ID   RDRP_ROTH3              Reviewed;        1088 AA.
AC   A4ZCW2;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   29-MAY-2007, sequence version 1.
DT   22-FEB-2023, entry version 54.
DE   RecName: Full=RNA-directed RNA polymerase;
DE            EC=2.7.7.48;
DE   AltName: Full=Protein VP1;
OS   Rotavirus A (strain RVA/Human/Japan/AU-1/1982/G3P3[9]) (RV-A).
OC   Viruses; Riboviria; Orthornavirae; Duplornaviricota; Resentoviricetes;
OC   Reovirales; Sedoreoviridae; Rotavirus; Rotavirus A.
OX   NCBI_TaxID=39013;
OH   NCBI_TaxID=9606; Homo sapiens (Human).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=18216098; DOI=10.1128/jvi.02257-07;
RA   Matthijnssens J., Ciarlet M., Heiman E.M., Arijs I., Delbeke T.,
RA   McDonald S.M., Palombo E.A., Iturriza-Gomara M., Maes P., Patton J.T.,
RA   Rahman M., Van Ranst M.;
RT   "Full genome-based classification of rotaviruses reveals a common origin
RT   between human Wa-Like and porcine rotavirus strains and human DS-1-like and
RT   bovine rotavirus strains.";
RL   J. Virol. 82:3204-3219(2008).
CC   -!- FUNCTION: RNA-directed RNA polymerase that is involved in both
CC       transcription and genome replication. Together with VP3 capping enzyme,
CC       forms an enzyme complex positioned near the channels situated at each
CC       of the five-fold vertices of the core. Following infection, the
CC       outermost layer of the virus is lost, leaving a double-layered particle
CC       (DLP) made up of the core and VP6 shell. VP1 then catalyzes the
CC       transcription of fully conservative plus-strand genomic RNAs that are
CC       extruded through the DLP's channels into the cytoplasm where they
CC       function as mRNAs for translation of viral proteins. One copy of each
CC       of the viral (+)RNAs is also recruited during core assembly, together
CC       with newly synthesized polymerase complexes and VP2. The polymerase of
CC       these novo-formed particles catalyzes the synthesis of complementary
CC       minus-strands leading to dsRNA formation. To do so, the polymerase
CC       specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved
CC       3'-sequence of plus-strand RNA templates. VP2 presumably activates the
CC       autoinhibited VP1-RNA complex to coordinate packaging and genome
CC       replication. Once dsRNA synthesis is complete, the polymerase switches
CC       to the transcriptional mode, thus providing secondary transcription (By
CC       similarity). {ECO:0000255|PROSITE-ProRule:PRU00539}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC         RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC         COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC         EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000305};
CC   -!- SUBUNIT: Interacts with VP3 (Potential). Interacts with VP2; this
CC       interaction activates VP1. Interacts with NSP5; this interaction is
CC       probably necessary for the formation of functional virus factories.
CC       Interacts with NSP2; this interaction is weak (By similarity).
CC       {ECO:0000250, ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: Virion {ECO:0000305}. Note=Attached inside the
CC       inner capsid as a minor component. Also found in spherical cytoplasmic
CC       structures, called virus factories, that appear early after infection
CC       and are the site of viral replication and packaging (By similarity).
CC       {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the reoviridae RNA-directed RNA polymerase
CC       family. {ECO:0000305}.
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DR   EMBL; DQ490533; ABF67540.1; -; Genomic_RNA.
DR   SMR; A4ZCW2; -.
DR   Proteomes; UP000001454; Genome.
DR   GO; GO:0044423; C:virion component; IEA:UniProtKB-KW.
DR   GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003968; F:RNA-dependent RNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0006351; P:DNA-templated transcription; IEA:InterPro.
DR   GO; GO:0019079; P:viral genome replication; IEA:InterPro.
DR   Gene3D; 1.10.357.80; -; 2.
DR   Gene3D; 1.20.120.1390; -; 1.
DR   Gene3D; 3.30.230.140; -; 2.
DR   Gene3D; 3.30.70.2480; -; 1.
DR   Gene3D; 1.10.10.1990; Viral RNA-directed RNA polymerase, 4-helical domain; 1.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR042032; RNA-dir_pol_4-hel_dom.
DR   InterPro; IPR001795; RNA-dir_pol_luteovirus.
DR   InterPro; IPR007097; RNA-dir_pol_reovirus.
DR   InterPro; IPR022071; Rotavirus_VP1_C.
DR   Pfam; PF02123; RdRP_4; 1.
DR   Pfam; PF12289; Rotavirus_VP1; 1.
DR   SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR   PROSITE; PS50523; RDRP_DSRNA_REO; 1.
PE   3: Inferred from homology;
KW   Magnesium; Nucleotide-binding; Nucleotidyltransferase; RNA-binding;
KW   RNA-directed RNA polymerase; Transferase; Viral RNA replication; Virion.
FT   CHAIN           1..1088
FT                   /note="RNA-directed RNA polymerase"
FT                   /id="PRO_0000368039"
FT   DOMAIN          501..687
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
SQ   SEQUENCE   1088 AA;  124847 MW;  DC2F1D88A0C76706 CRC64;
     MGKYNLILSE YLSFIYNSQS AVQIPIYYSS NSDLEKRCIE FHSKCLENSK KGLSLKNIFL
     EYKDVTENAT LLSILSYSYD KYNAVERKLV HYAKGKPLEA DLNANELDYE NNKLTSDLFP
     TAEEYTDSLM DPAILTSLSS NLNAVMFWLE RHANDTAERA KIYKRRLDLF AIVASTVNKY
     GVPRHNAKYR YEYEVMKDKP YYLVTWANSS IEMLMSVFSH EDYLIAKELI ILSYSNRSTL
     AKLVSSPMSI LVALVDINGT FITNEELELE FSNKYVRAIV PDQTFDELKE ILDNMKKAGL
     VDIPKMIQDW LVDCSIEKFP LMAKIYSWSF HVGFRKQKML DAALDQLKTE YTEDVDDEMY
     REYTMLIRDE VVKMLEEAVK HDDHLLQDSE LAGLLSMSSA SNGESRQLKF GRKTIFSTKK
     NMHVMDDMAN GKYTPGVIPP VNVDKPIPLG RRDVPGRRTR IIFILPYEYF IAQHAVVEKM
     LIYAKHTREY AEFYSQSNQL LSYGDVTRFL SNNAMVLYTD VSQWDSSQHN TQPFRKGIIM
     GLDILANMTN DAKVIQTLHL YKQTQINLMD SYVQIPDGNV IKKIQYGAVA SGEKQTKAAN
     SIANLALIKT VLSRIANKYS FVTKIIRVDG DDNYAVLQFN TEVTKQMVQD VSNDVRDTYA
     RMNAKVKALV STVGIEIAKR YIAGGKIFFR AGINLLNNEK RGQSTQWDQA AVLYSNYIVN
     RLRGFETDRE FILTKIMQMT SVAITGSLRL FPSERVLTTN STFKVFDSED FIIEYGTTDD
     EVYIQRAFMS LSSQKSGIAD EIAASQTFKN YVSKLSDQLL VSKNVIVSRG IALTEKAKLN
     SYAPVSLEKR RAQISALLTM LQKPVTFKSN KITINDILHD IKPYFVTSEA NLPIQYQKFM
     PTLPNNVQYI IQCIGSRTYQ IEDDGSKSAI SRLISKYSVY RPSIEELYKV ISLHEQEIQL
     YLVSLGIPKI DADTYVGSKI YSQDKYRILE SYVYNLLSIN YGCYQLFDFN SPDLEKLIRI
     PFKGKIPAVT FILHLYAKLE IINYAIKNGS WISLFCNYPK SEMIKLWKKM WNITSLRSPY
     TNANFFQD
//