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Protein

RNA-directed RNA polymerase

Gene

VP1

Organism
Avian infectious bursal disease virus (IBDV) (Gumboro disease virus)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

RNA-dependent RNA polymerase which is found both free and covalently attached to the genomic RNA. May also contain guanylyl and methyl transferase activities (By similarity).By similarity

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi259 – 2668GTPSequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, RNA-directed RNA polymerase, Transferase

Keywords - Biological processi

Viral RNA replication

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-directed RNA polymerase (EC:2.7.7.48)
Short name:
RDRP
Alternative name(s):
Protein VP1
Gene namesi
Name:VP1
OrganismiAvian infectious bursal disease virus (IBDV) (Gumboro disease virus)
Taxonomic identifieri10995 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesBirnaviridaeAvibirnavirus
Virus hostiGallus gallus (Chicken) [TaxID: 9031]
Meleagris gallopavo (Common turkey) [TaxID: 9103]

Subcellular locationi

  • Virion By similarity

  • Note: Minor amounts are incorporated in the virion.By similarity

GO - Cellular componenti

  • virion Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi401 – 4033ADN → GDD: Increases polymerase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 881881RNA-directed RNA polymerasePRO_0000227880Add
BLAST

Post-translational modificationi

May exist in multiple phosphorylated forms.

Keywords - PTMi

Covalent protein-RNA linkage, Phosphoprotein

Interactioni

Subunit structurei

Interacts with VP3 in the cytoplasm.1 Publication

Structurei

Secondary structure

1
881
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi47 – 5610Combined sources
Beta strandi67 – 748Combined sources
Helixi75 – 784Combined sources
Helixi80 – 823Combined sources
Turni83 – 864Combined sources
Beta strandi96 – 10611Combined sources
Beta strandi118 – 1203Combined sources
Helixi128 – 13912Combined sources
Beta strandi141 – 1433Combined sources
Helixi146 – 16116Combined sources
Beta strandi162 – 1654Combined sources
Helixi169 – 18416Combined sources
Beta strandi185 – 1873Combined sources
Helixi192 – 1943Combined sources
Helixi199 – 20911Combined sources
Beta strandi218 – 2203Combined sources
Beta strandi225 – 2273Combined sources
Helixi229 – 2324Combined sources
Beta strandi233 – 2375Combined sources
Beta strandi239 – 2413Combined sources
Beta strandi244 – 2474Combined sources
Beta strandi256 – 2594Combined sources
Helixi260 – 2623Combined sources
Helixi267 – 2693Combined sources
Helixi271 – 29121Combined sources
Helixi295 – 2973Combined sources
Helixi300 – 30910Combined sources
Helixi311 – 3144Combined sources
Beta strandi315 – 3206Combined sources
Beta strandi323 – 3264Combined sources
Helixi327 – 3293Combined sources
Turni330 – 3323Combined sources
Beta strandi336 – 3394Combined sources
Helixi342 – 35615Combined sources
Turni363 – 3653Combined sources
Turni378 – 3803Combined sources
Helixi381 – 39010Combined sources
Beta strandi395 – 4006Combined sources
Beta strandi403 – 4086Combined sources
Beta strandi411 – 4177Combined sources
Helixi420 – 4234Combined sources
Helixi426 – 43914Combined sources
Beta strandi441 – 4433Combined sources
Beta strandi446 – 4494Combined sources
Helixi451 – 4599Combined sources
Helixi461 – 4655Combined sources
Beta strandi469 – 4735Combined sources
Beta strandi475 – 4784Combined sources
Helixi486 – 50621Combined sources
Helixi515 – 5184Combined sources
Helixi520 – 5245Combined sources
Beta strandi528 – 5369Combined sources
Helixi537 – 54610Combined sources
Turni552 – 5543Combined sources
Beta strandi555 – 5573Combined sources
Beta strandi566 – 5705Combined sources
Beta strandi573 – 5786Combined sources
Turni579 – 5824Combined sources
Beta strandi583 – 5886Combined sources
Helixi590 – 5989Combined sources
Helixi613 – 62917Combined sources
Helixi631 – 6333Combined sources
Helixi635 – 65521Combined sources
Helixi659 – 6624Combined sources
Turni663 – 6653Combined sources
Helixi666 – 6683Combined sources
Helixi673 – 6753Combined sources
Turni676 – 6783Combined sources
Helixi687 – 6948Combined sources
Helixi713 – 7208Combined sources
Turni721 – 7233Combined sources
Turni728 – 7303Combined sources
Helixi731 – 74111Combined sources
Helixi744 – 7463Combined sources
Helixi747 – 76014Combined sources
Helixi771 – 78212Combined sources
Helixi793 – 8019Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PGGX-ray2.50A31-804[»]
2PUSX-ray2.40A1-845[»]
2QJ1X-ray3.48A5-845[»]
2R70X-ray2.70A1-845[»]
2R72X-ray3.15A1-845[»]
ProteinModelPortaliQ9Q6Q5.
SMRiQ9Q6Q5. Positions 31-804.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Q6Q5.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini398 – 598201RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di1.10.287.540. 1 hit.
InterProiIPR007100. RNA-dir_pol_birnavirus.
IPR007098. RNA-dir_pol_mononegavirus.
IPR023218. UPF0291_struct_dom.
[Graphical view]
PfamiPF04197. Birna_RdRp. 1 hit.
[Graphical view]
PROSITEiPS50524. RDRP_DSRNA_BIR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9Q6Q5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDIFNSPQA RSTISAAFGI KPTAGQDVEE LLIPKVWVPP EDPLASPSRL
60 70 80 90 100
AKFLRENGYK VLQPRSLPEN EEYETDQILP DLAWMRQIEG AVLKPTLSLP
110 120 130 140 150
IGDQEYFPKY YPTHRPSKEK PNAYPPDIAL LKQMIYLFLQ VPEANEGLKD
160 170 180 190 200
EVTLLTQNIR DKAYGSGTYM GQATRLVAMK EVATGRNPNK DPLKLGYTFE
210 220 230 240 250
SIAQLLDITL PVGPPGEDDK PWVPLTRVPS RMLVLTGDVD GDFEVEDYLP
260 270 280 290 300
KINLKSSSGL PYVGRTKGET IGEMIAISNQ FLRELSTLLK QGAGTKGSNK
310 320 330 340 350
KKLLSMLSDY WYLSCGLLFP KAERYDKSTW LTKTRNIWSA PSPTHLMISM
360 370 380 390 400
ITWPVMSNSP NNVLNIEGCP SLYKFNPFRG GLNRIVEWIL APEEPKALVY
410 420 430 440 450
ADNIYIVHSN TWYSIDLEKG EANCTRQHMQ AAMYYILTRG WSDNGDPMFN
460 470 480 490 500
QTWATFAMNI APALVVDSSC LIMNLQIKTY GQGSGNAATF INNHLLSTLV
510 520 530 540 550
LDQWNLMRQP RPDSEEFKSI EDKLGINFKI ERSIDDIRGK LRQLVLLAQP
560 570 580 590 600
GYLSGGVEPE QSSPTVELDL LGWSATYSKD LGIYVPVLDK ERLFCSAAYP
610 620 630 640 650
KGVENKSLKS KVGIEQAYKV VRYEALRLVG GWNYPLLNKA CKNNAGAARR
660 670 680 690 700
HLEAKGFPLD EFLAEWSELS EFGEAFEGFN IKLTVTSESL AELNKPVPPK
710 720 730 740 750
PPNVNRPVNT GGLKAVSNAL KTGRYRNEAG LSGLVLLATA RSRLQDAVKA
760 770 780 790 800
KAEAEKLHKS KPDDPDADWF ERSETLSDLL EKADIASKVA HSALVETSDA
810 820 830 840 850
LEAVQSTSVY TPKYPEVKNP QTASNPVVGL HLPAKRATGV QAALLGAGTS
860 870 880
RPMGMEAPTR SKNAVKMAKR RQRQKESRQQ P
Length:881
Mass (Da):97,911
Last modified:May 1, 2000 - v1
Checksum:i3FBB3EDB3B744D7B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF194429 mRNA. Translation: AAF16083.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF194429 mRNA. Translation: AAF16083.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PGGX-ray2.50A31-804[»]
2PUSX-ray2.40A1-845[»]
2QJ1X-ray3.48A5-845[»]
2R70X-ray2.70A1-845[»]
2R72X-ray3.15A1-845[»]
ProteinModelPortaliQ9Q6Q5.
SMRiQ9Q6Q5. Positions 31-804.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Q6Q5.

Family and domain databases

Gene3Di1.10.287.540. 1 hit.
InterProiIPR007100. RNA-dir_pol_birnavirus.
IPR007098. RNA-dir_pol_mononegavirus.
IPR023218. UPF0291_struct_dom.
[Graphical view]
PfamiPF04197. Birna_RdRp. 1 hit.
[Graphical view]
PROSITEiPS50524. RDRP_DSRNA_BIR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Efficient rescue of infectious bursal disease virus from cloned cDNA: evidence for involvement of the 3'-terminal sequence in genome replication."
    Boot H.J., ter Huurne A.A., Peeters B.P.H., Gielkens A.L.
    Virology 265:330-341(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Isolate CEF94.
  2. Pan J., Vakharia V.N., Tao Y.J.
    Submitted (MAY-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 19-29.
  3. "Infectious bursal disease virus capsid protein VP3 interacts both with VP1, the RNA-dependent RNA polymerase, and with viral double-stranded RNA."
    Tacken M.G., Peeters B.P.H., Thomas A.A.M., Rottier P.J.M., Boot H.J.
    J. Virol. 76:11301-11311(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VP3.
    Strain: Isolate CEF94.
  4. "The structure of a birnavirus polymerase reveals a distinct active site topology."
    Pan J., Vakharia V.N., Tao Y.J.
    Proc. Natl. Acad. Sci. U.S.A. 104:7385-7390(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), MUTAGENESIS OF 401-ALA--ASN-403.

Entry informationi

Entry nameiRDRP_IBDV
AccessioniPrimary (citable) accession number: Q9Q6Q5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: May 1, 2000
Last modified: December 9, 2015
This is version 52 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.