POLG_SOUV3
ID POLG_SOUV3 Reviewed; 1788 AA.
AC Q04544;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Genome polyprotein;
DE Contains:
DE RecName: Full=Protein p48;
DE Contains:
DE RecName: Full=NTPase;
DE EC=3.6.1.15;
DE AltName: Full=p41;
DE Contains:
DE RecName: Full=Protein p22;
DE Contains:
DE RecName: Full=Viral genome-linked protein;
DE AltName: Full=VPG;
DE Contains:
DE RecName: Full=3C-like protease;
DE Short=3CLpro;
DE EC=3.4.22.66;
DE AltName: Full=Calicivirin;
DE Contains:
DE RecName: Full=RNA-directed RNA polymerase;
DE Short=RdRp;
DE EC=2.7.7.48;
GN ORFNames=ORF1;
OS Southampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV)
OS (Hu/NV/SHV/1991/UK).
OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC Picornavirales; Caliciviridae; Norovirus.
OX NCBI_TaxID=37129;
OH NCBI_TaxID=9606; Homo sapiens (Human).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=8380940; DOI=10.1126/science.8380940;
RA Lambden P.R., Caul E.O., Ashley C.R., Clarke I.N.;
RT "Sequence and genome organization of a human small round-structured
RT (Norwalk-like) virus.";
RL Science 259:516-519(1993).
RN [2]
RP SEQUENCE REVISION.
RX PubMed=8560774; DOI=10.1007/bf01702595;
RA Lambden P.R., Liu B., Clarke I.N.;
RT "A conserved sequence motif at the 5' terminus of the Southampton virus
RT genome is characteristic of the Caliciviridae.";
RL Virus Genes 10:149-152(1995).
RN [3]
RP PROTEOLYTIC PROCESSING OF POLYPROTEIN.
RX PubMed=10073687; DOI=10.1099/0022-1317-80-2-291;
RA Liu B.L., Viljoen G.J., Clarke I.N., Lambden P.R.;
RT "Identification of further proteolytic cleavage sites in the Southampton
RT calicivirus polyprotein by expression of the viral protease in E. coli.";
RL J. Gen. Virol. 80:291-296(1999).
CC -!- FUNCTION: Protein p48 may play a role in viral replication by
CC interacting with host VAPA, a vesicle-associated membrane protein that
CC plays a role in SNARE-mediated vesicle fusion. This interaction may
CC target replication complex to intracellular membranes (By similarity).
CC {ECO:0000250}.
CC -!- FUNCTION: NTPase presumably plays a role in replication. Despite having
CC similarities with helicases, does not seem to display any helicase
CC activity (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Protein P22 may play a role in targeting replication complex
CC to intracellular membranes. {ECO:0000250}.
CC -!- FUNCTION: Viral genome-linked protein is covalently linked to the 5'-
CC end of the positive-strand, negative-strand genomic RNAs and subgenomic
CC RNA. Acts as a genome-linked replication primer. May recruit ribosome
CC to viral RNA thereby promoting viral proteins translation (By
CC similarity). {ECO:0000250}.
CC -!- FUNCTION: 3C-like protease processes the polyprotein: 3CLpro-RdRp is
CC first released by autocleavage, then all other proteins are cleaved.
CC May cleave polyadenylate-binding protein thereby inhibiting cellular
CC translation. {ECO:0000255|PROSITE-ProRule:PRU00870}.
CC -!- FUNCTION: RNA-directed RNA polymerase replicates genomic and
CC antigenomic RNA by recognizing replications specific signals.
CC Transcribes also a subgenomic mRNA by initiating RNA synthesis
CC internally on antigenomic RNA. This sgRNA codes for structural
CC proteins. Catalyzes the covalent attachment VPg with viral RNAs (By
CC similarity). {ECO:0000255|PROSITE-ProRule:PRU00539}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-
CC diphosphate + H(+) + phosphate; Xref=Rhea:RHEA:23680,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:61557; EC=3.6.1.15;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endopeptidase with a preference for cleavage when the P1
CC position is occupied by Glu-|-Xaa and the P1' position is occupied by
CC Gly-|-Yaa.; EC=3.4.22.66; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00870};
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 -!- SUBUNIT: [Protein p48]: Interacts with human VAPA.
CC {ECO:0000250|UniProtKB:Q83883}.
CC -!- PTM: Specific enzymatic cleavages in vivo yield mature proteins. 3CLpro
CC is first autocatalytically cleaved, then processes the whole
CC polyprotein. {ECO:0000255|PROSITE-ProRule:PRU00870}.
CC -!- PTM: VPg is uridylylated by the polymerase and is covalently attached
CC to the 5'-end of the polyadenylated genomic and subgenomic RNAs. This
CC uridylylated form acts as a nucleotide-peptide primer for the
CC polymerase (By similarity). {ECO:0000250}.
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DR EMBL; L07418; AAA92983.1; -; Genomic_RNA.
DR PIR; A37491; A37491.
DR PDB; 2IPH; X-ray; 1.75 A; A/B=1100-1280.
DR PDBsum; 2IPH; -.
DR SMR; Q04544; -.
DR MEROPS; C37.001; -.
DR PRIDE; Q04544; -.
DR BRENDA; 3.4.22.28; 5774.
DR BRENDA; 3.4.22.66; 5774.
DR BRENDA; 3.6.1.15; 5774.
DR EvolutionaryTrace; Q04544; -.
DR Proteomes; UP000007226; Genome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
DR GO; GO:0017111; F:nucleoside-triphosphatase activity; IEA:InterPro.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0003724; F:RNA helicase activity; IEA:InterPro.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0018144; P:RNA-protein covalent cross-linking; IEA:UniProtKB-KW.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR Gene3D; 2.40.10.10; -; 2.
DR Gene3D; 3.30.70.270; -; 2.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR000605; Helicase_SF3_ssDNA/RNA_vir.
DR InterPro; IPR014759; Helicase_SF3_ssRNA_vir.
DR InterPro; IPR001665; Norovirus_pept_C37.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR009003; Peptidase_S1_PA.
DR InterPro; IPR043504; Peptidase_S1_PA_chymotrypsin.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR001205; RNA-dir_pol_C.
DR InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR InterPro; IPR013614; Viral_PP_Calicivir_N.
DR Pfam; PF08405; Calici_PP_N; 1.
DR Pfam; PF05416; Peptidase_C37; 1.
DR Pfam; PF00680; RdRP_1; 1.
DR Pfam; PF00910; RNA_helicase; 1.
DR PRINTS; PR00917; SRSVCYSPTASE.
DR SUPFAM; SSF50494; SSF50494; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS51537; NV_3CL_PRO; 1.
DR PROSITE; PS50507; RDRP_SSRNA_POS; 1.
DR PROSITE; PS51218; SF3_HELICASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Covalent protein-RNA linkage;
KW Host-virus interaction; Hydrolase; Nucleotide-binding;
KW Nucleotidyltransferase; Phosphoprotein; Protease;
KW RNA-directed RNA polymerase; Thiol protease; Transferase;
KW Viral RNA replication.
FT CHAIN 1..1788
FT /note="Genome polyprotein"
FT /id="PRO_0000342021"
FT CHAIN 1..399
FT /note="Protein p48"
FT /id="PRO_0000036935"
FT CHAIN 400..762
FT /note="NTPase"
FT /id="PRO_0000036936"
FT CHAIN 763..961
FT /note="Protein p22"
FT /id="PRO_0000036937"
FT CHAIN 962..1099
FT /note="Viral genome-linked protein"
FT /id="PRO_0000036938"
FT CHAIN 1100..1280
FT /note="3C-like protease"
FT /id="PRO_0000036939"
FT CHAIN 1281..1788
FT /note="RNA-directed RNA polymerase"
FT /id="PRO_0000036940"
FT DOMAIN 533..698
FT /note="SF3 helicase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT DOMAIN 1100..1280
FT /note="Peptidase C37"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00870"
FT DOMAIN 1515..1636
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT REGION 58..86
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 948..979
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 1129
FT /note="For 3CLpro activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00870"
FT ACT_SITE 1153
FT /note="For 3CLpro activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00870"
FT ACT_SITE 1238
FT /note="For 3CLpro activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00870"
FT BINDING 561..568
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT SITE 399..400
FT /note="Cleavage; by 3CLpro"
FT /evidence="ECO:0000250"
FT SITE 762..763
FT /note="Cleavage; by 3CLpro"
FT /evidence="ECO:0000250"
FT SITE 961..962
FT /note="Cleavage; by 3CLpro"
FT /evidence="ECO:0000250"
FT SITE 1099..1100
FT /note="Cleavage; by 3CLpro"
FT /evidence="ECO:0000250"
FT SITE 1280..1281
FT /note="Cleavage; by 3CLpro"
FT /evidence="ECO:0000250"
FT MOD_RES 991
FT /note="O-(5'-phospho-RNA)-tyrosine"
FT /evidence="ECO:0000250"
FT HELIX 1102..1105
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1108..1111
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1114..1127
FT /evidence="ECO:0007829|PDB:2IPH"
FT HELIX 1128..1130
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1136..1138
FT /evidence="ECO:0007829|PDB:2IPH"
FT HELIX 1143..1145
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1146..1151
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1154..1161
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1181..1187
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1193..1208
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1211..1220
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1222..1224
FT /evidence="ECO:0007829|PDB:2IPH"
FT TURN 1229..1231
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1241..1246
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1249..1259
FT /evidence="ECO:0007829|PDB:2IPH"
FT STRAND 1261..1269
FT /evidence="ECO:0007829|PDB:2IPH"
SQ SEQUENCE 1788 AA; 198582 MW; 9ED4F6529793652F CRC64;
MMMASKDVVA TNVASNNNAN NTSATSRFLS RFKGLGGGAS PPSPIKIKST EMALGLIGRT
TPEPTGTAGP PPKQQRDRPP RTQEEVQYGM GWSDRPIDQN VKSWEELDTT VKEEILDNHK
EWFDAGGLGP CTMPPTYERV KDDSPPGEQV KWSARDGVNI GVERLTTVSG PEWNLCPLPP
IDLRNMEPAS EPTIGDMIEF YEGHIYHYSI YIGQGKTVGV HSPQAAFSVA RVTIQPIAAW
WRVCYIPQPK HRLSYDQLKE LENEPWPYAA ITNNCFEFCC QVMNLEDTWL QRRLVTSGRF
HHPTQSWSQQ TPEFQQDSKL ELVRDAILAA VNGLVSQPFK NFLGKLKPLN VLNILSNCDW
TFMGVVEMVI LLLELFGVFW NPPDVSNFIA SLLPDFHLQG PEDLARDLVP VILGGIGLAI
GFTRDKVTKV MKSAVDGLRA ATQLGQYGLE IFSLLKKYFF GGDQTERTLK GIEAAVIDME
VLSSTSVTQL VRDKQAAKAY MNILDNEEEK ARKLSAKNAD PHVISSTNAL ISRISMARSA
LAKAQAEMTS RMRPVVIMMC GPPGIGKTKA AEHLAKRLAN EIRPGGKVGL VPREAVDHWD
GYHGEEVMLW DDYGMTKILD DCNKLQAIAD SAPLTLNCDR IENKGMQFVS DAIVITTNAP
GPAPVDFVNL GPVCRRVDFL VYCSAPEVEQ IRRVSPGDTS ALKDCFKLDF SHLKMELAPQ
GGFDNQGNTP FGKGTMKPTT INRLLIQAVA LTMERQDEFQ LQGKMYDFDD DRVSAFTTMA
RDNGLGILSM AGLGKKLRGV TTMEGLKNAL KGYKISACTI KWQAKVYSLE SDGNSVNIKE
ERNILTQQQQ SVCTASVALT RLRAARAVAY ASCIQSAITS ILQIAGSALV VNRAVKRMFG
TRTATLSLEG PPREHKCRVH MAKAAGKGPI GHDDVVEKYG LCETEEDEEV AHTEIPSATM
EGKNKGKNKK GRGRRNNYNA FSRRGLNDEE YEEYKKIREE KGGNYSIQEY LEDRQRYEEE
LAEVQAGGDG GIGETEMEIR HRVFYKSKSR KHHQEERRQL GLVTGSDIRK RKPIDWTPPK
SAWADDEREV DYNEKISFEA PPTLWSRVTK FGSGWGFWVS PTVFITTTHV IPTSAKEFFG
EPLTSIAIHR AGEFTLFRFS KKIRPDLTGM ILEEGCPEGT VCSVLIKRDS GELLPLAVRM
GAIASMRIQG RLVHGQSGML LTGANAKGMD LGTIPGDCGA PYVYKRANDW VVCGVHAAAT
KSGNTVVCAV QASEGETTLE GGDKGHYAGH EIIKHGCGPA LSTKTKFWKS SPEPLPPGVY
EPAYLGGRDP RVTVGPSLQQ VLRDQLKPFA EPRGRMPEPG LLEAAVETVT SSLEQVMDTP
VPWSYSDACQ SLDKTTSSGF PYHRRKNDDW NGTTFVRELG EQAAHANNMY EQAKSMKPMY
TGALKDELVK PEKVYQKVKK RLLWGADLGT VVRAARAFGP FCDAIKSHTI KLPIKVGMNS
IEDGPLIYAE HSKYKYHFDA DYTAWDSTQN RQIMTESFSI MCRLTASPEL ASVVAQDLLA
PSEMDVGDYV IRVKEGLPSG FPCTSQVNSI NHWLITLCAL SEVTGLSPDV IQSMSYFSFY
GDDEIVSTDI EFDPAKLTQV LREYGLRPTR PDKSEGPIIV RKSVDGLVFL RRTISRDAAG
FQGRLDRASI ERQIYWTRGP NHSDPFETLV PHQQRKVQLI SLLGEASLHG EKFYRKISSK
VIQEIKTGGL EMYVPGWQAM FRWMRFHDLG LWTGDRNLLP EFVNDDGV
