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P27410 (POLG_RHDVF) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 104. 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 Rabbit/Germany/FRG/1989) (Ra/LV/RHDV/GH/1989/GE) (RHDV-FRG) [Reference proteome]
Taxonomic identifier314536 [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. Ref.2 Ref.11

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. Ref.2 Ref.11

3C-like protease processes the polyprotein: 3CLpro-RdRp (p72) is first released by autocleavage, then all other proteins are cleaved By similarity. Ref.2 Ref.11

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. Ref.2 Ref.11

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. Ref.2 Ref.11

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.

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. Ref.4 Ref.6 Ref.7 Ref.8 Ref.10

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 By similarity.

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 By similarity.

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: P27410-1)

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: P27410-2)

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_0000341645
Chain1 – 143143Protein p16
PRO_0000036959
Chain144 – 339196Protein p23
PRO_0000036960
Chain340 – 718379NTPase
PRO_0000036961
Chain719 – 1108390Precursor p41
PRO_0000341646
Chain719 – 993275Protein p29
PRO_0000036962
Chain719 – 936218Protein p23/2
PRO_0000341647
Chain937 – 1108172Protein p18
PRO_0000341648
Chain994 – 1108115Viral genome-linked protein
PRO_0000036963
Chain1109 – 12511433C-like protease
PRO_0000036964
Chain1252 – 1767516RNA-directed RNA polymerase
PRO_0000036965
Chain1768 – 2344577Capsid protein VP60
PRO_0000036967

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

Amino acid modifications

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

Natural variations

Alternative sequence1 – 17651765Missing in isoform Subgenomic capsid protein VP60.
VSP_034381

Experimental info

Mutagenesis11351H → N: Complete loss of 3CLpro activity in vitro. Ref.3
Mutagenesis11521D → E: Partial loss of 3CLpro activity in vitro. Ref.3
Mutagenesis11521D → G or N: Complete loss of 3CLpro activity in vitro. Ref.3
Mutagenesis11751D → G or E: Complete loss of 3CLpro activity in vitro. Ref.3
Mutagenesis11751D → N: Partial loss of 3CLpro activity in vitro. Ref.3
Mutagenesis12121C → G: Complete loss of 3CLpro activity in vitro. Ref.3
Mutagenesis12121C → S: Partial loss of 3CLpro activity in vitro. Ref.3
Mutagenesis12271H → L or N: Complete loss of 3CLpro activity in vitro. Ref.3

Secondary structure

................................................................................... 2344
Helix Strand Turn

Details...

Sequences

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

Last modified August 1, 1992. Version 1.
Checksum: 1454C248F81E9212

FASTA2,344257,068
        10         20         30         40         50         60 
MAAMSRLTGM TTAILPEKKP LDFFLDLRDK TPPCCIRATG RLAWPVFPGQ NGKEGPLETC 

        70         80         90        100        110        120 
NKCGKWLNGF GNFGLEDLGD VCLCSIAQQK HKFGPVCLCN RVYIHDCGRW RRRSRFLKHY 

       130        140        150        160        170        180 
KALNKVIPCA YQFDESFPTP IFEGEVDDLF VELGAPTSMG FMDKKLLKKG KKLMDKFVDV 

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

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

       310        320        330        340        350        360 
NLLAILMDWN NDLTGFITTL VRLLELYGVV QATVNLIIEG VKSFWDKVVC ATDRCFDLLK 

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

       430        440        450        460        470        480 
TLWITINQHM VAKDLTSVQQ KVMTVVKMAN EAATLDQLEI VSCLCSDLET 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 HGSKPGKSCY 

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

       730        740        750        760        770        780 
NKFNFVYPDA 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 AYGTLVRTLT GAATFSDDPV 

       910        920        930        940        950        960 
STTIICSNCT IQLHSCGGLL 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 SIMFRSWWTR RQLRPEEDQV TIVGRSGVRN 

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

      1150       1160       1170       1180       1190       1200 
CSEIVTCSPT TDLCLVKGES 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 VPDEYKTGYR PANLGRSDPD SDKSLMNIAV 

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

      1390       1400       1410       1420       1430       1440 
VPGKKIDHVK DGVMDQVLAK 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 
KTTSRHMVIE ETYDLAKEER GVQLEELQVA AAAHGQEFFN FVCRELERQQ AYTQFSVYSY 

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

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

      1870       1880       1890       1900       1910       1920 
SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVR 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 GWSSPRFGDI DHRRGSASYS GSNATNVLQF WYANAGSAID NPISQVAPDG 

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

      2170       2180       2190       2200       2210       2220 
GAQTVAKSIY AVVTGTAQNP AGLFVMASGI ISTPNASAIT 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: 20857900C4107D20
Show »

FASTA57960,257

References

[1]"Rabbit hemorrhagic disease virus -- molecular cloning and nucleotide sequencing of a calicivirus genome."
Meyers G., Wirblich C., Thiel H.-J.
Virology 184:664-676(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]"Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles."
Meyers G., Wirblich C., Thiel H.-J.
Virology 184:677-686(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF VPG.
[3]"Identification and characterization of a 3C-like protease from rabbit hemorrhagic disease virus, a calicivirus."
Boniotti B., Wirblich C., Sibilia M., Meyers G., Thiel H.J., Rossi C.
J. Virol. 68:6487-6495(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF HIS-1135; ASP-1152; ASP-1175; CYS-1212 AND HIS-1227.
[4]"3C-like protease of rabbit hemorrhagic disease virus: identification of cleavage sites in the ORF1 polyprotein and analysis of cleavage specificity."
Wirblich C., Sibilia M., Boniotti M.B., Rossi C., Thiel H.-J., Meyers G.
J. Virol. 69:7159-7168(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[5]"Two independent pathways of expression lead to self-assembly of the rabbit hemorrhagic disease virus capsid protein."
Sibilia M., Boniotti M.B., Angoscini P., Capucci L., Rossi C.
J. Virol. 69:5812-5815(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBGENOMIC ORIGIN OF VP60.
[6]"Detection of viral proteins after infection of cultured hepatocytes with rabbit hemorrhagic disease virus."
Konig M., Thiel H.J., Meyers G.
J. Virol. 72:4492-4497(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[7]"Rabbit hemorrhagic disease virus: genome organization and polyprotein processing of a calicivirus studied after transient expression of cDNA constructs."
Meyers G., Wirblich C., Thiel H.J., Thumfart J.O.
Virology 276:349-363(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[8]"Identification of a new cleavage site of the 3C-like protease of rabbit haemorrhagic disease virus."
Joubert P., Pautigny C., Madelaine M.-F., Rasschaert D.
J. Gen. Virol. 81:481-488(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[9]"Characterisation of the RNA-dependent RNA polymerase from Rabbit hemorrhagic disease virus produced in Escherichia coli."
Lopez Vazquez A.L., Martin Alonso J.M., Parra F.
Arch. Virol. 146:59-69(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF RNA-DIRECTED RNA POLYMERASE.
[10]"Rabbit hemorrhagic disease virus: identification of a cleavage site in the viral polyprotein that is not processed by the known calicivirus protease."
Thumfart J.O., Meyers G.
Virology 304:352-363(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[11]"The coat protein of Rabbit hemorrhagic disease virus contains a molecular switch at the N-terminal region facing the inner surface of the capsid."
Barcena J., Verdaguer N., Roca R., Morales M., Angulo I., Risco C., Carrascosa J.L., Torres J.M., Caston J.R.
Virology 322:118-134(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF CAPSID PROTEIN VP60.
[12]"Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase."
Ng K.K.S., Cherney M.M., Vazquez A.L., Machin A., Martin-Alonso J.M., Parra F., James M.N.G.
J. Biol. Chem. 277:1381-1387(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1252-1767.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M67473 Genomic RNA. Translation: AAA47285.1.
PIRRRWWRH. A41039.
RefSeqNP_062875.1. NC_001543.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1KHVX-ray2.50A/B1252-1767[»]
1KHWX-ray2.70A/B1252-1767[»]
ProteinModelPortalP27410.
SMRP27410. Positions 1256-1752.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1491968.

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...

Other

EvolutionaryTraceP27410.

Entry information

Entry namePOLG_RHDVF
AccessionPrimary (citable) accession number: P27410
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: April 16, 2014
This is version 104 of the entry and version 1 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