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Q89273

- POLG_RHDVB

UniProt

Q89273 - POLG_RHDVB

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Protein

Genome polyprotein

Gene

ORF1

Organism
Rabbit hemorrhagic disease virus (strain BS89) (Ra/LV/RHDV/BS89/1989/IT) (RHDV-BS89)
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).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).PROSITE-ProRule annotation
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).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).PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei143 – 1442Cleavage; by 3CLproBy similarity
Sitei339 – 3402Cleavage; by 3CLproBy similarity
Sitei718 – 7192Cleavage; by 3CLproBy similarity
Sitei936 – 9372Cleavage; by hostBy similarity
Sitei993 – 9942Cleavage; by 3CLproBy similarity
Sitei1108 – 11092Cleavage; by 3CLproBy similarity
Active sitei1135 – 11351For 3CLpro activityBy similarity
Active sitei1159 – 11591For 3CLpro activityBy similarity
Active sitei1212 – 12121For 3CLpro activitySequence Analysis
Sitei1251 – 12522Cleavage; by 3CLproBy similarity
Sitei1767 – 17682Cleavage; by 3CLproBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi522 – 5298ATPPROSITE-ProRule annotation

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 BS89) (Ra/LV/RHDV/BS89/1989/IT) (RHDV-BS89)
Taxonomic identifieri314537 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeLagovirus
Virus hostiOryctolagus cuniculus (Rabbit) [TaxID: 9986]

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 23442344Genome polyproteinPRO_0000342003Add
BLAST
Chaini1 – 143143Protein p16By similarityPRO_0000036950Add
BLAST
Chaini144 – 339196Protein p23By similarityPRO_0000036951Add
BLAST
Chaini340 – 718379NTPaseBy similarityPRO_0000036952Add
BLAST
Chaini719 – 1108390Precursor p41PRO_0000342004Add
BLAST
Chaini719 – 993275Protein p29By similarityPRO_0000036953Add
BLAST
Chaini719 – 936218Protein p23/2PRO_0000342005Add
BLAST
Chaini937 – 1108172Protein p18PRO_0000342006Add
BLAST
Chaini994 – 1108115Viral genome-linked proteinBy similarityPRO_0000036954Add
BLAST
Chaini1109 – 12511433C-like proteaseBy similarityPRO_0000036955Add
BLAST
Chaini1252 – 1767516RNA-directed RNA polymeraseBy similarityPRO_0000036956Add
BLAST
Chaini1768 – 2344577Capsid protein VP60By similarityPRO_0000036958Add
BLAST

Amino acid modifications

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

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

Structurei

3D structure databases

ProteinModelPortaliQ89273.
SMRiQ89273. Positions 1256-1752.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini492 – 653162SF3 helicasePROSITE-ProRule annotationAdd
BLAST
Domaini1120 – 121899Peptidase C24Add
BLAST
Domaini1495 – 1619125RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 peptidase C24 domain.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

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: Q89273-1) [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

        10         20         30         40         50
MAAMSRLTGM TTAILPEKKP LNFFLDLRDK TPPCCIRATG KLAWPVFPGQ
60 70 80 90 100
NGKEGPLKTC NKCGKWLNGF GYFGLEDLGD VCLCSIAQQK HKFGPVCLCN
110 120 130 140 150
RAYIHDCGRW RRRSRFLKHY KALNKVIPCA YQFDESFSTP VFEGEVDDLF
160 170 180 190 200
VELGAPTSMG FMDKKLLKKG KKLMDKFVDV DEPCLTSRDA SLLDSIASDT
210 220 230 240 250
TIRAKLEEEY GVEMVQAARD RKDFMKNLRL ALDNRPANPV TWYTKLGNIT
260 270 280 290 300
EKGKQWAKKV VYGACKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFKPV
310 320 330 340 350
NLLAILMDWT NDLAGFVTTL VRLLELYGVV QATVNLIIEG VKSFWDKVVC
360 370 380 390 400
ATERCFDLLK RLFDTFEDSV PTGPTAGCLI FMAFVFSTVV GYLPNNSVIT
410 420 430 440 450
TFMKGAGKLT TFAGVIGAIR TLWITINQHM VAKDLTSIQQ KVMTVVKMAN
460 470 480 490 500
EAATLDQLEI VSCLCSDLEN TLTNRCTLPS YNQHLGILNA SQKVISDLHT
510 520 530 540 550
MVLGKINMTK QRPQPVAVIF KGAPGIGKTY LVHRIARDLG CQHPSTINFG
560 570 580 590 600
LDHFDSYTGE EVAIADEFNT CGDGESWVEL FIQMVNTNPC PLNCDKAENK
610 620 630 640 650
NKVFNSKYLL CTTNSNMILN ATHPRAGAFY RRVMIVEARN KAVESWQATR
660 670 680 690 700
HGSKPGKSCY SKDMSHLTFQ VYPHNMPAPG FVFVGDKLVK SQVAPREYKY
710 720 730 740 750
SELLDLIKSE HPDVASFDGA NRFNFVYPDA QYDQALLMWK QYFVMYGCVA
760 770 780 790 800
RLAKNFVDDI PYNQVHISRA SDPKIEGCVE YQCKFQHLWR MVPQFVLGCV
810 820 830 840 850
NMTNQLGTPL TQQQLDRITN GVEGVTVTTV NNILAFHSQT TLINPSFLKL
860 870 880 890 900
IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGSLVRTLT GAATFSDEPV
910 920 930 940 950
STTIICSNCT IQIHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL
960 970 980 990 1000
ISGFSWRQIA HLFVEVISHL CANHLVNLAT MAALGPVATK AFQGVKGKTK
1010 1020 1030 1040 1050
RGRGARVNLG NDEYDEWQAA RREFVNAHDM TAEEYLAMKN KAAMGSDDQD
1060 1070 1080 1090 1100
SVMFRSWWTR RQLRPDEDQV TIVGRGGVRN EVIRTRVRQT PKGPKTLDDG
1110 1120 1130 1140 1150
GFYDNDYEGL PGFMRHNGSG WMIHIGNGLY ISNTHTARSS CSEIVTCSPT
1160 1170 1180 1190 1200
TDLCLVKGEA IRSVAQIAEG TPVCDWKKSP ISTYGIKKTL SDSTKIDVLA
1210 1220 1230 1240 1250
YDGCTQTTHG DCGLPLYDSS GKIVAIHTGK LLGFSKMCTL IDLTITKGVY
1260 1270 1280 1290 1300
ETSNFFCGEP IDYRGITAHR LVGAEPRPPV SGTRYAKVPG VPDEYKTGYR
1310 1320 1330 1340 1350
PANLGRSDPD SDKSLMNIAV KNLQVYQQEP KLDKVDEFIE RAAADVLGYL
1360 1370 1380 1390 1400
RFLTKGERQA NLNFKAAFNT LDLSTSCGPF VPGKKIDHVK DGVMDQVLAK
1410 1420 1430 1440 1450
HLYKCWSVAN SGKALHHIYA CGLKDELRPL DKVREGKKRL LWGCDVGVAV
1460 1470 1480 1490 1500
CRAAVFHNIC YKLKMVARFG PIAVGVDMTS RDVDVIINNL TSKASDFLCL
1510 1520 1530 1540 1550
DYSKWDSTMS PCVVRLAIDI LADCCEQTEL TKSVVLTLKS HPMTILDAMI
1560 1570 1580 1590 1600
VQTKRGLPSG MPFTSVINSI CHWLLWSAAV YKSCAEIGLH CSNLYEDAPF
1610 1620 1630 1640 1650
YTYGDDGVYA MTPMMVSLLP AIIENLRDYG LSPTAADKTE FIDVCPLNKI
1660 1670 1680 1690 1700
SFLKRTFELT DIGWVSKLDK SSILRQLEWS KTTSRHMMIE ETYDLAKEER
1710 1720 1730 1740 1750
GVQLEELQVP AAAHGQEFFN FVCKELERQQ AYTQFSVYSY DAARKILADR
1760 1770 1780 1790 1800
KRVVSVVPDD EFVNVMEGKA RTAPQGEAAG TATTASVPGT TTDGLDPGVV
1810 1820 1830 1840 1850
ATTSVVTAEN SSASIATAGI GGPPQQVDQQ ETWRTNFYYN DVFTWSVADA
1860 1870 1880 1890 1900
PGSILYTVQH SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVA
1910 1920 1930 1940 1950
AVIPPGIEIG PGLEVRQFPH VVIDARSLEP VTITMPDLRP NMYHPTGDPG
1960 1970 1980 1990 2000
LVPTLVLSVY NNLINPFGGS TSAIQVTVET RPSEDFEFVM IRAPSSKTVD
2010 2020 2030 2040 2050
SISPAGLLTT PVLTGVGNDN RWNGQIVGLQ PVPGGFSTCN RHWNLNGSTY
2060 2070 2080 2090 2100
GWSSPRFADI DHRRGSASYP GSNATNVLQF WYANAGSAVD NPISQVAPDG
2110 2120 2130 2140 2150
FPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP
2160 2170 2180 2190 2200
GNLQPTTNTS GAQTVAKSIY AVVTGTAQNP AGLFVMASGV ISTPNANAIT
2210 2220 2230 2240 2250
YTPQPDRIVT TPGTPAAAPV GKNTPIMFAS VVRRTGDVNA TAGSANGTQY
2260 2270 2280 2290 2300
GTGSQPLPVT IGLSLNNYSS ALMPGQFFVW QLTFASGFME IGLSVDGYFY
2310 2320 2330 2340
AGTGASTTLI DLTELIDVRP VGPRPSKSTL VFNLGGTANG FSYV

Note: Produced from the genomic RNA.

Length:2,344
Mass (Da):256,898
Last modified:November 1, 1996 - v1
Checksum:iB92411C5067EB0C2
GO
Isoform Subgenomic capsid protein VP60 (identifier: Q89273-2) [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):60,193
Checksum:iD070C2232C0ACA4C
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 17651765Missing in isoform Subgenomic capsid protein VP60. CuratedVSP_034380Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X87607 Genomic RNA. Translation: CAA60910.1.
PIRiS55399.

Keywords - Coding sequence diversityi

Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X87607 Genomic RNA. Translation: CAA60910.1 .
PIRi S55399.

3D structure databases

ProteinModelPortali Q89273.
SMRi Q89273. 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. "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: NUCLEOTIDE SEQUENCE [GENOMIC RNA], CHARACTERIZATION OF 3C-LIKE PROTEASE.

Entry informationi

Entry nameiPOLG_RHDVB
AccessioniPrimary (citable) accession number: Q89273
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: November 1, 1996
Last modified: October 29, 2014
This is version 84 of the entry and version 1 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 (By similarity).By similarity

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3