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Protein

RNA replicase polyprotein

Gene
N/A
Organism
Turnip yellow mosaic virus
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as a cysteine protease, methyltransferase and deubiquitinase. The cyteine protease activity cleaves the polyprotein giving rise to mature proteins. The methyltransferase domain is probably involved in viral RNA capping. The deubiquitylating activity counteracts the degradation of the viral polymerase mediated by the host ubiquitin-proteasome system. The polymerase is thus stabilized and infectivity is increased.1 Publication
RNA-directed RNA polymerase is responsible for the replication and transcription of the genome.PROSITE-ProRule annotation1 Publication

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei783For protease activityPROSITE-ProRule annotation1
Active sitei869For protease activityPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi976 – 983ATPBy similarity8

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Methyltransferase, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

Keywords - Biological processi

Host-virus interaction, Modulation of host ubiquitin pathway by viral deubiquitinase, Modulation of host ubiquitin pathway by virus, Viral RNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA replicase polyprotein
Alternative name(s):
206 kDa polyprotein
Cleaved into the following 3 chains:
Alternative name(s):
98 kDa protein
MET/PRO
Alternative name(s):
42 kDa protein
HEL
Alternative name(s):
66 kDa protein
POL
OrganismiTurnip yellow mosaic virus
Taxonomic identifieri12154 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageTymoviralesTymoviridaeTymovirus
Virus hostiBrassica [TaxID: 3705]
Cardamine lilacina [TaxID: 82359]
Proteomesi
  • UP000000401 Componenti: Genome

Subcellular locationi

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002229381 – 1844RNA replicase polyproteinAdd BLAST1844
ChainiPRO_00004180481 – 879Methyltransferase/ProteaseAdd BLAST879
ChainiPRO_0000418049880 – 1259Putative helicaseAdd BLAST380
ChainiPRO_00004180501260 – 1844RNA-directed RNA polymeraseAdd BLAST585

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei879 – 880Cleavage; by viral protease2
Sitei1259 – 1260Cleavage; by viral protease2

Structurei

Secondary structure

11844
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi734 – 737Combined sources4
Beta strandi742 – 748Combined sources7
Helixi749 – 752Combined sources4
Beta strandi764 – 769Combined sources6
Helixi783 – 792Combined sources10
Helixi796 – 803Combined sources8
Turni804 – 806Combined sources3
Helixi809 – 811Combined sources3
Helixi815 – 820Combined sources6
Helixi824 – 834Combined sources11
Beta strandi836 – 842Combined sources7
Beta strandi845 – 850Combined sources6
Beta strandi855 – 863Combined sources9
Beta strandi865 – 867Combined sources3
Beta strandi869 – 873Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4A5UX-ray2.00A728-879[»]
ProteinModelPortaliP10358.
SMRiP10358.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini58 – 219Alphavirus-like MTPROSITE-ProRule annotationAdd BLAST162
Domaini730 – 884Peptidase C21PROSITE-ProRule annotationAdd BLAST155
Domaini946 – 1103(+)RNA virus helicase ATP-bindingAdd BLAST158
Domaini1104 – 1236(+)RNA virus helicase C-terminalAdd BLAST133
Domaini1572 – 1678RdRp catalyticPROSITE-ProRule annotationAdd BLAST107

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi475 – 478Poly-Leu4
Compositional biasi564 – 758Pro-richAdd BLAST195

Domaini

The OTU-like region is responsible for the deubiquitination activity of this protein.

Sequence similaritiesi

Contains 1 alphavirus-like MT (methyltransferase) domain.PROSITE-ProRule annotation
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

InterProiIPR027351. (+)RNA_virus_helicase_core_dom.
IPR002588. Alphavirus-like_MT_dom.
IPR008043. Peptidase_C21.
IPR007094. RNA-dir_pol_PSvirus.
IPR001788. Tymovirus_RNA-dep_RNA_pol.
[Graphical view]
PfamiPF05381. Peptidase_C21. 1 hit.
PF00978. RdRP_2. 1 hit.
PF01443. Viral_helicase1. 1 hit.
PF01660. Vmethyltransf. 1 hit.
[Graphical view]
PROSITEiPS51743. ALPHAVIRUS_MT. 1 hit.
PS51738. PEPTIDASE_C21. 1 hit.
PS51657. PSRV_HELICASE. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P10358-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAFQLALDAL APTTHRDPSL HPILESTVDS IRSSIQTYPW SIPKELLPLL
60 70 80 90 100
NSYGIPTSGL GTSHHPHAAH KTIETFLLCT HWSFQATTPS SVMFMKPSKF
110 120 130 140 150
NKLAQVNSNF RELKNYRLHP NDSTRYPFTS PDLPVFPTIF MHDALMYYHP
160 170 180 190 200
SQIMDLFLRK PNLERLYASL VVPPEAHLSD QSFYPKLYTY TTTRHTLHYV
210 220 230 240 250
PEGHEAGSYN QPSDAHSWLR INSIRLGNHH LSVTILESWG PVHSLLIQRG
260 270 280 290 300
TPPPDPSLQA PPTLMTSDLF RSYQEPRLDV VSFRIPDAIE LPQATFLQQP
310 320 330 340 350
LRDRLVPRAV YNALFTYTRA VRTLRTSDPA AFVRMHSSKP DHDWVTSNAW
360 370 380 390 400
DNLQTFALLN VPLRPNVVYH VLQSPIASLS LYLRQHWRRL TATAVPILSF
410 420 430 440 450
LTLLQRFLPL PIPLAEVKSI TAFRRELYRK KEPHHPLDVF HLQHRVRNYH
460 470 480 490 500
SAISAVRPAS PPHQKLPHAL QKAALLLLRP ISPLLTATPF FRSEQKSMLP
510 520 530 540 550
NAELSWTLKR FALPWQASLV LLALSESSIL LHKLFSPPTL QAQHDTYHRH
560 570 580 590 600
LHPGSYSLQW ERTPLSIPRT TAFLPFTPTT STAPPDRSEA SLPPAFASTF
610 620 630 640 650
VPRPPPAASS PGAQPPTTTA APPTPIEPTQ RTHQNSDLAL ESSTSTEPPP
660 670 680 690 700
PPIRSPDMTP SAPVLFPEIN SPRRFPPQLP ATPDLEPAHT PPPLSIPHQD
710 720 730 740 750
PTDSADPLMG SHLLHHSLPA PPTHPLPSSQ LLPAPLTNDP TAIGPVLPFE
760 770 780 790 800
ELHPRRYPEN TATFLTRLRS LPSNHLPQPT LNCLLSAVSD QTKVSEEHLW
810 820 830 840 850
ESLQTILPDS QLSNEETNTL GLSTEHLTAL AHLYNFQATV YSDRGPILFG
860 870 880 890 900
PSDTIKRIDI THTTGPPSHF SPGKRLLGSQ PSAKGHPSDP LIRAMKSFKV
910 920 930 940 950
SGNYLPFSEA HNHPTSISHA KNLISNMKNG FDGVLSLLDV STGQRTGPTP
960 970 980 990 1000
KERIIQIDHY LDTNPGKTTP VVHFAGFAGC GKTYPIQQLL KTKLFKDFRV
1010 1020 1030 1040 1050
SCPTTELRTE WKTAMELHGS QSWRFNTWES SILKSSRILV IDEIYKMPRG
1060 1070 1080 1090 1100
YLDLSILADP ALELVIILGD PLQGEYHSQS KDSSNHRLPS ETLRLLPYID
1110 1120 1130 1140 1150
MYCWWSYRIP QCIARLFQIH SFNAWQGVIG SVSTPHDQSP VLTNSHASSL
1160 1170 1180 1190 1200
TFNSLGYRSC TISSSQGLTF CDPAIIVLDN YTKWLSSANG LVALTRSRSG
1210 1220 1230 1240 1250
VQFMGPSSYV GGTNGSSAMF SDAFNNSLII MDRYFPSLFP QLKLITSPLT
1260 1270 1280 1290 1300
TRGPKLNGAT PSASPTHRSP NFHLPPHIPL SYDRDFVTVN PTLPDQGPET
1310 1320 1330 1340 1350
RLDTHFLPPS RLPLHFDLPP AITPPPVSTS VDPPQAKASP VYPGEFFDSL
1360 1370 1380 1390 1400
AAFFLPAHDP STREILHKDQ SSNQFPWFDR PFSLSCQPSS LISAKHAPNH
1410 1420 1430 1440 1450
DPTLLPASIN KRLRFRPSDS PHQITADDVV LGLQLFHSLC RAYSRQPNST
1460 1470 1480 1490 1500
VPFNPELFAE CISLNEYAQL SSKTQSTIVA NASRSDPDWR HTTVKIFAKA
1510 1520 1530 1540 1550
QHKVNDGSIF GSWKACQTLA LMHDYVILVL GPVKKYQRIF DNADRPPNIY
1560 1570 1580 1590 1600
SHCGKTPNQL RDWCQEHLTH STPKIANDYT AFDQSQHGES VVLEALKMKR
1610 1620 1630 1640 1650
LNIPSHLIQL HVHLKTNVST QFGPLTCMRL TGEPGTYDDN TDYNLAVIYS
1660 1670 1680 1690 1700
QYDVGSCPIM VSGDDSLIDH PLPTRHDWPS VLKRLHLRFK LELTSHPLFC
1710 1720 1730 1740 1750
GYYVGPAGCI RNPLALFCKL MIAVDDDALD DRRLSYLTEF TTGHLLGESL
1760 1770 1780 1790 1800
WHLLPETHVQ YQSACFDFFC RRCPRHEKML LDDSTPALSL LERITSSPRW
1810 1820 1830 1840
LTKNAMYLLP AKLRLAITSL SQTQSFPESI EVSHAESELL HYVQ
Length:1,844
Mass (Da):206,641
Last modified:August 1, 1992 - v2
Checksum:iA016D758C83D128C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07441 Genomic RNA. Translation: CAA30322.1. Sequence problems.
PIRiS01956.
RefSeqiNP_663297.1. NC_004063.1.

Genome annotation databases

GeneIDi951158.
KEGGivg:951158.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07441 Genomic RNA. Translation: CAA30322.1. Sequence problems.
PIRiS01956.
RefSeqiNP_663297.1. NC_004063.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4A5UX-ray2.00A728-879[»]
ProteinModelPortaliP10358.
SMRiP10358.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi951158.
KEGGivg:951158.

Family and domain databases

InterProiIPR027351. (+)RNA_virus_helicase_core_dom.
IPR002588. Alphavirus-like_MT_dom.
IPR008043. Peptidase_C21.
IPR007094. RNA-dir_pol_PSvirus.
IPR001788. Tymovirus_RNA-dep_RNA_pol.
[Graphical view]
PfamiPF05381. Peptidase_C21. 1 hit.
PF00978. RdRP_2. 1 hit.
PF01443. Viral_helicase1. 1 hit.
PF01660. Vmethyltransf. 1 hit.
[Graphical view]
PROSITEiPS51743. ALPHAVIRUS_MT. 1 hit.
PS51738. PEPTIDASE_C21. 1 hit.
PS51657. PSRV_HELICASE. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLR_TYMV
AccessioniPrimary (citable) accession number: P10358
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: August 1, 1992
Last modified: November 2, 2016
This is version 94 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

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.