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O37061

- RDRP_ROTSP

UniProt

O37061 - RDRP_ROTSP

Protein

RNA-directed RNA polymerase

Gene
N/A
Organism
Rotavirus A (strain SA11-Patton G3-Px[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx) (RV-A) (Simian Agent 11 (strain Patton))
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 51 (01 Oct 2014)
      Sequence version 2 (24 Mar 2009)
      Previous versions | rss
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    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.2 PublicationsPROSITE-ProRule annotation

    Catalytic activityi

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

    Cofactori

    Magnesium.Curated

    GO - Molecular functioni

    1. nucleotide binding Source: UniProtKB-KW
    2. RNA binding Source: UniProtKB-KW
    3. RNA-directed RNA polymerase activity Source: UniProtKB-KW

    GO - Biological processi

    1. transcription, DNA-templated Source: InterPro
    2. viral genome replication Source: InterPro

    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 SA11-Patton G3-Px[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx) (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

    1. virion Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Virion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 10881088RNA-directed RNA polymerasePRO_0000367812Add
    BLAST

    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

    1
    1088
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 1512
    Beta strandi23 – 286
    Helixi32 – 4918
    Turni50 – 523
    Helixi58 – 614
    Helixi63 – 686
    Beta strandi69 – 779
    Helixi85 – 895
    Helixi90 – 923
    Helixi108 – 1103
    Helixi115 – 1184
    Turni122 – 1243
    Turni128 – 1303
    Beta strandi134 – 1363
    Helixi138 – 15114
    Turni152 – 1543
    Helixi157 – 17822
    Helixi193 – 1964
    Helixi203 – 21412
    Helixi220 – 23213
    Turni233 – 2353
    Beta strandi237 – 2393
    Helixi240 – 2456
    Helixi248 – 2514
    Turni252 – 2543
    Beta strandi257 – 2637
    Beta strandi269 – 2768
    Helixi282 – 29716
    Helixi302 – 3109
    Turni311 – 3133
    Turni316 – 3194
    Helixi320 – 3289
    Helixi329 – 3324
    Helixi339 – 3446
    Helixi361 – 37313
    Helixi376 – 3805
    Helixi384 – 3874
    Helixi389 – 3968
    Beta strandi399 – 41012
    Beta strandi413 – 4197
    Helixi420 – 4289
    Turni429 – 4313
    Beta strandi442 – 4454
    Beta strandi447 – 4526
    Beta strandi455 – 4573
    Beta strandi460 – 4634
    Helixi468 – 48518
    Turni491 – 4933
    Helixi499 – 50810
    Beta strandi514 – 5207
    Helixi522 – 5254
    Helixi528 – 54619
    Helixi552 – 56918
    Beta strandi571 – 5766
    Beta strandi578 – 5869
    Beta strandi593 – 5953
    Helixi596 – 61621
    Beta strandi622 – 6298
    Beta strandi632 – 6387
    Helixi645 – 66016
    Turni661 – 6633
    Beta strandi667 – 6737
    Beta strandi675 – 6773
    Beta strandi681 – 6833
    Beta strandi686 – 6883
    Beta strandi695 – 6973
    Helixi706 – 72318
    Helixi729 – 74012
    Beta strandi742 – 75211
    Helixi754 – 7585
    Beta strandi759 – 7613
    Helixi779 – 79012
    Helixi797 – 8048
    Helixi806 – 81914
    Helixi826 – 83712
    Helixi838 – 8414
    Helixi843 – 86018
    Helixi874 – 8818
    Helixi882 – 8843
    Beta strandi885 – 8906
    Helixi905 – 91410
    Helixi929 – 9379
    Helixi944 – 9518
    Helixi955 – 96410
    Helixi969 – 9757
    Helixi979 – 99618
    Turni997 – 10004
    Turni1002 – 10065
    Helixi1012 – 10165
    Helixi1027 – 104822
    Beta strandi1049 – 10568
    Helixi1060 – 107011
    Helixi1079 – 10879

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO37061.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini501 – 687187RdRp catalyticPROSITE-ProRule annotationAdd
    BLAST

    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.
    [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

    MGKYNLILSE YLSFIYNSQS AVQIPIYYSS NSELENRCIE FHSKCLENSK     50
    NGLSLRKLFV EYNDVIENAT LLSILSYSYD KYNAVERKLV KYAKGKPLEA 100
    DLTVNELDYE NNKMTSELFP TAEEYTDSLM DPAILTSLSS NLNAVMFWLE 150
    KHENDVAEKL KVYKRRLDLF TIVASTINKY GVPRHNAKYR YEYDVMKDKP 200
    YYLVTWANSS IEMLMSVFSH DDYLIAKELI VLSYSNRSTL AKLVSSPMSI 250
    LVALVDINGT FITNEELELE FSNKYVRAIV PDQTFDELNQ MLDNMRKAGL 300
    VDIPKMIQDW LVDRSIEKFP LMAKIYSWSF HVGFRKQKML DAALDQLKTE 350
    YTENVDDEMY REYTMLIRDE VVKMLEEPVK HDDHLLRDSE LAGLLSMSSA 400
    SNGESRQLKF GRKTIFSTKK NMHVMDDMAN ERYTPGIIPP VNVDKPIPLG 450
    RRDVPGRRTR IIFILPYEYF IAQHAVVEKM LIYAKHTREY AEFYSQSNQL 500
    LSYGDVTRFL SNNTMVLYTD VSQWDSSQHN TQPFRKGIIM GLDILANMTN 550
    DAKVLQTLNL YKQTQINLMD SYVQIPDGNV IKKIQYGAVA SGEKQTKAAN 600
    SIANLALIKT VLSRISNKHS FATKIIRVDG DDNYAVLQFN TEVTKQMIQD 650
    VSNDVRETYA RMNAKVKALV STVGIEIAKR YIAGGKIFFR AGINLLNNEK 700
    RGQSTQWDQA AILYSNYIVN RLRGFETDRE FILTKIMQMT SVAITGSLRL 750
    FPSERVLTTN STFKVFDSED FIIEYGTTVD EVYIQRAFMS LSSQKSGIAD 800
    EIAASSTFKN YVTRLSEQLL FSKNNIVSRG IALTEKAKLN SYAPISLEKR 850
    RAQISALLTM LQKPVTFKSS KITINDILRD IKPFFTVSDA HLPIQYQKFM 900
    PTLPDNVQYI IQCIGSRTYQ IEDDGSKSAI SRLISKYSVY KPSIEELYKV 950
    ISLHENEIQL YLISLGIPKI DADTYVGSKI YSRDKYRILE SYVYNLLSIN 1000
    YGCYQLFDFN SPDLEKLIRI PFKGKIPAVT FILHLYAKLE VINYAIKNGS 1050
    WISLFCNYPK SEMIKLWKKM WNITSLRSPY TNANFFQE 1088
    Length:1,088
    Mass (Da):125,252
    Last modified:March 24, 2009 - v2
    Checksum:i7A5AD04A37BA0E8C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF015955 mRNA. Translation: AAC58684.1. Different termination.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF015955 mRNA. Translation: AAC58684.1 . Different termination.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2R7O X-ray 3.35 A 1-1088 [» ]
    2R7Q X-ray 2.90 A 1-1088 [» ]
    2R7R X-ray 2.60 A 1-1088 [» ]
    2R7S X-ray 3.24 A 1-1088 [» ]
    2R7T X-ray 3.00 A 1-1088 [» ]
    2R7U X-ray 3.10 A 1-1088 [» ]
    2R7V X-ray 2.80 A 1-1088 [» ]
    2R7W X-ray 2.60 A 1-1088 [» ]
    2R7X X-ray 2.80 A/B 1-1088 [» ]
    4F5X X-ray 5.00 W 1-1088 [» ]
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei O37061.

    Family and domain databases

    InterProi IPR001795. RNA-dir_pol_luteovirus.
    IPR007097. RNA-dir_pol_reovirus.
    IPR022071. Rotavirus_VP1.
    [Graphical view ]
    Pfami PF02123. RdRP_4. 1 hit.
    PF12289. Rotavirus_VP1. 1 hit.
    [Graphical view ]
    PROSITEi PS50523. RDRP_DSRNA_REO. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Rotavirus RNA polymerase requires the core shell protein to synthesize the double-stranded RNA genome."
      Patton J.T., Jones M.T., Kalbach A.N., He Y.-W., Xiaobo J.
      J. Virol. 71:9618-9626(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
    2. "The rotavirus RNA-binding protein NS35 (NSP2) forms 10S multimers and interacts with the viral RNA polymerase."
      Kattoura M.D., Chen X., Patton J.T.
      Virology 202:803-813(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH NSP2.
    3. "Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1."
      Lu X., McDonald S.M., Tortorici M.A., Tao Y.J., Vasquez-Del Carpio R., Nibert M.L., Patton J.T., Harrison S.C.
      Structure 16:1678-1688(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), COFACTOR, FUNCTION.

    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: October 1, 2014
    This is version 51 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

    External Data

    Dasty 3