Q86119 (POLG_RHDVA) Reviewed, UniProtKB/Swiss-Prot
Last modified May 1, 2013. Version 81. History...
Names and origin
|Protein names||Recommended name:|
Cleaved into the following 11 chains:
|Organism||Rabbit hemorrhagic disease virus (strain AST89) (Ra/LV/RHDV/AST89/1989/SP) (RHDV-AST89) [Complete proteome]|
|Taxonomic identifier||314538 [NCBI]|
|Taxonomic lineage||Viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Lagovirus ›|
|Virus host||Oryctolagus cuniculus (Rabbit) [TaxID: 9986]|
|Sequence length||2344 AA.|
|Sequence processing||The displayed sequence is further processed into a mature form.|
|Protein existence||Evidence at protein level|
General annotation (Comments)
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 encodes 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.
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).
Binds to histo-blood group antigens at surface of target cells By similarity. Ref.8
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.
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.
Contains 1 peptidase C24 domain.
Contains 1 RdRp catalytic domain.
Contains 1 SF3 helicase domain.
|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:
|Note: Produced from the subgenomic RNA.|
Sequence annotation (Features)
|Feature key||Position(s)||Length||Description||Graphical view||Feature identifier|
|Chain||1 – 2344||2344||Genome polyprotein||PRO_0000341999|
|Chain||1 – 143||143||Protein p16 By similarity||PRO_0000036941|
|Chain||144 – 339||196||Protein p23 By similarity||PRO_0000036942|
|Chain||340 – 718||379||NTPase By similarity||PRO_0000036943|
|Chain||712 – 1108||397||Precursor p41 By similarity||PRO_0000342000|
|Chain||712 – 936||225||Protein p23/2 By similarity||PRO_0000342001|
|Chain||719 – 993||275||Protein p29 By similarity||PRO_0000036944|
|Chain||937 – 1108||172||Protein p18 By similarity||PRO_0000342002|
|Chain||994 – 1108||115||Viral genome-linked protein By similarity||PRO_0000036945|
|Chain||1109 – 1251||143||3C-like protease By similarity||PRO_0000036946|
|Chain||1252 – 1767||516||RNA-directed RNA polymerase By similarity||PRO_0000036947|
|Chain||1768 – 2344||577||Capsid protein VP60 By similarity||PRO_0000036949|
|Domain||492 – 653||162||SF3 helicase|
|Domain||1120 – 1218||99||Peptidase C24|
|Domain||1495 – 1619||125||RdRp catalytic|
|Nucleotide binding||522 – 529||8||ATP Potential|
|Active site||1135||1||For 3CLpro activity By similarity|
|Active site||1159||1||For 3CLpro activity By similarity|
|Active site||1212||1||For 3CLpro activity Potential|
|Site||143 – 144||2||Cleavage; by 3CLpro By similarity|
|Site||339 – 340||2||Cleavage; by 3CLpro By similarity|
|Site||718 – 719||2||Cleavage; by 3CLpro By similarity|
|Site||936 – 937||2||Cleavage; by host By similarity|
|Site||993 – 994||2||Cleavage; by 3CLpro By similarity|
|Site||1108 – 1109||2||Cleavage; by 3CLpro By similarity|
|Site||1251 – 1252||2||Cleavage; by 3CLpro By similarity|
|Site||1767 – 1768||2||Cleavage; by 3CLpro By similarity|
Amino acid modifications
|Disulfide bond||1584 ↔ 1591||By similarity|
|Alternative sequence||1 – 1765||1765||Missing in isoform Subgenomic capsid protein VP60.||VSP_034379|
|Mutagenesis||1767||1||E → G: Loss of cleavage between RNA-directed RNA polymerase and VP60. Ref.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.
|||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.
|||"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.
|||"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.
|||"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.
|||"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.
|||"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.
|||"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.|
|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.
3D structure databases
|SMR||Q86119. Positions 1256-1752. |
Protocols and materials databases
Family and domain databases
|InterPro||IPR003593. AAA+_ATPase. |
|Pfam||PF00915. Calici_coat. 1 hit. |
PF03510. Peptidase_C24. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00910. RNA_helicase. 1 hit.
|PRINTS||PR00916. 2CENDOPTASE. |
|SMART||SM00382. AAA. 1 hit. |
|SUPFAM||SSF50494. Pept_Ser_Cys. 1 hit. |
|PROSITE||PS50507. RDRP_SSRNA_POS. 1 hit. |
PS51218. SF3_HELICASE_2. 1 hit.
|Accession||Primary (citable) accession number: Q86119|
Secondary accession number(s): Q7THT7 Q9IBM0
|Entry status||Reviewed (UniProtKB/Swiss-Prot)|
|Annotation program||Viral Protein Annotation Program|