /evidence="ECO:0007829|PDB:2IMU"
FT HELIX 468..474
FT /evidence="ECO:0007829|PDB:2IMU"
FT HELIX 476..481
FT /evidence="ECO:0007829|PDB:2IMU"
SQ SEQUENCE 1012 AA; 109671 MW; 1C58BCEB0FDB9EE1 CRC64;
MTNLQDQTQQ IVPFIRSLLM PTTGPASIPD DTLEKHTLRS ETSTYNLTVG DTGSGLIVFF
PGFPGSIVGA HYTLQSNGNY KFDQMLLTAQ NLPASYNYCR LVSRSLTVRS STLPGGVYAL
NGTINAVTFQ GSLSELTDVS YNGLMSATAN INDKIGNVLV GEGVTVLSLP TSYDLGYVRL
GDPIPAIGLD PKMVATCDSS DRPRVYTITA ADDYQFSSQY QPGGVTITLF SANIDAITSL
SVGGELVFQT SVHGLVLGAT IYLIGFDGTA VITRAVAANN GLTTGTDNLL PFNLVIPTNE
ITQPITSIKL EIVTSKSGGQ AGDQMSWSAR GSLAVTIHGG NYPGALRPVT LVAYERVATG
SVVTVAGVSN FELIPNPELA KNLVTEYGRF DPGAMNYTKL ILSERDRLGI KTVWPTREYT
DFREYFMEVA DLNSPLKIAG AFGFKDIIRA IRRIAVPVVS TLFPPAAPLA HAIGEGVDYL
LGDEAQAASG TARAASGKAR AASGRIRQLT LAADKGYEVV ANLFQVPQNP VVDGILASPG
VLRGAHNLDC VLREGATLFP VVITTVEDAM TPKALNSKMF AVIEGVREDL QPPSQRGSFI
RTLSGHRVYG YAPDGVLPLE TGRDYTVVPI DDVWDDSIML SKDPIPPIVG NSGNLAIAYM
DVFRPKVPIH VAMTGALNAC GEIEKVSFRS TKLATAHRLG LKLAGPGAFD VNTGPNWATF
IKRFPHNPRD WDRLPYLNLP YLPPNAGRQY HLAMAASEFK ETPELESAVR AMEAAANVDP
LFQSALSVFM WLEENGIVTD MANFALSDPN AHRMRNFLAN APQAGSKSQR AKYGTAGYGV
EARGPTPEEA QREKDTRISK KMETMGIYFA TPEWVALNGH RGPSPGQLKY WQNTREIPDP
NEDYLDYVHA EKSRLASEEQ ILRAATSIYG APGQAEPPQA FIDEVAKVYE INHGRGPNQE
QMKDLLLTAM EMKHRNPRRA LPKPKPKPNA PTQRPPGRLG RWIRTVSDED LE
