RDRP_BPPH6
ID RDRP_BPPH6 Reviewed; 665 AA.
AC P11124;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=RNA-directed RNA polymerase;
DE EC=2.7.7.48;
DE AltName: Full=Protein P2;
GN Name=P2;
OS Pseudomonas phage phi6 (Bacteriophage phi-6).
OC Viruses; Riboviria; Orthornavirae; Duplornaviricota; Vidaverviricetes;
OC Mindivirales; Cystoviridae; Cystovirus.
OX NCBI_TaxID=10879;
OH NCBI_TaxID=319; Pseudomonas savastanoi pv. phaseolicola (Pseudomonas syringae pv. phaseolicola).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA], AND PARTIAL PROTEIN SEQUENCE.
RX PubMed=3346944; DOI=10.1128/jvi.62.4.1180-1185.1988;
RA Mindich L., Nemhauser I., Gottlieb P., Romantschuk M., Carton J.,
RA Frucht S., Strassman J., Bamford D.H., Kalkkinen N.;
RT "Nucleotide sequence of the large double-stranded RNA segment of
RT bacteriophage phi 6: genes specifying the viral replicase and
RT transcriptase.";
RL J. Virol. 62:1180-1185(1988).
RN [2]
RP IDENTIFICATION IN THE PACKAGING COMPLEX, AND INTERACTION WITH P7.
RX PubMed=23077625; DOI=10.1371/journal.pone.0047489;
RA Katz G., Wei H., Alimova A., Katz A., Morgan D.G., Gottlieb P.;
RT "Protein P7 of the cystovirus phi6 is located at the three-fold axis of the
RT unexpanded procapsid.";
RL PLoS ONE 7:E47489-E47489(2012).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=11242087; DOI=10.1038/35065653;
RA Butcher S.J., Grimes J.M., Makeyev E.V., Bamford D.H., Stuart D.I.;
RT "A mechanism for initiating RNA-dependent RNA polymerization.";
RL Nature 410:235-240(2001).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RX PubMed=14962391; DOI=10.1016/j.str.2004.01.012;
RA Salgado P.S., Makeyev E.V., Butcher S.J., Bamford D.H., Stuart D.I.,
RA Grimes J.M.;
RT "The structural basis for RNA specificity and Ca2+ inhibition of an RNA-
RT dependent RNA polymerase.";
RL Structure 12:307-316(2004).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RX PubMed=15659773; DOI=10.1099/vir.0.80492-0;
RA Laurila M.R., Salgado P.S., Stuart D.I., Grimes J.M., Bamford D.H.;
RT "Back-priming mode of phi6 RNA-dependent RNA polymerase.";
RL J. Gen. Virol. 86:521-526(2005).
CC -!- FUNCTION: Rna-dependent RNA polymerase part of the packaging complex
CC that packages the viral RNA segments, replicate them into a double-
CC stranded form and transcribe them.
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;
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC -!- SUBUNIT: Part of the packaging complex composed of RDRP, P4 and P7.
CC Interacts with P7 (Probable). {ECO:0000305|PubMed:23077625}.
CC -!- SUBCELLULAR LOCATION: Virion. Note=Found in the capsid (12 copies).
CC Prior to RNA packaging, localizes on the inner procapsid surface near
CC the three-fold axis of symmetry.
CC -!- CAUTION: Was originally thought to be a capsid protein.
CC {ECO:0000305|PubMed:3346944}.
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DR EMBL; M17461; AAA32355.1; -; Genomic_RNA.
DR PIR; B29885; P2BPF6.
DR RefSeq; NP_620346.1; NC_003715.1.
DR PDB; 1HHS; X-ray; 2.00 A; A/B/C=2-665.
DR PDB; 1HHT; X-ray; 2.90 A; P/Q/R=2-665.
DR PDB; 1HI0; X-ray; 3.00 A; P/Q/R=2-665.
DR PDB; 1HI1; X-ray; 3.00 A; A/B/C=2-665.
DR PDB; 1HI8; X-ray; 2.50 A; A/B=2-665.
DR PDB; 1UVI; X-ray; 2.15 A; A/B/C=2-665.
DR PDB; 1UVJ; X-ray; 1.90 A; A/B/C=2-665.
DR PDB; 1UVK; X-ray; 2.45 A; A/C/E=2-665.
DR PDB; 1UVL; X-ray; 2.00 A; A/C/E=2-665.
DR PDB; 1UVM; X-ray; 2.00 A; A/B/C=2-665.
DR PDB; 1UVN; X-ray; 3.00 A; A/C/E=2-665.
DR PDB; 1WAC; X-ray; 3.00 A; A/B/C=2-665.
DR PDB; 2JL9; X-ray; 3.20 A; A/B/C=1-665.
DR PDB; 2JLF; X-ray; 3.20 A; A/B/C=2-665.
DR PDB; 2JLG; X-ray; 2.80 A; A/B/C=2-665.
DR PDB; 4A8F; X-ray; 3.30 A; A/B/C=1-665.
DR PDB; 4A8K; X-ray; 3.50 A; A/B/C=1-665.
DR PDB; 4A8M; X-ray; 2.92 A; P/Q/R=1-665.
DR PDB; 4A8O; X-ray; 2.67 A; A/B/C=1-665.
DR PDB; 4A8Q; X-ray; 3.06 A; A/B/C=1-665.
DR PDB; 4A8S; X-ray; 2.90 A; A/B/C=1-665.
DR PDB; 4A8W; X-ray; 3.04 A; A/B/C=1-665.
DR PDB; 4A8Y; X-ray; 3.41 A; A/B/C=1-665.
DR PDB; 4B02; X-ray; 3.30 A; A/B/C=2-665.
DR PDB; 5FJ6; EM; 7.90 A; A=2-665.
DR PDB; 5FJ7; EM; 7.90 A; C=2-665.
DR PDBsum; 1HHS; -.
DR PDBsum; 1HHT; -.
DR PDBsum; 1HI0; -.
DR PDBsum; 1HI1; -.
DR PDBsum; 1HI8; -.
DR PDBsum; 1UVI; -.
DR PDBsum; 1UVJ; -.
DR PDBsum; 1UVK; -.
DR PDBsum; 1UVL; -.
DR PDBsum; 1UVM; -.
DR PDBsum; 1UVN; -.
DR PDBsum; 1WAC; -.
DR PDBsum; 2JL9; -.
DR PDBsum; 2JLF; -.
DR PDBsum; 2JLG; -.
DR PDBsum; 4A8F; -.
DR PDBsum; 4A8K; -.
DR PDBsum; 4A8M; -.
DR PDBsum; 4A8O; -.
DR PDBsum; 4A8Q; -.
DR PDBsum; 4A8S; -.
DR PDBsum; 4A8W; -.
DR PDBsum; 4A8Y; -.
DR PDBsum; 4B02; -.
DR PDBsum; 5FJ6; -.
DR PDBsum; 5FJ7; -.
DR SMR; P11124; -.
DR DrugBank; DB04137; Guanosine-5'-Triphosphate.
DR GeneID; 956436; -.
DR KEGG; vg:956436; -.
DR BRENDA; 2.7.7.48; 718.
DR EvolutionaryTrace; P11124; -.
DR Proteomes; UP000002610; Genome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0050265; F:RNA uridylyltransferase activity; IDA:CACAO.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IDA:CACAO.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR Gene3D; 1.10.490.60; -; 2.
DR InterPro; IPR016406; Cystovir_RNA-dir_pol.
DR InterPro; IPR043110; Cystovir_RNA-dir_pol_N.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR001205; RNA-dir_pol_C.
DR InterPro; IPR007096; RNA-dir_Rpol_phage_catalytic.
DR Pfam; PF00680; RdRP_1; 1.
DR PIRSF; PIRSF004131; RNA_pol_phage_P2; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS50522; RDRP_PHAGE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Magnesium; Manganese;
KW Metal-binding; Nucleotide-binding; Nucleotidyltransferase;
KW Reference proteome; RNA-directed RNA polymerase; Transferase;
KW Viral RNA replication; Virion.
FT INIT_MET 1
FT /note="Removed; by host"
FT CHAIN 2..665
FT /note="RNA-directed RNA polymerase"
FT /id="PRO_0000164635"
FT DOMAIN 310..485
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT BINDING 454
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 491
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 495
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 13..16
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 23..30
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 39..41
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 49..65
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 90..95
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 107..112
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 122..136
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:1UVJ"
FT TURN 154..156
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 161..183
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 187..194
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 200..207
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 212..215
FT /evidence="ECO:0007829|PDB:1UVJ"
FT TURN 216..219
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 220..223
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 231..235
FT /evidence="ECO:0007829|PDB:1UVJ"
FT TURN 236..238
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 239..241
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 252..257
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 266..275
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 278..297
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 300..303
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 308..316
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 319..328
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 329..332
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 335..348
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 352..361
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 366..368
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 378..381
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 396..398
FT /evidence="ECO:0007829|PDB:2JLG"
FT HELIX 399..419
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 421..426
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 430..441
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 445..452
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 455..460
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 462..464
FT /evidence="ECO:0007829|PDB:2JLG"
FT HELIX 465..478
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 485..487
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 489..491
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 500..503
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 510..512
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 514..517
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 519..527
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 540..542
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 543..546
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 548..550
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 551..559
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 565..580
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 584..599
FT /evidence="ECO:0007829|PDB:1UVJ"
FT TURN 600..602
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 604..606
FT /evidence="ECO:0007829|PDB:1UVL"
FT STRAND 608..610
FT /evidence="ECO:0007829|PDB:2JLG"
FT HELIX 612..614
FT /evidence="ECO:0007829|PDB:1HI1"
FT HELIX 617..624
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 626..629
FT /evidence="ECO:0007829|PDB:1UVJ"
FT TURN 630..632
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 635..637
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 640..646
FT /evidence="ECO:0007829|PDB:1UVJ"
FT STRAND 647..649
FT /evidence="ECO:0007829|PDB:1UVJ"
FT HELIX 652..662
FT /evidence="ECO:0007829|PDB:1UVJ"
SQ SEQUENCE 665 AA; 74922 MW; F785B034C85DD5D2 CRC64;
MPRRAPAFPL SDIKAQMLFA NNIKAQQASK RSFKEGAIET YEGLLSVDPR FLSFKNELSR
YLTDHFPANV DEYGRVYGNG VRTNFFGMRH MNGFPMIPAT WPLASNLKKR ADADLADGPV
SERDNLLFRA AVRLMFSDLE PVPLKIRKGS STCIPYFSND MGTKIEIAER ALEKAEEAGN
LMLQGKFDDA YQLHQMGGAY YVVYRAQSTD AITLDPKTGK FVSKDRMVAD FEYAVTGGEQ
GSLFAASKDA SRLKEQYGID VPDGFFCERR RTAMGGPFAL NAPIMAVAQP VRNKIYSKYA
YTFHHTTRLN KEEKVKEWSL CVATDVSDHD TFWPGWLRDL ICDELLNMGY APWWVKLFET
SLKLPVYVGA PAPEQGHTLL GDPSNPDLEV GLSSGQGATD LMGTLLMSIT YLVMQLDHTA
PHLNSRIKDM PSACRFLDSY WQGHEEIRQI SKSDDAILGW TKGRALVGGH RLFEMLKEGK
VNPSPYMKIS YEHGGAFLGD ILLYDSRREP GSAIFVGNIN SMLNNQFSPE YGVQSGVRDR
SKRKRPFPGL AWASMKDTYG ACPIYSDVLE AIERCWWNAF GESYRAYRED MLKRDTLELS
RYVASMARQA GLAELTPIDL EVLADPNKLQ YKWTEADVSA NIHEVLMHGV SVEKTERFLR
SVMPR
