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Protein

Genome polyprotein

Gene

ORF1

Organism
Rabbit hemorrhagic disease virus (strain Rabbit/Germany/FRG/1989) (Ra/LV/RHDV/GH/1989/GE) (RHDV-FRG)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Active sitei1135For 3CLpro activityBy similarity1
Active sitei1159For 3CLpro activityBy similarity1
Active sitei1212For 3CLpro activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi522 – 529ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

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

Enzyme and pathway databases

BRENDAi3.4.22.B15. 5265.

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 Rabbit/Germany/FRG/1989) (Ra/LV/RHDV/GH/1989/GE) (RHDV-FRG)
Taxonomic identifieri314536 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeLagovirus
Virus hostiOryctolagus cuniculus (Rabbit) [TaxID: 9986]
Proteomesi
  • UP000000413 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1135H → N: Complete loss of 3CLpro activity in vitro. 1 Publication1
Mutagenesisi1152D → E: Partial loss of 3CLpro activity in vitro. 1 Publication1
Mutagenesisi1152D → G or N: Complete loss of 3CLpro activity in vitro. 1 Publication1
Mutagenesisi1175D → G or E: Complete loss of 3CLpro activity in vitro. 1 Publication1
Mutagenesisi1175D → N: Partial loss of 3CLpro activity in vitro. 1 Publication1
Mutagenesisi1212C → G: Complete loss of 3CLpro activity in vitro. 1 Publication1
Mutagenesisi1212C → S: Partial loss of 3CLpro activity in vitro. 1 Publication1
Mutagenesisi1227H → L or N: Complete loss of 3CLpro activity in vitro. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003416451 – 2344Genome polyproteinAdd BLAST2344
ChainiPRO_00000369591 – 143Protein p16Add BLAST143
ChainiPRO_0000036960144 – 339Protein p23Add BLAST196
ChainiPRO_0000036961340 – 718NTPaseAdd BLAST379
ChainiPRO_0000341646719 – 1108Precursor p41Add BLAST390
ChainiPRO_0000036962719 – 993Protein p29Add BLAST275
ChainiPRO_0000341647719 – 936Protein p23/2Add BLAST218
ChainiPRO_0000341648937 – 1108Protein p18Add BLAST172
ChainiPRO_0000036963994 – 1108Viral genome-linked proteinAdd BLAST115
ChainiPRO_00000369641109 – 12513C-like proteaseAdd BLAST143
ChainiPRO_00000369651252 – 1767RNA-directed RNA polymeraseAdd BLAST516
ChainiPRO_00000369671768 – 2344Capsid protein VP60Add BLAST577

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1014O-(5'-phospho-RNA)-tyrosineBy similarity1
Disulfide bondi1584 ↔ 1591

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 p18.5 Publications
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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei143 – 144Cleavage; by 3CLpro2
Sitei339 – 340Cleavage; by 3CLpro2
Sitei718 – 719Cleavage; by 3CLpro2
Sitei936 – 937Cleavage; by host2
Sitei993 – 994Cleavage; by 3CLpro2
Sitei1108 – 1109Cleavage; by 3CLpro2
Sitei1251 – 1252Cleavage; by 3CLpro2
Sitei1767 – 1768Cleavage; by 3CLpro2

Keywords - PTMi

Covalent protein-RNA linkage, Disulfide bond, Phosphoprotein

Proteomic databases

PRIDEiP27410.

Interactioni

Subunit structurei

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

Structurei

Secondary structure

12344
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1257 – 1263Combined sources7
Beta strandi1266 – 1271Combined sources6
Beta strandi1282 – 1287Combined sources6
Helixi1293 – 1295Combined sources3
Beta strandi1300 – 1302Combined sources3
Helixi1305 – 1307Combined sources3
Helixi1315 – 1324Combined sources10
Helixi1325 – 1327Combined sources3
Helixi1337 – 1353Combined sources17
Turni1354 – 1356Combined sources3
Helixi1364 – 1370Combined sources7
Beta strandi1373 – 1376Combined sources4
Beta strandi1379 – 1381Combined sources3
Helixi1385 – 1387Combined sources3
Beta strandi1391 – 1393Combined sources3
Helixi1396 – 1410Combined sources15
Beta strandi1418 – 1423Combined sources6
Beta strandi1440 – 1444Combined sources5
Helixi1446 – 1465Combined sources20
Turni1466 – 1469Combined sources4
Beta strandi1470 – 1472Combined sources3
Helixi1482 – 1493Combined sources12
Beta strandi1495 – 1502Combined sources8
Helixi1505 – 1508Combined sources4
Helixi1511 – 1522Combined sources12
Helixi1529 – 1539Combined sources11
Beta strandi1543 – 1545Combined sources3
Beta strandi1547 – 1551Combined sources5
Helixi1564 – 1586Combined sources23
Helixi1594 – 1597Combined sources4
Beta strandi1600 – 1603Combined sources4
Beta strandi1606 – 1611Combined sources6
Helixi1613 – 1617Combined sources5
Helixi1619 – 1628Combined sources10
Beta strandi1633 – 1637Combined sources5
Helixi1647 – 1649Combined sources3
Beta strandi1655 – 1660Combined sources6
Beta strandi1663 – 1668Combined sources6
Helixi1670 – 1678Combined sources9
Beta strandi1679 – 1689Combined sources11
Helixi1698 – 1712Combined sources15
Helixi1716 – 1729Combined sources14
Turni1730 – 1732Combined sources3
Helixi1740 – 1750Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KHVX-ray2.50A/B1252-1767[»]
1KHWX-ray2.70A/B1252-1767[»]
ProteinModelPortaliP27410.
SMRiP27410.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP27410.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini492 – 653SF3 helicasePROSITE-ProRule annotationAdd BLAST162
Domaini1120 – 1218Peptidase C24Add BLAST99
Domaini1495 – 1619RdRp catalyticPROSITE-ProRule annotationAdd BLAST125

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

CDDicd00205. rhv_like. 1 hit.
Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR004005. 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.
IPR009003. Peptidase_S1_PA.
IPR033703. Rhv-like.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
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.
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. AlignAdd to basket

Isoform Genome polyprotein (identifier: P27410-1) [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 LDFFLDLRDK TPPCCIRATG RLAWPVFPGQ
60 70 80 90 100
NGKEGPLETC NKCGKWLNGF GNFGLEDLGD VCLCSIAQQK HKFGPVCLCN
110 120 130 140 150
RVYIHDCGRW RRRSRFLKHY KALNKVIPCA YQFDESFPTP IFEGEVDDLF
160 170 180 190 200
VELGAPTSMG FMDKKLLKKG KKLMDKFVDV DEPCLTSRDT SLLDSIASDN
210 220 230 240 250
TIRAKLEEEY GVEMVQAARD RKDFMKNLRL ALDNRPANPV TWYTKLGNIT
260 270 280 290 300
EKGKQWAKKV VYGARKVTDP LKTLASILLV GLHNVIAVDT TVMLSTFKPV
310 320 330 340 350
NLLAILMDWN NDLTGFITTL VRLLELYGVV QATVNLIIEG VKSFWDKVVC
360 370 380 390 400
ATDRCFDLLK RLFDTFEDSV PTGPTAGCLI FMAFVFSTVV GYLPNNSVIT
410 420 430 440 450
TFMKGAGKLT TFAGVVGAIR TLWITINQHM VAKDLTSVQQ KVMTVVKMAN
460 470 480 490 500
EAATLDQLEI VSCLCSDLET 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 SQVTPREYKY
710 720 730 740 750
SELLDLIKSE HPDVASFEGA NKFNFVYPDA QYDQALLMWK QYFVMYGCVA
760 770 780 790 800
RLAKNFVDDI PYNQVHISRA SDPKIEGCVE YQCKFQHLWR MVPQFVLGCV
810 820 830 840 850
NMTNQLGTPL TQQQLDRITN GVEGVTVTTV NNILPFHSQT TLINPSFIKL
860 870 880 890 900
IWAVRKHLKG LSGVTKVAQF IWRVMTNPVD AYGTLVRTLT GAATFSDDPV
910 920 930 940 950
STTIICSNCT IQLHSCGGLL VRYSRDPVPV ASDNVDRGDQ GVDVFTDPNL
960 970 980 990 1000
ISGFSWRQIA HLFVEVISHL CANHLVNLAT MAALGAVATK AFQGVKGKTK
1010 1020 1030 1040 1050
RGRGARVNLG NDEYDEWQAA RREFVNAHDM TAEEYLAMKN KAAMGSDDQD
1060 1070 1080 1090 1100
SIMFRSWWTR RQLRPEEDQV TIVGRSGVRN EVIRTRVRQT PRGPKTLDDG
1110 1120 1130 1140 1150
GFYDNDYEGL PGFMRHNGSG WMIHIGNGLY ISNTHTARSS CSEIVTCSPT
1160 1170 1180 1190 1200
TDLCLVKGES 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 DKVKEGKKRL LWGCDVGVAV
1460 1470 1480 1490 1500
CAAAVFHNIC 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 KTTSRHMVIE ETYDLAKEER
1710 1720 1730 1740 1750
GVQLEELQVA AAAHGQEFFN FVCRELERQQ AYTQFSVYSY DAARKILADR
1760 1770 1780 1790 1800
KRVVSVVPDD EFVNVMEGKA RAAPQGEAAG TATTASVPGT TTDGMDPGVV
1810 1820 1830 1840 1850
ATTSVITAEN SSASIATAGI GGPPQQVDQQ ETWRTNFYYN DVFTWSVADA
1860 1870 1880 1890 1900
PGSILYTVQH SPQNNPFTAV LSQMYAGWAG GMQFRFIVAG SGVFGGRLVR
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
GWSSPRFGDI DHRRGSASYS GSNATNVLQF WYANAGSAID NPISQVAPDG
2110 2120 2130 2140 2150
FPDMSFVPFN GPGIPAAGWV GFGAIWNSNS GAPNVTTVQA YELGFATGAP
2160 2170 2180 2190 2200
GNLQPTTNTS GAQTVAKSIY AVVTGTAQNP AGLFVMASGI ISTPNASAIT
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):257,068
Last modified:August 1, 1992 - v1
Checksum:i1454C248F81E9212
GO
Isoform Subgenomic capsid protein VP60 (identifier: P27410-2) [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):60,257
Checksum:i20857900C4107D20
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0343811 – 1765Missing in isoform Subgenomic capsid protein VP60. CuratedAdd BLAST1765

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M67473 Genomic RNA. Translation: AAA47285.1.
PIRiA41039. RRWWRH.
RefSeqiNP_062875.1. NC_001543.1.

Genome annotation databases

GeneIDi1491968.
KEGGivg:1491968.

Keywords - Coding sequence diversityi

Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M67473 Genomic RNA. Translation: AAA47285.1.
PIRiA41039. RRWWRH.
RefSeqiNP_062875.1. NC_001543.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KHVX-ray2.50A/B1252-1767[»]
1KHWX-ray2.70A/B1252-1767[»]
ProteinModelPortaliP27410.
SMRiP27410.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP27410.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1491968.
KEGGivg:1491968.

Enzyme and pathway databases

BRENDAi3.4.22.B15. 5265.

Miscellaneous databases

EvolutionaryTraceiP27410.

Family and domain databases

CDDicd00205. rhv_like. 1 hit.
Gene3Di2.60.120.20. 1 hit.
3.40.50.300. 2 hits.
InterProiIPR004005. 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.
IPR009003. Peptidase_S1_PA.
IPR033703. Rhv-like.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
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.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_RHDVF
AccessioniPrimary (citable) accession number: P27410
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: November 30, 2016
This is version 120 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.