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Q86119 (POLG_RHDVA) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 86. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Genome polyprotein
Alternative name(s):
p254

Cleaved into the following 11 chains:

  1. Protein p16
  2. Protein p23
  3. NTPase
    EC=3.6.1.15
    Alternative name(s):
    2C-like protein
    P2C
    p37
  4. Precursor p41
  5. Protein p29
  6. Protein p23/2
  7. Protein p18
  8. Viral genome-linked protein
    Alternative name(s):
    VPg
    p13
  9. 3C-like protease
    Short name=3CLpro
    EC=3.4.22.66
    Alternative name(s):
    Calicivirin
    Thiol protease P3C
    p15
  10. RNA-directed RNA polymerase
    EC=2.7.7.48
    Alternative name(s):
    3Dpol
    p58
  11. Capsid protein VP60
Gene names
ORF Names:ORF1
OrganismRabbit hemorrhagic disease virus (strain AST89) (Ra/LV/RHDV/AST89/1989/SP) (RHDV-AST89) [Complete proteome]
Taxonomic identifier314538 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeLagovirus
Virus hostOryctolagus cuniculus (Rabbit) [TaxID: 9986]

Protein attributes

Sequence length2344 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

NTPase presumably plays a role in replication By similarity.

Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation By similarity.

3C-like protease processes the polyprotein: 3CLpro-RdRp (p72) is first released by autocleavage, then all other proteins are cleaved By similarity.

RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA codes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs By similarity.

Capsid protein VP60 self assembles to form an icosahedral capsid with a T=3 symmetry, about 35 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate VP2 proteins and genomic or subgenomic RNA. Attaches virion to target cells by binding histo-blood group antigens, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm By similarity.

Catalytic activity

NTP + H2O = NDP + phosphate.

Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|-Xaa and the P1' position is occupied by Gly-|-Yaa.

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Subunit structure

Binds to histo-blood group antigens at surface of target cells By similarity. Ref.8

Subcellular location

Capsid protein VP60: Virion. Host cytoplasm By similarity.

Post-translational modification

Specific enzymatic cleavages by its own cysteine protease yield mature proteins. The protease cleaves itself from the nascent polyprotein autocatalytically. Precursor p41 can be cleaved by viral 3CLpro into protein p19 and VPg, or cleaved by host protease into protein p23/2 and protein p18 By similarity. Ref.1

VPg is uridylylated by the polymerase and is covalently attached to the 5'-end of the polyadenylated genomic and subgenomic RNAs. This uridylylated form acts as a nucleotide-peptide primer for the polymerase.

Miscellaneous

Two differents RNAs lead the expression of the capsid protein. One arises from the cleavage of the polyprotein translated from the genomic RNA and the other from the translation of a subgenomic RNA derived from the (-)RNA template. Capsid protein expressed from the subgenomic mRNA is produced in much larger amounts than the cleaved one.

Sequence similarities

Contains 1 peptidase C24 domain.

Contains 1 RdRp catalytic domain.

Contains 1 SF3 helicase domain.

Alternative products

This entry describes 2 isoforms produced by alternative promoter usage. [Align] [Select]
Isoform Genome polyprotein (identifier: Q86119-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Note: Produced from the genomic RNA.
Isoform Subgenomic capsid protein VP60 (identifier: Q86119-2)

Also known as: VP1;

The sequence of this isoform differs from the canonical sequence as follows:
     1-1765: Missing.
Note: Produced from the subgenomic RNA.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 23442344Genome polyprotein
PRO_0000341999
Chain1 – 143143Protein p16 By similarity
PRO_0000036941
Chain144 – 339196Protein p23 By similarity
PRO_0000036942
Chain340 – 718379NTPase By similarity
PRO_0000036943
Chain712 – 1108397Precursor p41 By similarity
PRO_0000342000
Chain712 – 936225Protein p23/2 By similarity
PRO_0000342001
Chain719 – 993275Protein p29 By similarity
PRO_0000036944
Chain937 – 1108172Protein p18 By similarity
PRO_0000342002
Chain994 – 1108115Viral genome-linked protein By similarity
PRO_0000036945
Chain1109 – 12511433C-like protease By similarity
PRO_0000036946
Chain1252 – 1767516RNA-directed RNA polymerase By similarity
PRO_0000036947
Chain1768 – 2344577Capsid protein VP60 By similarity
PRO_0000036949

Regions

Domain492 – 653162SF3 helicase
Domain1120 – 121899Peptidase C24
Domain1495 – 1619125RdRp catalytic
Nucleotide binding522 – 5298ATP Potential

Sites

Active site11351For 3CLpro activity By similarity
Active site11591For 3CLpro activity By similarity
Active site12121For 3CLpro activity Potential
Site143 – 1442Cleavage; by 3CLpro By similarity
Site339 – 3402Cleavage; by 3CLpro By similarity
Site718 – 7192Cleavage; by 3CLpro By similarity
Site936 – 9372Cleavage; by host By similarity
Site993 – 9942Cleavage; by 3CLpro By similarity
Site1108 – 11092Cleavage; by 3CLpro By similarity
Site1251 – 12522Cleavage; by 3CLpro By similarity
Site1767 – 17682Cleavage; by 3CLpro By similarity

Amino acid modifications

Modified residue10141O-(5'-phospho-RNA)-tyrosine
Disulfide bond1584 ↔ 1591 By similarity

Natural variations

Alternative sequence1 – 17651765Missing in isoform Subgenomic capsid protein VP60.
VSP_034379

Experimental info

Mutagenesis17671E → G: Loss of cleavage between RNA-directed RNA polymerase and VP60. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform Genome polyprotein [UniParc].

Last modified October 1, 2003. Version 2.
Checksum: E1C61F038111F092

FASTA2,344256,817
        10         20         30         40         50         60 
MAAMSRLTGM TTAILPEKKP LNFFLDLRDK TPPCCIRATG KLAWPVFLGQ NGKEGPLETC 

        70         80         90        100        110        120 
NKCGKWLNGF GCFGLEDLGD VCLCSIAQQK HKFGPVCLCN RAYIHDCGRW RRRSRFLKHY 

       130        140        150        160        170        180 
KALNKVIPCA YQFDESFSTP VFEGEVDDLF VELGAPTSMG FMDKKLLKKG KKLMDKFVDV 

       190        200        210        220        230        240 
DEPCLTSRDA SLLDSIASDN TIRAKLEEEY GVEMVQAARD RKDFMKNLRL ALDNRPANPV 

       250        260        270        280        290        300 
TWYTKLGNIT EKGKQWAKKV VYGACKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFKPV 

       310        320        330        340        350        360 
NLLAILMDWT NDLTGFVTTL VRLLELYGVV QATVNLIVEG VKSFWDKVVC ATDRCFDLLK 

       370        380        390        400        410        420 
RLFDTFEDSV PTGPTAGCLI FMAFVFSTVV GYLPNNSVIT TFMKGAGKLT TFAGVIGAIR 

       430        440        450        460        470        480 
TLWITINQHM VAKDLTSIQQ KVMTVVKMAN EAATLDQLEI VSCLCSDLEN TLTNRCTLPS 

       490        500        510        520        530        540 
YNQHLGILNA SQKVISDLHT MVLGKINMTK QRPQPVAVIF KGAPGIGKTY LVHRIARDLG 

       550        560        570        580        590        600 
CQHPSTINFG LDHFDSYTGE EVAIADEFNT CGDGESWVEL FIQMVNTNPC PLNCDKAENK 

       610        620        630        640        650        660 
NKVFNSKYLL CTTNSNMILN ATHPRAGAFY RRVMIVEARN KAVESWQATR HGSKPGRSCY 

       670        680        690        700        710        720 
SKDMSHLTFQ VYPHNMPAPG FVFVGDKLVK SQVAPREYKY SELLDLIKSE HPDVASFEGA 

       730        740        750        760        770        780 
NRFNFVYPDA QYDQALLMWK QYFVMYGCVA RLAKNFVDDI PYNQVHISRA SDPKIEGCVE 

       790        800        810        820        830        840 
YQCKFQHLWR MVPQFVLGCV NMTNQLGTPL TQQQLDRITN GVEGVTVTTV NNILPFHSQT 

       850        860        870        880        890        900 
TLINPSFIKL IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGSLVRTLT GAATFSDDPV 

       910        920        930        940        950        960 
STTIICSNCT IQIHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL ISGFSWRQIA 

       970        980        990       1000       1010       1020 
HLFVEVISHL CANHLVNLAT MAALGAVATK AFQGVKGKTK RGRGARVNLG NDEYDEWQAA 

      1030       1040       1050       1060       1070       1080 
RREFVNAHDM TAEEYLAMKN KAAMGSDDQD SVMFRSWWTR RQLRPDEDQV TVVGRGGVRN 

      1090       1100       1110       1120       1130       1140 
EVIRTRVRQT PKGPKTLDDG GFYDNDYEGL PGFMRHNGSG WMIHIGNGLY ISNTHTARSS 

      1150       1160       1170       1180       1190       1200 
CSEVVTCSPT TDLCLVKGEA IRSVAQIAEG TPVCDWKKSP ISTYGIKKTL SDSTKIDVLA 

      1210       1220       1230       1240       1250       1260 
YDGCTQTTHG DCGLPLYDSS GKIVAIHTGK LLGFSKMCTL IDLTITKGVY ETSNFFCGEP 

      1270       1280       1290       1300       1310       1320 
IDYRGITAHR LVGAEPRPPV SGTRYAKVPG VPEEYKTGYR PANLGRSDPD SDKSLMNIAV 

      1330       1340       1350       1360       1370       1380 
KNLQVYQQEP KLDKVDEFIE RAAADVLGYL RFLTKGERQA NLNFKAAFNT LDLSTSCGPF 

      1390       1400       1410       1420       1430       1440 
VPGKKIDHVK DGVMDQVHAK HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVKEGKKRL 

      1450       1460       1470       1480       1490       1500 
LWGCDVGVAV CAAAVFHNIC YKLKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL 

      1510       1520       1530       1540       1550       1560 
DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI VQTKRGLPSG 

      1570       1580       1590       1600       1610       1620 
MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF YTYGDDGVYA MTPMMVSLLP 

      1630       1640       1650       1660       1670       1680 
AIIENLRDYG LSPTAADKTE FIDVCPLNKI SFLKRTFELT DIGWVSKLDK SSILRQLEWS 

      1690       1700       1710       1720       1730       1740 
KTTSRHMMIE ETYDLAKEER GVQLEELQVA AAAHGQEFFN FVCKELERQQ AYTQFSVYSY 

      1750       1760       1770       1780       1790       1800 
DAARKILADR KRVVSVVPDD EFVNVMEGKA RTAPQGEAAG TATTASVPGT TTDGMDPGVV 

      1810       1820       1830       1840       1850       1860 
ATTSVVTAEN SSASIATAGI GGPPQQVDQQ ETWRTNFYYN DVFTWSVADA PGSILYTVQH 

      1870       1880       1890       1900       1910       1920 
SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVA AVIPPGIEIG PGLEVRQFPH 

      1930       1940       1950       1960       1970       1980 
VVIDARSLEP VTITMPDLRP NMYHPTGDPG LVPTLVLSVY NNLINPFGGS TSAIQVTVET 

      1990       2000       2010       2020       2030       2040 
RPSEDFEFVM IRAPSSKTVD SISPAGLLTT PVLTGVGNDN RWNGQIVGLQ PVPGGFSTCN 

      2050       2060       2070       2080       2090       2100 
RHWNLNGSTY GWSSPRFADI DHRRGSASYP GNNATNVLQF WYANAGSAID NPISQVAPDG 

      2110       2120       2130       2140       2150       2160 
FPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP GNLQPTTNTS 

      2170       2180       2190       2200       2210       2220 
GSQTVAKSIY AVVTGTAQNP AGLFVMASGV ISTPSANAIT YTPQPDRIVT TPGTPAAAPV 

      2230       2240       2250       2260       2270       2280 
GKNTPIMFAS VVRRTGDVNA TAGSANGTQY GTGSQPLPVT IGLSLNNYSS ALMPGQFFVW 

      2290       2300       2310       2320       2330       2340 
QLTFASGFME IGLSVDGYFY AGTGASTTLI DLTELIDVRP VGPRPSKSTL VFNLGGTANG 


FSYV 

« Hide

Isoform Subgenomic capsid protein VP60 (VP1) [UniParc].

Checksum: 7BA463B7C7D77BAC
Show »

FASTA57960,241

References

[1]"Processing of rabbit hemorrhagic disease virus polyprotein."
Martin-Alonso J.M., Casais R., Boga J.A., Parra F.
J. Virol. 70:1261-1265(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], PROTEIN SEQUENCE OF 719-724 AND 1009-1114, MUTAGENESIS OF GLU-1767, PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[2]Casais R., Martin-Alonso J.M., Boga J.A., Parra F.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: SEQUENCE REVISION TO 1891; 2058 AND 2061.
[3]"Molecular cloning, sequence and expression of the capsid protein gene from rabbit hemorrhagic disease virus (Spanish isolate AST/89)."
Boga J.A., Casais R., Marin M.S., Martin-Alonso J.M., Carmenes R., Prieto M., Parra F.
J. Gen. Virol. 75:2409-2413(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1650-2344.
[4]"The amino terminal sequence of VP60 from rabbit hemorrhagic disease virus supports its putative subgenomic origin."
Parra F., Boga J.A., Marin M.S., Casais R.
Virus Res. 27:219-228(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1766-1797, PROTEIN SEQUENCE OF 1767-1780.
[5]"In vitro translation of a subgenomic mRNA from purified virions of the Spanish field isolate AST/89 of rabbit hemorrhagic disease virus (RHDV)."
Boga J.A., Marin M.S., Casais R., Prieto M., Parra F.
Virus Res. 26:33-40(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBGENOMIC ORIGIN OF VP60.
[6]"Identification of the amino acid residue involved in rabbit hemorrhagic disease virus VPg uridylylation."
Machin A., Martin Alonso J.M., Parra F.
J. Biol. Chem. 276:27787-27792(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: COVALENT RNA-LINKAGE OF VPG, URIDYLYLATION AT TYR-1014.
[7]"Synthesis in vitro of rabbit hemorrhagic disease virus subgenomic RNA by internal initiation on (-)sense genomic RNA: mapping of a subgenomic promoter."
Morales M., Barcena J., Ramirez M.A., Boga J.A., Parra F., Torres J.M.
J. Biol. Chem. 279:17013-17018(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBGENOMIC ORIGIN OF VP60.
[8]"NMR experiments reveal the molecular basis of receptor recognition by a calicivirus."
Rademacher C., Krishna N.R., Palcic M., Parra F., Peters T.
J. Am. Chem. Soc. 130:3669-3675(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION OF VP60 WITH HISTO-BLOOD GROUP ANTIGENS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z49271 Genomic RNA. Translation: CAA89265.2.
Z49271 Genomic RNA. Translation: CAD91718.1.
Z24757 Genomic RNA. Translation: CAA80881.1. Sequence problems.
Z24757 Genomic RNA. Translation: CAA80883.1. Sequence problems.
X73046 mRNA. Translation: CAA51524.1.
PIRS64740.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZUEelectron microscopy10.30A/B/C1766-2344[»]
ProteinModelPortalQ86119.
SMRQ86119. Positions 1256-1752.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR003593. AAA+_ATPase.
IPR004005. Calicivirus_coat.
IPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000317. Peptidase_C24.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]
PfamPF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLG_RHDVA
AccessionPrimary (citable) accession number: Q86119
Secondary accession number(s): Q7THT7 expand/collapse secondary AC list , Q86123, Q86124, Q9IBM0
Entry history
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: October 1, 2003
Last modified: April 16, 2014
This is version 86 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references