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Q86119

- POLG_RHDVA

UniProt

Q86119 - POLG_RHDVA

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Protein

Genome polyprotein

Gene
ORF1
Organism
Rabbit hemorrhagic disease virus (strain AST89) (Ra/LV/RHDV/AST89/1989/SP) (RHDV-AST89)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 activityi

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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei143 – 1442Cleavage; by 3CLpro By similarity
Sitei339 – 3402Cleavage; by 3CLpro By similarity
Sitei718 – 7192Cleavage; by 3CLpro By similarity
Sitei936 – 9372Cleavage; by host By similarity
Sitei993 – 9942Cleavage; by 3CLpro By similarity
Sitei1108 – 11092Cleavage; by 3CLpro By similarity
Active sitei1135 – 11351For 3CLpro activity By similarity
Active sitei1159 – 11591For 3CLpro activity By similarity
Active sitei1212 – 12121For 3CLpro activity Reviewed prediction
Sitei1251 – 12522Cleavage; by 3CLpro By similarity
Sitei1767 – 17682Cleavage; by 3CLpro By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi522 – 5298ATP Reviewed prediction

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. cysteine-type endopeptidase activity Source: InterPro
  3. RNA binding Source: InterPro
  4. RNA-directed RNA polymerase activity Source: UniProtKB-KW
  5. RNA helicase activity Source: InterPro

GO - Biological processi

  1. RNA-protein covalent cross-linking Source: UniProtKB-KW
  2. transcription, DNA-templated Source: InterPro
  3. viral RNA genome replication Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

Keywords - Biological processi

Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Alternative name(s):
p254
Cleaved into the following 11 chains:
Alternative name(s):
2C-like protein
P2C
p37
Alternative name(s):
VPg
p13
3C-like protease (EC:3.4.22.66)
Short name:
3CLpro
Alternative name(s):
Calicivirin
Thiol protease P3C
p15
Alternative name(s):
3Dpol
p58
Gene namesi
ORF Names:ORF1
OrganismiRabbit hemorrhagic disease virus (strain AST89) (Ra/LV/RHDV/AST89/1989/SP) (RHDV-AST89)
Taxonomic identifieri314538 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeLagovirus
Virus hostiOryctolagus cuniculus (Rabbit) [TaxID: 9986]
ProteomesiUP000008653: Genome

Subcellular locationi

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-SubCell
  2. viral capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1767 – 17671E → G: Loss of cleavage between RNA-directed RNA polymerase and VP60. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 23442344Genome polyproteinPRO_0000341999Add
BLAST
Chaini1 – 143143Protein p16 By similarityPRO_0000036941Add
BLAST
Chaini144 – 339196Protein p23 By similarityPRO_0000036942Add
BLAST
Chaini340 – 718379NTPase By similarityPRO_0000036943Add
BLAST
Chaini712 – 1108397Precursor p41 By similarityPRO_0000342000Add
BLAST
Chaini712 – 936225Protein p23/2 By similarityPRO_0000342001Add
BLAST
Chaini719 – 993275Protein p29 By similarityPRO_0000036944Add
BLAST
Chaini937 – 1108172Protein p18 By similarityPRO_0000342002Add
BLAST
Chaini994 – 1108115Viral genome-linked protein By similarityPRO_0000036945Add
BLAST
Chaini1109 – 12511433C-like protease By similarityPRO_0000036946Add
BLAST
Chaini1252 – 1767516RNA-directed RNA polymerase By similarityPRO_0000036947Add
BLAST
Chaini1768 – 2344577Capsid protein VP60 By similarityPRO_0000036949Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1014 – 10141O-(5'-phospho-RNA)-tyrosine
Disulfide bondi1584 ↔ 1591 By similarity

Post-translational modificationi

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.1 Publication
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.

Keywords - PTMi

Covalent protein-RNA linkage, Disulfide bond, Phosphoprotein

Interactioni

Subunit structurei

Binds to histo-blood group antigens at surface of target cells By similarity.1 Publication

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZUEelectron microscopy10.30A/B/C1766-2344[»]
ProteinModelPortaliQ86119.
SMRiQ86119. Positions 1256-1752.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini492 – 653162SF3 helicaseAdd
BLAST
Domaini1120 – 121899Peptidase C24Add
BLAST
Domaini1495 – 1619125RdRp catalyticAdd
BLAST

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR003593. 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.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative promoter usage. Align

Isoform Genome polyprotein (identifier: Q86119-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MAAMSRLTGM TTAILPEKKP LNFFLDLRDK TPPCCIRATG KLAWPVFLGQ     50
NGKEGPLETC NKCGKWLNGF GCFGLEDLGD VCLCSIAQQK HKFGPVCLCN 100
RAYIHDCGRW RRRSRFLKHY KALNKVIPCA YQFDESFSTP VFEGEVDDLF 150
VELGAPTSMG FMDKKLLKKG KKLMDKFVDV DEPCLTSRDA SLLDSIASDN 200
TIRAKLEEEY GVEMVQAARD RKDFMKNLRL ALDNRPANPV TWYTKLGNIT 250
EKGKQWAKKV VYGACKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFKPV 300
NLLAILMDWT NDLTGFVTTL VRLLELYGVV QATVNLIVEG VKSFWDKVVC 350
ATDRCFDLLK RLFDTFEDSV PTGPTAGCLI FMAFVFSTVV GYLPNNSVIT 400
TFMKGAGKLT TFAGVIGAIR TLWITINQHM VAKDLTSIQQ KVMTVVKMAN 450
EAATLDQLEI VSCLCSDLEN TLTNRCTLPS YNQHLGILNA SQKVISDLHT 500
MVLGKINMTK QRPQPVAVIF KGAPGIGKTY LVHRIARDLG CQHPSTINFG 550
LDHFDSYTGE EVAIADEFNT CGDGESWVEL FIQMVNTNPC PLNCDKAENK 600
NKVFNSKYLL CTTNSNMILN ATHPRAGAFY RRVMIVEARN KAVESWQATR 650
HGSKPGRSCY SKDMSHLTFQ VYPHNMPAPG FVFVGDKLVK SQVAPREYKY 700
SELLDLIKSE HPDVASFEGA NRFNFVYPDA QYDQALLMWK QYFVMYGCVA 750
RLAKNFVDDI PYNQVHISRA SDPKIEGCVE YQCKFQHLWR MVPQFVLGCV 800
NMTNQLGTPL TQQQLDRITN GVEGVTVTTV NNILPFHSQT TLINPSFIKL 850
IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGSLVRTLT GAATFSDDPV 900
STTIICSNCT IQIHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL 950
ISGFSWRQIA HLFVEVISHL CANHLVNLAT MAALGAVATK AFQGVKGKTK 1000
RGRGARVNLG NDEYDEWQAA RREFVNAHDM TAEEYLAMKN KAAMGSDDQD 1050
SVMFRSWWTR RQLRPDEDQV TVVGRGGVRN EVIRTRVRQT PKGPKTLDDG 1100
GFYDNDYEGL PGFMRHNGSG WMIHIGNGLY ISNTHTARSS CSEVVTCSPT 1150
TDLCLVKGEA IRSVAQIAEG TPVCDWKKSP ISTYGIKKTL SDSTKIDVLA 1200
YDGCTQTTHG DCGLPLYDSS GKIVAIHTGK LLGFSKMCTL IDLTITKGVY 1250
ETSNFFCGEP IDYRGITAHR LVGAEPRPPV SGTRYAKVPG VPEEYKTGYR 1300
PANLGRSDPD SDKSLMNIAV KNLQVYQQEP KLDKVDEFIE RAAADVLGYL 1350
RFLTKGERQA NLNFKAAFNT LDLSTSCGPF VPGKKIDHVK DGVMDQVHAK 1400
HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVKEGKKRL LWGCDVGVAV 1450
CAAAVFHNIC YKLKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL 1500
DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI 1550
VQTKRGLPSG MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF 1600
YTYGDDGVYA MTPMMVSLLP AIIENLRDYG LSPTAADKTE FIDVCPLNKI 1650
SFLKRTFELT DIGWVSKLDK SSILRQLEWS KTTSRHMMIE ETYDLAKEER 1700
GVQLEELQVA AAAHGQEFFN FVCKELERQQ AYTQFSVYSY DAARKILADR 1750
KRVVSVVPDD EFVNVMEGKA RTAPQGEAAG TATTASVPGT TTDGMDPGVV 1800
ATTSVVTAEN SSASIATAGI GGPPQQVDQQ ETWRTNFYYN DVFTWSVADA 1850
PGSILYTVQH SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVA 1900
AVIPPGIEIG PGLEVRQFPH VVIDARSLEP VTITMPDLRP NMYHPTGDPG 1950
LVPTLVLSVY NNLINPFGGS TSAIQVTVET RPSEDFEFVM IRAPSSKTVD 2000
SISPAGLLTT PVLTGVGNDN RWNGQIVGLQ PVPGGFSTCN RHWNLNGSTY 2050
GWSSPRFADI DHRRGSASYP GNNATNVLQF WYANAGSAID NPISQVAPDG 2100
FPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP 2150
GNLQPTTNTS GSQTVAKSIY AVVTGTAQNP AGLFVMASGV ISTPSANAIT 2200
YTPQPDRIVT TPGTPAAAPV GKNTPIMFAS VVRRTGDVNA TAGSANGTQY 2250
GTGSQPLPVT IGLSLNNYSS ALMPGQFFVW QLTFASGFME IGLSVDGYFY 2300
AGTGASTTLI DLTELIDVRP VGPRPSKSTL VFNLGGTANG FSYV 2344

Note: Produced from the genomic RNA.

Length:2,344
Mass (Da):256,817
Last modified:October 1, 2003 - v2
Checksum:iE1C61F038111F092
GO
Isoform Subgenomic capsid protein VP60 (identifier: Q86119-2) [UniParc]FASTAAdd to Basket

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.

Show »
Length:579
Mass (Da):60,241
Checksum:i7BA463B7C7D77BAC
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 17651765Missing in isoform Subgenomic capsid protein VP60. VSP_034379Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiS64740.

Keywords - Coding sequence diversityi

Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi S64740.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3ZUE electron microscopy 10.30 A/B/C 1766-2344 [» ]
ProteinModelPortali Q86119.
SMRi Q86119. Positions 1256-1752.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

Gene3Di 2.60.120.20. 1 hit.
3.40.50.300. 2 hits.
InterProi IPR003593. 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.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF00915. Calici_coat. 1 hit.
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view ]
PRINTSi PR00916. 2CENDOPTASE.
PR00918. CALICVIRUSNS.
SMARTi SM00382. AAA. 1 hit.
[Graphical view ]
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEi PS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiPOLG_RHDVA
AccessioniPrimary (citable) accession number: Q86119
Secondary accession number(s): Q7THT7
, Q86123, Q86124, Q9IBM0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: October 1, 2003
Last modified: July 9, 2014
This is version 89 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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