POL2_BPMV
ID POL2_BPMV Reviewed; 1018 AA.
AC P23009;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-1992, sequence version 2.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=RNA2 polyprotein;
DE AltName: Full=Genome polyprotein M;
DE AltName: Full=M RNA polyprotein;
DE AltName: Full=Middle component RNA polyprotein;
DE AltName: Full=P2;
DE Contains:
DE RecName: Full=VP58;
DE AltName: Full=P58;
DE Contains:
DE RecName: Full=Movement protein;
DE Short=MP;
DE Contains:
DE RecName: Full=Large capsid protein;
DE Short=LCP;
DE AltName: Full=Coat protein VP42;
DE AltName: Full=L subunit;
DE AltName: Full=Large coat protein;
DE Contains:
DE RecName: Full=Small capsid protein precursor;
DE AltName: Full=S subunit;
DE Contains:
DE RecName: Full=Mature small capsid protein;
DE Short=SCP;
DE AltName: Full=Coat protein VP22;
DE AltName: Full=Small capsid protein, N-terminus part;
DE AltName: Full=Small coat protein, N-terminus part;
DE Contains:
DE RecName: Full=Small capsid protein C-terminus part;
DE AltName: Full=Small coat protein C-terminus part;
OS Bean-pod mottle virus (strain Kentucky G7) (BPMV).
OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC Picornavirales; Secoviridae; Comovirinae; Comovirus.
OX NCBI_TaxID=31715;
OH NCBI_TaxID=53866; Desmodium.
OH NCBI_TaxID=3847; Glycine max (Soybean) (Glycine hispida).
OH NCBI_TaxID=3885; Phaseolus vulgaris (Kidney bean) (French bean).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=2053290; DOI=10.1016/0042-6822(91)90155-5;
RA Macfarlane S.A., Shanks M., Davies J.W., Zlotnick A., Lomonossoff G.P.;
RT "Analysis of the nucleotide sequence of bean pod mottle virus middle
RT component RNA.";
RL Virology 183:405-409(1991).
RN [2]
RP POSSIBLE PROTEOLYTIC CLEAVAGE (SMALL CAPSID PROTEIN PRECURSOR).
RX PubMed=1716655; DOI=10.1099/0022-1317-72-9-2225;
RA Joisson C., Van Regenmortel M.H.;
RT "Influence of the C terminus of the small protein subunit of bean pod
RT mottle virus on the antigenicity of the virus determined using monoclonal
RT antibodies and anti-peptide antiserum.";
RL J. Gen. Virol. 72:2225-2232(1991).
RN [3]
RP ALTERNATIVE INITIATION, AND FUNCTION (VP58).
RX PubMed=24390330; DOI=10.1128/jvi.03301-13;
RA Lin J., Guo J., Finer J., Dorrance A.E., Redinbaugh M.G., Qu F.;
RT "The bean pod mottle virus RNA2-encoded 58-kilodalton protein P58 is
RT required in cis for RNA2 accumulation.";
RL J. Virol. 88:3213-3222(2014).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 447-1018, FUNCTION (LARGE CAPSID
RP PROTEIN), FUNCTION (MATURE SMALL CAPSID PROTEIN), SUBCELLULAR LOCATION
RP (LARGE CAPSID PROTEIN), AND SUBCELLULAR LOCATION (MATURE SMALL CAPSID
RP PROTEIN).
RX PubMed=2749253; DOI=10.1126/science.2749253;
RA Chen Z., Stauffacher C., Li Y., Schmidt T., Bomu W., Kamer G., Shanks M.,
RA Lomonossoff G., Johnson J.E.;
RT "Protein-RNA interactions in an icosahedral virus at 3.0-A resolution.";
RL Science 245:154-159(1989).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 447-1005, FUNCTION (LARGE CAPSID
RP PROTEIN), FUNCTION (MATURE SMALL CAPSID PROTEIN), SUBCELLULAR LOCATION
RP (LARGE CAPSID PROTEIN), AND SUBCELLULAR LOCATION (MATURE SMALL CAPSID
RP PROTEIN).
RX PubMed=14517057; DOI=10.1016/s0042-6822(03)00457-4;
RA Lin T., Cavarelli J., Johnson J.E.;
RT "Evidence for assembly-dependent folding of protein and RNA in an
RT icosahedral virus.";
RL Virology 314:26-33(2003).
CC -!- FUNCTION: [VP58]: Responsible for viral RNA2 accumulation. May function
CC by recruiting the RNA1-encoded polyprotein that contains the
CC replication protein to RNA2 and enable its replication.
CC {ECO:0000269|PubMed:24390330}.
CC -!- FUNCTION: [Movement protein]: Transports the viral genome to
CC neighboring plant cells directly through plasmosdesmata, without any
CC budding. The movement protein allows efficient cell to cell
CC propagation, by bypassing the host cell wall barrier. Acts by forming a
CC tubular structure at the host plasmodesmata, enlarging it enough to
CC allow free passage of virion capsids. Binds to GTP and to single-
CC stranded RNA and single-stranded DNA in a non-sequence-specific manner.
CC {ECO:0000250|UniProtKB:P03599}.
CC -!- FUNCTION: [Small capsid protein precursor]: The cleavable C-terminus of
CC small capsid protein seems to be involved in viral assembly and RNA
CC packaging. After virus assembly, these amino acids are cleaved off
CC during the normal maturation of the virus. Also seems to act as
CC suppressor of post-transcriptional gene silencing (PTGS), a mechanism
CC of plant viral defense that limits the accumulation of viral RNAs.
CC {ECO:0000250|UniProtKB:P03599}.
CC -!- FUNCTION: [Small capsid protein C-terminus part]: Acts as a suppressor
CC of RNA-mediated gene silencing, also known as post-transcriptional gene
CC silencing (PTGS), a mechanism of plant viral defense that limits the
CC accumulation of viral RNAs. {ECO:0000250|UniProtKB:P03599}.
CC -!- FUNCTION: [Large capsid protein]: Together with the mature small capsid
CC protein, forms an icosahedral capsid (T=3) enclosing the viral positive
CC strand RNA genome, with a diameter of approximately 300 Angstroms. The
CC capsid is formed from 60 copies each of the large and the mature small
CC capsid protein. The large capsid protein interacts with the viral RNA.
CC {ECO:0000269|PubMed:14517057, ECO:0000269|PubMed:2749253}.
CC -!- FUNCTION: [Mature small capsid protein]: Together with the large capsid
CC protein, forms an icosahedral capsid (T=3) enclosing the viral positive
CC strand RNA genome, with a diameter of approximately 300 Angstroms. The
CC capsid is formed from 60 copies each of the large and the mature small
CC capsid protein. The mature small capsid protein forms the turrets at
CC the fivefold axes of the viral particle. {ECO:0000269|PubMed:14517057,
CC ECO:0000269|PubMed:2749253}.
CC -!- SUBUNIT: [Mature small capsid protein]: Interacts with the large capsid
CC protein. {ECO:0000250|UniProtKB:P03599}.
CC -!- SUBUNIT: [Large capsid protein]: Interacts with the small capsid
CC protein. Homomultimer; assembles as pentons. Interacts with the
CC movement protein (via C-terminus). {ECO:0000250|UniProtKB:P03599}.
CC -!- SUBUNIT: [Movement protein]: Interacts (via C-terminus) with the large
CC capsid protein. {ECO:0000250|UniProtKB:P03599}.
CC -!- SUBCELLULAR LOCATION: [Movement protein]: Host cell junction, host
CC plasmodesma {ECO:0000250|UniProtKB:P03599}. Note=Assembles in tubules
CC that are embedded within modified plasmodesmata.
CC {ECO:0000250|UniProtKB:P03599}.
CC -!- SUBCELLULAR LOCATION: [Large capsid protein]: Virion
CC {ECO:0000269|PubMed:14517057, ECO:0000269|PubMed:2749253}.
CC -!- SUBCELLULAR LOCATION: [Mature small capsid protein]: Virion
CC {ECO:0000269|PubMed:14517057, ECO:0000269|PubMed:2749253}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=1; Synonyms=RNA2 polyprotein;
CC IsoId=P23009-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P23009-2; Sequence=VSP_059980;
CC -!- DOMAIN: [Small capsid protein precursor]: The C-terminus is required
CC for efficient assembly and RNA packaging.
CC {ECO:0000250|UniProtKB:P03599}.
CC -!- DOMAIN: [Large capsid protein]: Contains a beta-sheet structure called
CC beta-barrel jelly roll. {ECO:0000250|UniProtKB:P03599}.
CC -!- DOMAIN: [Mature small capsid protein]: Contains a beta-sheet structure
CC called beta-barrel jelly roll. {ECO:0000250|UniProtKB:P03599}.
CC -!- DOMAIN: [Movement protein]: The C-terminus is involved in binding to
CC the large capsid protein, and hence to the virion.
CC {ECO:0000250|UniProtKB:P03599}.
CC -!- PTM: [Small capsid protein precursor]: The C-terminal amino acids of
CC the small capsid protein is specifically cleaved by the RNA1 encoded
CC picornain 3C-like protease during maturation.
CC {ECO:0000250|UniProtKB:P03599, ECO:0000305|PubMed:1716655}.
CC -!- PTM: [RNA2 polyprotein]: Specific enzymatic cleavages by picornain 3C-
CC like protease in vivo yield mature proteins.
CC {ECO:0000250|UniProtKB:P03599}.
CC -!- CAUTION: It is uncertain whether Met-1 or Met-103 is the initiator.
CC {ECO:0000305}.
CC -!- WEB RESOURCE: Name=Virus Particle ExploreR db; Note=Icosahedral capsid
CC structure;
CC URL="https://viperdb.scripps.edu/Info_Page.php?VDB=1pgl";
CC -!- WEB RESOURCE: Name=Virus Particle ExploreR db; Note=Icosahedral capsid
CC structure;
CC URL="https://viperdb.scripps.edu/Info_Page.php?VDB=1pgw";
CC -!- WEB RESOURCE: Name=Virus Particle ExploreR db; Note=Icosahedral capsid
CC structure;
CC URL="https://viperdb.scripps.edu/Info_Page.php?VDB=1bmv";
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DR EMBL; M62738; AAA42801.1; -; Genomic_RNA.
DR PIR; A40321; GNWXG7.
DR RefSeq; NP_612348.1; NC_003495.1.
DR PDB; 1BMV; X-ray; 3.00 A; 1=821-1005, 2=447-820.
DR PDB; 1PGL; X-ray; 2.80 A; 1=821-1005, 2=447-816.
DR PDB; 1PGW; X-ray; 2.90 A; 1=821-1005, 2=466-816.
DR PDBsum; 1BMV; -.
DR PDBsum; 1PGL; -.
DR PDBsum; 1PGW; -.
DR SMR; P23009; -.
DR PRIDE; P23009; -.
DR GeneID; 956616; -.
DR KEGG; vg:956616; -.
DR EvolutionaryTrace; P23009; -.
DR Proteomes; UP000007610; Genome.
DR GO; GO:0044219; C:host cell plasmodesma; IEA:UniProtKB-SubCell.
DR GO; GO:0039617; C:T=3 icosahedral viral capsid; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR GO; GO:0046740; P:transport of virus in host, cell to cell; IEA:UniProtKB-KW.
DR Gene3D; 2.60.120.20; -; 2.
DR InterPro; IPR003181; Como_LCP.
DR InterPro; IPR003182; RNA2_polyprotein.
DR InterPro; IPR029053; Viral_coat.
DR Pfam; PF02247; Como_LCP; 1.
DR Pfam; PF02248; Como_SCP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative initiation; Capsid protein; DNA-binding;
KW GTP-binding; Host cell junction; Nucleotide-binding; RNA-binding;
KW Suppressor of RNA silencing; T=3 icosahedral capsid protein; Transport;
KW Viral movement protein; Virion.
FT CHAIN 1..1018
FT /note="RNA2 polyprotein"
FT /id="PRO_0000445846"
FT CHAIN 1..446
FT /note="VP58"
FT /id="PRO_0000037031"
FT CHAIN 103..446
FT /note="Movement protein"
FT /id="PRO_0000445847"
FT CHAIN 447..820
FT /note="Large capsid protein"
FT /id="PRO_0000037032"
FT CHAIN 821..1018
FT /note="Small capsid protein precursor"
FT /id="PRO_0000037033"
FT CHAIN 821..1005
FT /note="Mature small capsid protein"
FT /id="PRO_0000445848"
FT CHAIN 1006..1018
FT /note="Small capsid protein C-terminus part"
FT /id="PRO_0000445849"
FT REGION 401..407
FT /note="Involved in tubule formation by the movement
FT protein"
FT /evidence="ECO:0000250|UniProtKB:P03599"
FT SITE 446..447
FT /note="Cleavage; by viral protease"
FT /evidence="ECO:0000250|UniProtKB:P03599"
FT SITE 463
FT /note="Interaction with the viral RNA"
FT /evidence="ECO:0000250|UniProtKB:P03599"
FT SITE 819..820
FT /note="Cleavage; by viral protease"
FT /evidence="ECO:0000250|UniProtKB:P03599"
FT SITE 1005..1006
FT /note="Cleavage"
FT /evidence="ECO:0000305|PubMed:1716655"
FT VAR_SEQ 1..102
FT /note="Missing (in isoform 2)"
FT /id="VSP_059980"
FT HELIX 451..453
FT /evidence="ECO:0007829|PDB:1PGL"
FT TURN 466..469
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 470..478
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 487..492
FT /evidence="ECO:0007829|PDB:1PGL"
FT HELIX 493..496
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 498..500
FT /evidence="ECO:0007829|PDB:1BMV"
FT HELIX 505..510
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 516..523
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 533..542
FT /evidence="ECO:0007829|PDB:1PGL"
FT HELIX 550..553
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 554..561
FT /evidence="ECO:0007829|PDB:1PGL"
FT TURN 563..565
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 567..573
FT /evidence="ECO:0007829|PDB:1PGL"
FT HELIX 584..590
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 593..600
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 610..622
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 628..632
FT /evidence="ECO:0007829|PDB:1BMV"
FT STRAND 635..648
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 650..652
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 657..661
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 667..669
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 672..674
FT /evidence="ECO:0007829|PDB:1PGL"
FT HELIX 677..682
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 685..698
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 708..713
FT /evidence="ECO:0007829|PDB:1PGL"
FT HELIX 724..726
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 727..732
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 740..745
FT /evidence="ECO:0007829|PDB:1PGL"
FT HELIX 747..749
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 754..756
FT /evidence="ECO:0007829|PDB:1PGL"
FT TURN 764..766
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 771..778
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 783..785
FT /evidence="ECO:0007829|PDB:1BMV"
FT STRAND 788..805
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 829..835
FT /evidence="ECO:0007829|PDB:1PGL"
FT TURN 842..844
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 846..853
FT /evidence="ECO:0007829|PDB:1PGL"
FT TURN 854..857
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 858..861
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 863..865
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 868..871
FT /evidence="ECO:0007829|PDB:1PGL"
FT HELIX 875..882
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 883..897
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 900..902
FT /evidence="ECO:0007829|PDB:1BMV"
FT HELIX 904..906
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 910..917
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 921..923
FT /evidence="ECO:0007829|PDB:1BMV"
FT STRAND 926..931
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 934..945
FT /evidence="ECO:0007829|PDB:1PGL"
FT TURN 948..950
FT /evidence="ECO:0007829|PDB:1PGL"
FT TURN 958..961
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 966..973
FT /evidence="ECO:0007829|PDB:1PGL"
FT TURN 974..976
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 979..986
FT /evidence="ECO:0007829|PDB:1PGL"
FT STRAND 991..997
FT /evidence="ECO:0007829|PDB:1PGL"
SQ SEQUENCE 1018 AA; 113352 MW; B11B35D0A7F0F872 CRC64;
MFASFIFSGD NKLTEKTIFN CGDLDILVVY YTIATQFRKF LPHYIRWHLY TLLIYILPSF
LTTEIKYKRN LSNIHISGLF YDNRFKFWTK HDKNLALTEE EKMEVIRNRG IPADVLAKRA
HEFEKHVAHE SLKDQIPAVD KLYSTKVNKF AKIMNLRQSV VGDLKLLTDG KLYEGKHIPV
SNISAGENHV VQIPLMAQEE ILSSSASDFK TAMVSKSSKP QATAMHVGAI EIIIDSFASP
DCNIVGAMLL VDTYHTNPEN AVRSIFVAPF RGGRPIRVVT FPNTIVQIEP DMNSRFQLLS
TTTNGDFVQG KDLAMVKVNV ACAAVGLTSS YTPTPLLESG LQKDRGLIVE YFGRMSYVAH
NINQPQEKDL LEGNFSFDIK SRSRLEKVSS TKAQFVSGRT FKYDIIGAGS QSSEELSEEK
IQGKAKQVDA RLRQRIDPQY NEVQAQMETN LFKLSLDDVE TPKGSMLDLK ISQSKIALPK
NTVGGTILRS DLLANFLTEG NFRASVDLQR THRIKGMIKM VATVGIPENT GIALACAMNS
SIRGRASSDI YTICSQDCEL WNPACTKAMT MSFNPNPCSD AWSLEFLKRT GFHCDIICVT
GWTATPMQDV QVTIDWFISS QECVPRTYCV LNPQNPFVLN RWMGKLTFPQ GTSRSVKRMP
LSIGGGAGAK SAILMNMPNA VLSMWRYFVG DLVFEVSKMT SPYIKCTVSF FIAFGNLADD
TINFEAFPHK LVQFGEIQEK VVLKFSQEEF LTAWSTQVRP ATTLLADGCP YLYAMVHDSS
VSTIPGDFVI GVKLTIIENM CAYGLNPGIS GSRLLGTIPQ SISQQTVWNQ MATVRTPLNF
DSSKQSFCQF SVDLLGGGIS VDKTGDWITL VQNSPISNLL RVAAWKKGCL MVKVVMSGNA
AVKRSDWASL VQVFLTNSNS TEHFDACRWT KSEPHSWELI FPIEVCGPNN GFEMWSSEWA
NQTSWHLSFL VDNPKQSTTF DVLLGISQNF EIAGNTLMPA FSVPQANARS SENAESSA
