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Protein

RNA-directed RNA polymerase

Gene

ORF1

Organism
Red clover necrotic mosaic virus (RCNMV)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

RNA-dependent RNA polymerase that plays an essential role in the virus replication.1 Publication

Catalytic activityi

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

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

Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-directed RNA polymerase (EC:2.7.7.48)
Alternative name(s):
Protein p88
Gene namesi
ORF Names:ORF1
OrganismiRed clover necrotic mosaic virus (RCNMV)
Taxonomic identifieri12267 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageTombusviridaeDianthovirus
Virus hostiMedicago sativa (Alfalfa) [TaxID: 3879]
Melilotus officinalis (Yellow sweet clover) (Trifolium officinale) [TaxID: 47083]
Trifolium pratense (Red clover) [TaxID: 57577]
Trifolium repens (Creeping white clover) [TaxID: 3899]
ProteomesiUP000008651 Componenti: Genome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 767767RNA-directed RNA polymerasePRO_0000040206Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliP22956.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini463 – 580118RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

InterProiIPR007094. RNA-dir_pol_PSvirus.
IPR002166. RNA_pol_HCV.
[Graphical view]
PfamiPF00998. RdRP_3. 1 hit.
[Graphical view]
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Isoform RNA-directed RNA polymerase p88 (identifier: P22956-1) [UniParc]FASTAAdd to basket

Also known as: 88 kDa protein

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
MGFINLSLFD VDKLMVWVSK FNPGKILSAI CNLGIDCWNR FRKWFFGLNF
60 70 80 90 100
DAHMWAVDAF IPLMPHYTEQ MERVVDDFCS ETPESKLEDC LELDTSVNEF
110 120 130 140 150
FDEEVYKKDE EGVMKLQRSA ARKHIKRVRP GMMQAAIKAV ETRIRNRHTI
160 170 180 190 200
FGDDMGKVDE AAVRATASDI CGEFKINEHH TNALVYAAAY LAMTPDQRSI
210 220 230 240 250
DSVKLAYNPK SQARRTLVSA IRENKAVAGF KSLEDFLGGP LSFPVEDAPY
260 270 280 290 300
PILGIPEIRV AEKRASRVMK SKRVVGLPAV SAGLKVCVHQ TSLHNMIVSL
310 320 330 340 350
ERRVFRVKNS AGELVVPPKP IQNAFDSISY FREEWLRKLS HKGQILKSSL
360 370 380 390 400
ADVVACYSSE KRKLYQKAAD SLEKKPVQWR DSKVQAFIKV EKLECDTKDP
410 420 430 440 450
VPRTIQPRSK RYNLAIGQYL RLNEKKMLDS IDDVFKEKTV LSGLDNRAQG
460 470 480 490 500
RAIAHKWRKY QNPIGIGLDA SRFDQHCSVD ALKFEQTFYK ACFPGDQQLE
510 520 530 540 550
TLLKWQLSNT GSALLPTGEL VRYRTKGCRM SGDINTGLGN KILMCSMVHA
560 570 580 590 600
FLKETGVRAS LANNGDDCVL FCEKGDYEQI NRNLEQWFLC RGFEMTVEKP
610 620 630 640 650
VDVLEKVAFC RSQPVCIATQ WAMVRQLGSL SRDCFSTQDW LNPKTFKDAM
660 670 680 690 700
NALGQCNGII NDGVPIHMAQ AKLMHRIGGN RKFNLDALHK QMEYSWRDRL
710 720 730 740 750
GKRTNLLWSE VEDATRLSYF RAFGIEPYIQ RIVEEYFSQV EITCEGRSTN
760
VLPTHYSRIH KDLIKAR
Note: Produced by ribosomal frameshifting between codons 236 and 237.
Length:767
Mass (Da):87,544
Last modified:November 1, 1991 - v2
Checksum:i3515C03BFF4F7A1B
GO
Isoform protein p27 (identifier: P22956-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     237-767: Missing.

Note: Produced by conventional translation.
Show »
Length:236
Mass (Da):27,015
Checksum:i44AD4823A36CB73B
GO

Sequence cautioni

The sequence AAB02541.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti237 – 2371Missing in AAB02540 (PubMed:2763465).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei237 – 767531Missing in isoform protein p27. CuratedVSP_032886Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04357 Genomic RNA. Translation: AAB02539.1.
J04357 Genomic RNA. Translation: AAB02540.1.
J04357 Genomic RNA. Translation: AAB02541.1. Sequence problems.
PIRiT10779. B43684.
RefSeqiNP_620523.1. NC_003756.1.
NP_620524.1. NC_003756.1. [P22956-2]

Genome annotation databases

GeneIDi956630.
956631.
KEGGivg:956630.
vg:956631.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04357 Genomic RNA. Translation: AAB02539.1.
J04357 Genomic RNA. Translation: AAB02540.1.
J04357 Genomic RNA. Translation: AAB02541.1. Sequence problems.
PIRiT10779. B43684.
RefSeqiNP_620523.1. NC_003756.1.
NP_620524.1. NC_003756.1. [P22956-2]

3D structure databases

ProteinModelPortaliP22956.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi956630.
956631.
KEGGivg:956630.
vg:956631.

Family and domain databases

InterProiIPR007094. RNA-dir_pol_PSvirus.
IPR002166. RNA_pol_HCV.
[Graphical view]
PfamiPF00998. RdRP_3. 1 hit.
[Graphical view]
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The complete nucleotide sequence and genome organization of red clover necrotic mosaic virus RNA-1."
    Xiong Z., Lommel S.A.
    Virology 171:543-554(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Australian.
  2. "Synthesis of the putative red clover necrotic mosaic virus RNA polymerase by ribosomal frameshifting in vitro."
    Xiong Z., Kim K.H., Kendall T.L., Lommel S.A.
    Virology 193:213-221(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: RIBOSOMAL FRAMESHIFT.
  3. "A plant RNA virus suppresses RNA silencing through viral RNA replication."
    Takeda A., Tsukuda M., Mizumoto H., Okamoto K., Kaido M., Mise K., Okuno T.
    EMBO J. 24:3147-3157(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiRDRP_RCNMV
AccessioniPrimary (citable) accession number: P22956
Secondary accession number(s): P22957, Q86156, Q86157
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: November 1, 1991
Last modified: June 24, 2015
This is version 77 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Caution

The 57-kDa protein cited in PubMed:2763465 has only been seen in vitro and is likely not expressed in vivo.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.