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O37061 (RDRP_ROTSP) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 47. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
RNA-directed RNA polymerase
EC=2.7.7.48
Alternative name(s):
Protein VP1
OrganismRotavirus A (strain SA11-Patton G3-Px[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx) (RV-A) (Simian Agent 11 (strain Patton))
Taxonomic identifier36434 [NCBI]
Taxonomic lineageViruses › dsRNA viruses › Reoviridae › Sedoreovirinae › Rotavirus › Rotavirus A ›
Virus hostMacaca mulatta (Rhesus macaque) [TaxID: 9544]

Protein attributes

Sequence length1088 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.3

Catalytic activity

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Cofactor

Magnesium Potential. Ref.3

Subunit structure

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. Ref.2

Subcellular location

Virion Potential. 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.

Sequence similarities

Belongs to the reoviridae RNA-directed RNA polymerase family.

Contains 1 RdRp catalytic domain.

Ontologies

Keywords
   Biological processViral RNA replication
   Cellular componentVirion
   LigandMagnesium
Nucleotide-binding
RNA-binding
   Molecular functionNucleotidyltransferase
RNA-directed RNA polymerase
Transferase
   Technical term3D-structure
Gene Ontology (GO)
   Biological_processtranscription, DNA-dependent

Inferred from electronic annotation. Source: InterPro

viral genome replication

Inferred from electronic annotation. Source: InterPro

   Cellular_componentvirion

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionRNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA-directed RNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

nucleotide binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10881088RNA-directed RNA polymerase
PRO_0000367812

Regions

Domain501 – 687187RdRp catalytic

Secondary structure

1 ....................................................................................................................................................................... 1088
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O37061 [UniParc].

Last modified March 24, 2009. Version 2.
Checksum: 7A5AD04A37BA0E8C

FASTA1,088125,252
        10         20         30         40         50         60 
MGKYNLILSE YLSFIYNSQS AVQIPIYYSS NSELENRCIE FHSKCLENSK NGLSLRKLFV 

        70         80         90        100        110        120 
EYNDVIENAT LLSILSYSYD KYNAVERKLV KYAKGKPLEA DLTVNELDYE NNKMTSELFP 

       130        140        150        160        170        180 
TAEEYTDSLM DPAILTSLSS NLNAVMFWLE KHENDVAEKL KVYKRRLDLF TIVASTINKY 

       190        200        210        220        230        240 
GVPRHNAKYR YEYDVMKDKP YYLVTWANSS IEMLMSVFSH DDYLIAKELI VLSYSNRSTL 

       250        260        270        280        290        300 
AKLVSSPMSI LVALVDINGT FITNEELELE FSNKYVRAIV PDQTFDELNQ MLDNMRKAGL 

       310        320        330        340        350        360 
VDIPKMIQDW LVDRSIEKFP LMAKIYSWSF HVGFRKQKML DAALDQLKTE YTENVDDEMY 

       370        380        390        400        410        420 
REYTMLIRDE VVKMLEEPVK HDDHLLRDSE LAGLLSMSSA SNGESRQLKF GRKTIFSTKK 

       430        440        450        460        470        480 
NMHVMDDMAN ERYTPGIIPP VNVDKPIPLG RRDVPGRRTR IIFILPYEYF IAQHAVVEKM 

       490        500        510        520        530        540 
LIYAKHTREY AEFYSQSNQL LSYGDVTRFL SNNTMVLYTD VSQWDSSQHN TQPFRKGIIM 

       550        560        570        580        590        600 
GLDILANMTN DAKVLQTLNL YKQTQINLMD SYVQIPDGNV IKKIQYGAVA SGEKQTKAAN 

       610        620        630        640        650        660 
SIANLALIKT VLSRISNKHS FATKIIRVDG DDNYAVLQFN TEVTKQMIQD VSNDVRETYA 

       670        680        690        700        710        720 
RMNAKVKALV STVGIEIAKR YIAGGKIFFR AGINLLNNEK RGQSTQWDQA AILYSNYIVN 

       730        740        750        760        770        780 
RLRGFETDRE FILTKIMQMT SVAITGSLRL FPSERVLTTN STFKVFDSED FIIEYGTTVD 

       790        800        810        820        830        840 
EVYIQRAFMS LSSQKSGIAD EIAASSTFKN YVTRLSEQLL FSKNNIVSRG IALTEKAKLN 

       850        860        870        880        890        900 
SYAPISLEKR RAQISALLTM LQKPVTFKSS KITINDILRD IKPFFTVSDA HLPIQYQKFM 

       910        920        930        940        950        960 
PTLPDNVQYI IQCIGSRTYQ IEDDGSKSAI SRLISKYSVY KPSIEELYKV ISLHENEIQL 

       970        980        990       1000       1010       1020 
YLISLGIPKI DADTYVGSKI YSRDKYRILE SYVYNLLSIN YGCYQLFDFN SPDLEKLIRI 

      1030       1040       1050       1060       1070       1080 
PFKGKIPAVT FILHLYAKLE VINYAIKNGS WISLFCNYPK SEMIKLWKKM WNITSLRSPY 


TNANFFQE

« Hide

References

[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AF015955 mRNA. Translation: AAC58684.1. Different termination.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

InterProIPR001795. RNA-dir_pol_luteovirus.
IPR007097. RNA-dir_pol_reovirus.
IPR022071. Rotavirus_VP1.
[Graphical view]
PfamPF02123. RdRP_4. 1 hit.
PF12289. Rotavirus_VP1. 1 hit.
[Graphical view]
PROSITEPS50523. RDRP_DSRNA_REO. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO37061.

Entry information

Entry nameRDRP_ROTSP
AccessionPrimary (citable) accession number: O37061
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: March 24, 2009
Last modified: April 3, 2013
This is version 47 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents