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Protein

RNA-directed RNA polymerase

Gene
N/A
Organism
Rotavirus A (strain RVA/SA11-Patton/G3P[X]) (RV-A) (Simian Agent 11 (strain Patton))
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription.PROSITE-ProRule annotation2 Publications

Catalytic activityi

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

Cofactori

Mg2+Curated

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

Magnesium, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-directed RNA polymerase (EC:2.7.7.48)
Alternative name(s):
Protein VP1
OrganismiRotavirus A (strain RVA/SA11-Patton/G3P[X]) (RV-A) (Simian Agent 11 (strain Patton))
Taxonomic identifieri36434 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirusRotavirus A
Virus hostiMacaca mulatta (Rhesus macaque) [TaxID: 9544]

Subcellular locationi

  • Virion Curated

  • Note: Attached inside the inner capsid as a minor component. Also found in spherical cytoplasmic structures, called virus factories, that appear early after infection and are the site of viral replication and packaging (By similarity).By similarity

GO - Cellular componenti

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

Keywords - Cellular componenti

Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003678121 – 1088RNA-directed RNA polymeraseAdd BLAST1088

Interactioni

Subunit structurei

Interacts with VP3 (Potential). Interacts with VP2; this interaction activates VP1. Interacts with NSP5; this interaction is probably necessary for the formation of functional virus factories. Interacts with NSP2; this interaction is weak (By similarity).By similarityCurated

Structurei

Secondary structure

11088
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 15Combined sources12
Beta strandi23 – 28Combined sources6
Helixi32 – 49Combined sources18
Turni50 – 52Combined sources3
Helixi58 – 61Combined sources4
Helixi63 – 68Combined sources6
Beta strandi69 – 77Combined sources9
Helixi85 – 89Combined sources5
Helixi90 – 92Combined sources3
Helixi108 – 110Combined sources3
Helixi115 – 118Combined sources4
Turni122 – 124Combined sources3
Turni128 – 130Combined sources3
Beta strandi134 – 136Combined sources3
Helixi138 – 151Combined sources14
Turni152 – 154Combined sources3
Helixi157 – 178Combined sources22
Helixi193 – 196Combined sources4
Helixi203 – 214Combined sources12
Helixi220 – 232Combined sources13
Turni233 – 235Combined sources3
Beta strandi237 – 239Combined sources3
Helixi240 – 245Combined sources6
Helixi248 – 251Combined sources4
Turni252 – 254Combined sources3
Beta strandi257 – 263Combined sources7
Beta strandi269 – 276Combined sources8
Helixi282 – 297Combined sources16
Helixi302 – 310Combined sources9
Turni311 – 313Combined sources3
Turni316 – 319Combined sources4
Helixi320 – 328Combined sources9
Helixi329 – 332Combined sources4
Helixi339 – 344Combined sources6
Helixi361 – 373Combined sources13
Helixi376 – 380Combined sources5
Helixi384 – 387Combined sources4
Helixi389 – 396Combined sources8
Beta strandi399 – 410Combined sources12
Beta strandi413 – 419Combined sources7
Helixi420 – 428Combined sources9
Turni429 – 431Combined sources3
Beta strandi442 – 445Combined sources4
Beta strandi447 – 452Combined sources6
Beta strandi455 – 457Combined sources3
Beta strandi460 – 463Combined sources4
Helixi468 – 485Combined sources18
Turni491 – 493Combined sources3
Helixi499 – 508Combined sources10
Beta strandi514 – 520Combined sources7
Helixi522 – 525Combined sources4
Helixi528 – 546Combined sources19
Helixi552 – 569Combined sources18
Beta strandi571 – 576Combined sources6
Beta strandi578 – 586Combined sources9
Beta strandi593 – 595Combined sources3
Helixi596 – 616Combined sources21
Beta strandi622 – 629Combined sources8
Beta strandi632 – 638Combined sources7
Helixi645 – 660Combined sources16
Turni661 – 663Combined sources3
Beta strandi667 – 673Combined sources7
Beta strandi675 – 677Combined sources3
Beta strandi681 – 683Combined sources3
Beta strandi686 – 688Combined sources3
Beta strandi695 – 697Combined sources3
Helixi706 – 723Combined sources18
Helixi729 – 740Combined sources12
Beta strandi742 – 752Combined sources11
Helixi754 – 758Combined sources5
Beta strandi759 – 761Combined sources3
Helixi779 – 790Combined sources12
Helixi797 – 804Combined sources8
Helixi806 – 819Combined sources14
Helixi826 – 837Combined sources12
Helixi838 – 841Combined sources4
Helixi843 – 860Combined sources18
Helixi874 – 881Combined sources8
Helixi882 – 884Combined sources3
Beta strandi885 – 890Combined sources6
Helixi905 – 914Combined sources10
Helixi929 – 937Combined sources9
Helixi944 – 951Combined sources8
Helixi955 – 964Combined sources10
Helixi969 – 975Combined sources7
Helixi979 – 996Combined sources18
Turni997 – 1000Combined sources4
Turni1002 – 1006Combined sources5
Helixi1012 – 1016Combined sources5
Helixi1027 – 1048Combined sources22
Beta strandi1049 – 1056Combined sources8
Helixi1060 – 1070Combined sources11
Helixi1079 – 1087Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2R7OX-ray3.35A1-1088[»]
2R7QX-ray2.90A1-1088[»]
2R7RX-ray2.60A1-1088[»]
2R7SX-ray3.24A1-1088[»]
2R7TX-ray3.00A1-1088[»]
2R7UX-ray3.10A1-1088[»]
2R7VX-ray2.80A1-1088[»]
2R7WX-ray2.60A1-1088[»]
2R7XX-ray2.80A/B1-1088[»]
4F5XX-ray5.00W1-1088[»]
SMRiO37061.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO37061.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini501 – 687RdRp catalyticPROSITE-ProRule annotationAdd BLAST187

Sequence similaritiesi

Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Family and domain databases

InterProiIPR001795. RNA-dir_pol_luteovirus.
IPR007097. RNA-dir_pol_reovirus.
IPR022071. Rotavirus_VP1_C.
[Graphical view]
PfamiPF02123. RdRP_4. 1 hit.
PF12289. Rotavirus_VP1. 1 hit.
[Graphical view]
PROSITEiPS50523. RDRP_DSRNA_REO. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O37061-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKYNLILSE YLSFIYNSQS AVQIPIYYSS NSELENRCIE FHSKCLENSK
60 70 80 90 100
NGLSLRKLFV EYNDVIENAT LLSILSYSYD KYNAVERKLV KYAKGKPLEA
110 120 130 140 150
DLTVNELDYE NNKMTSELFP TAEEYTDSLM DPAILTSLSS NLNAVMFWLE
160 170 180 190 200
KHENDVAEKL KVYKRRLDLF TIVASTINKY GVPRHNAKYR YEYDVMKDKP
210 220 230 240 250
YYLVTWANSS IEMLMSVFSH DDYLIAKELI VLSYSNRSTL AKLVSSPMSI
260 270 280 290 300
LVALVDINGT FITNEELELE FSNKYVRAIV PDQTFDELNQ MLDNMRKAGL
310 320 330 340 350
VDIPKMIQDW LVDRSIEKFP LMAKIYSWSF HVGFRKQKML DAALDQLKTE
360 370 380 390 400
YTENVDDEMY REYTMLIRDE VVKMLEEPVK HDDHLLRDSE LAGLLSMSSA
410 420 430 440 450
SNGESRQLKF GRKTIFSTKK NMHVMDDMAN ERYTPGIIPP VNVDKPIPLG
460 470 480 490 500
RRDVPGRRTR IIFILPYEYF IAQHAVVEKM LIYAKHTREY AEFYSQSNQL
510 520 530 540 550
LSYGDVTRFL SNNTMVLYTD VSQWDSSQHN TQPFRKGIIM GLDILANMTN
560 570 580 590 600
DAKVLQTLNL YKQTQINLMD SYVQIPDGNV IKKIQYGAVA SGEKQTKAAN
610 620 630 640 650
SIANLALIKT VLSRISNKHS FATKIIRVDG DDNYAVLQFN TEVTKQMIQD
660 670 680 690 700
VSNDVRETYA RMNAKVKALV STVGIEIAKR YIAGGKIFFR AGINLLNNEK
710 720 730 740 750
RGQSTQWDQA AILYSNYIVN RLRGFETDRE FILTKIMQMT SVAITGSLRL
760 770 780 790 800
FPSERVLTTN STFKVFDSED FIIEYGTTVD EVYIQRAFMS LSSQKSGIAD
810 820 830 840 850
EIAASSTFKN YVTRLSEQLL FSKNNIVSRG IALTEKAKLN SYAPISLEKR
860 870 880 890 900
RAQISALLTM LQKPVTFKSS KITINDILRD IKPFFTVSDA HLPIQYQKFM
910 920 930 940 950
PTLPDNVQYI IQCIGSRTYQ IEDDGSKSAI SRLISKYSVY KPSIEELYKV
960 970 980 990 1000
ISLHENEIQL YLISLGIPKI DADTYVGSKI YSRDKYRILE SYVYNLLSIN
1010 1020 1030 1040 1050
YGCYQLFDFN SPDLEKLIRI PFKGKIPAVT FILHLYAKLE VINYAIKNGS
1060 1070 1080
WISLFCNYPK SEMIKLWKKM WNITSLRSPY TNANFFQE
Length:1,088
Mass (Da):125,252
Last modified:March 24, 2009 - v2
Checksum:i7A5AD04A37BA0E8C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF015955 mRNA. Translation: AAC58684.1. Different termination.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF015955 mRNA. Translation: AAC58684.1. Different termination.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2R7OX-ray3.35A1-1088[»]
2R7QX-ray2.90A1-1088[»]
2R7RX-ray2.60A1-1088[»]
2R7SX-ray3.24A1-1088[»]
2R7TX-ray3.00A1-1088[»]
2R7UX-ray3.10A1-1088[»]
2R7VX-ray2.80A1-1088[»]
2R7WX-ray2.60A1-1088[»]
2R7XX-ray2.80A/B1-1088[»]
4F5XX-ray5.00W1-1088[»]
SMRiO37061.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiO37061.

Family and domain databases

InterProiIPR001795. RNA-dir_pol_luteovirus.
IPR007097. RNA-dir_pol_reovirus.
IPR022071. Rotavirus_VP1_C.
[Graphical view]
PfamiPF02123. RdRP_4. 1 hit.
PF12289. Rotavirus_VP1. 1 hit.
[Graphical view]
PROSITEiPS50523. RDRP_DSRNA_REO. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRDRP_ROTSP
AccessioniPrimary (citable) accession number: O37061
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: March 24, 2009
Last modified: November 30, 2016
This is version 59 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

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.