R1A_BEV
ID R1A_BEV Reviewed; 4569 AA.
AC P0C6F3; P18458;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 10-JUN-2008, sequence version 1.
DT 03-AUG-2022, entry version 68.
DE RecName: Full=Replicase polyprotein 1a;
DE Short=pp1a;
DE AltName: Full=ORF1a polyprotein;
DE Contains:
DE RecName: Full=Non-structural protein 1;
DE Short=nsp1;
DE Contains:
DE RecName: Full=Non-structural protein 2;
DE Short=nsp2;
DE Contains:
DE RecName: Full=3C-like serine proteinase;
DE Short=3CLSP;
DE EC=3.4.21.-;
DE AltName: Full=M-PRO;
DE AltName: Full=nsp3;
DE AltName: Full=p27;
DE Contains:
DE RecName: Full=Non-structural protein 4;
DE Short=nsp4;
DE Contains:
DE RecName: Full=Non-structural protein 5;
DE Short=nsp5;
DE Contains:
DE RecName: Full=Non-structural protein 6;
DE Short=nsp6;
DE Contains:
DE RecName: Full=Non-structural protein 7;
DE Short=nsp7;
DE Contains:
DE RecName: Full=Non-structural protein 8;
DE Short=nsp8;
DE Contains:
DE RecName: Full=Non-structural protein 9;
DE Short=nsp9;
GN ORFNames=1a;
OS Berne virus (BEV).
OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC Nidovirales; Tornidovirineae; Tobaniviridae; Torovirinae; Torovirus;
OC Renitovirus; Equine torovirus.
OX NCBI_TaxID=11156;
OH NCBI_TaxID=9796; Equus caballus (Horse).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA], CHARACTERIZATION OF 3C-LIKE PROTEINASE
RP M-PRO, AND PROTEOLYTIC PROCESSING OF POLYPROTEIN.
RX PubMed=16571831; DOI=10.1128/jvi.80.8.4157-4167.2006;
RA Smits S.L., Snijder E.J., de Groot R.J.;
RT "Characterization of a torovirus main proteinase.";
RL J. Virol. 80:4157-4167(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1-252.
RX PubMed=1856694; DOI=10.1099/0022-1317-72-7-1635;
RA Snijder E.J., den Boon J.A., Horzinek M.C., Spaan J.M.;
RT "Characterization of defective interfering RNAs of Berne virus.";
RL J. Gen. Virol. 72:1635-1643(1991).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 4219-4569.
RC STRAIN=Isolate P138/72;
RX PubMed=2388833; DOI=10.1093/nar/18.15.4535;
RA Snijder E.J., den Boon J.A., Bredenbeek P.J., Horzinek M.C., Rijnbrand R.,
RA Spaan W.J.M.;
RT "The carboxyl-terminal part of the putative Berne virus polymerase is
RT expressed by ribosomal frameshifting and contains sequence motifs which
RT indicate that toro- and coronaviruses are evolutionarily related.";
RL Nucleic Acids Res. 18:4535-4542(1990).
CC -!- FUNCTION: The 3C-like serine proteinase is responsible for the majority
CC of cleavages.
CC -!- SUBCELLULAR LOCATION: [Non-structural protein 1]: Host membrane
CC {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Non-structural protein 2]: Host membrane
CC {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Non-structural protein 4]: Host membrane
CC {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Ribosomal frameshifting; Named isoforms=2;
CC Name=Replicase polyprotein 1a; Synonyms=pp1a, ORF1a polyprotein;
CC IsoId=P0C6F3-1; Sequence=Displayed;
CC Name=Replicase polyprotein 1ab; Synonyms=pp1ab;
CC IsoId=P0C6V7-1; Sequence=External;
CC -!- DOMAIN: The hydrophobic domains (HD) could mediate the membrane
CC association of the replication complex and thereby alter the
CC architecture of the host cell membrane. {ECO:0000250}.
CC -!- PTM: Specific enzymatic cleavages in vivo by its own protease yield
CC mature proteins. 3CL-PRO is autocatalytically processed (By
CC similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: [Isoform Replicase polyprotein 1a]: Produced by
CC conventional translation.
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DR EMBL; DQ310701; ABC26008.1; -; Genomic_RNA.
DR EMBL; X56016; CAA39493.1; -; Genomic_RNA.
DR EMBL; X52374; CAA36600.1; -; Genomic_RNA.
DR PIR; S11237; S11237.
DR PIR; S11238; S11238.
DR SMR; P0C6F3; -.
DR MEROPS; S65.001; -.
DR PRIDE; P0C6F3; -.
DR Proteomes; UP000006571; Genome.
DR GO; GO:0033644; C:host cell membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0008234; F:cysteine-type peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR CDD; cd21557; Macro_X_Nsp3-like; 1.
DR Gene3D; 2.40.10.10; -; 2.
DR Gene3D; 3.40.220.10; -; 1.
DR InterPro; IPR002589; Macro_dom.
DR InterPro; IPR043472; Macro_dom-like.
DR InterPro; IPR044371; Macro_X_NSP3-like.
DR InterPro; IPR039573; NS2A-like.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR009003; Peptidase_S1_PA.
DR InterPro; IPR043504; Peptidase_S1_PA_chymotrypsin.
DR Pfam; PF05213; Corona_NS2A; 1.
DR Pfam; PF01661; Macro; 1.
DR SMART; SM00506; A1pp; 1.
DR SUPFAM; SSF50494; SSF50494; 1.
DR SUPFAM; SSF52949; SSF52949; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS51154; MACRO; 1.
PE 1: Evidence at protein level;
KW Host membrane; Hydrolase; Membrane; Metal-binding; Protease;
KW Reference proteome; Repeat; Ribosomal frameshifting; Thiol protease;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1..4569
FT /note="Replicase polyprotein 1a"
FT /id="PRO_0000338016"
FT CHAIN 1..2873
FT /note="Non-structural protein 1"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338017"
FT CHAIN 2874..3251
FT /note="Non-structural protein 2"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338018"
FT CHAIN 3252..3543
FT /note="3C-like serine proteinase"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338020"
FT CHAIN 3544..3802
FT /note="Non-structural protein 4"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338021"
FT CHAIN 3803..3979
FT /note="Non-structural protein 5"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338022"
FT CHAIN 3980..4161
FT /note="Non-structural protein 6"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338023"
FT CHAIN 4162..4246
FT /note="Non-structural protein 7"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338024"
FT CHAIN 4247..4399
FT /note="Non-structural protein 8"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338025"
FT CHAIN 4400..4569
FT /note="Non-structural protein 9"
FT /evidence="ECO:0000255"
FT /id="PRO_0000338026"
FT TRANSMEM 2303..2323
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 2330..2350
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 2385..2405
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 2535..2555
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 2639..2659
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 2664..2684
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 2889..2909
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3057..3077
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3106..3126
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3142..3162
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3556..3575
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3580..3602
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3611..3631
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3640..3660
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3663..3683
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3698..3718
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 3723..3738
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 1679..1860
FT /note="Macro"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00490"
FT REGION 2158..2191
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2303..2683
FT /note="HD1"
FT REGION 2889..3162
FT /note="HD2"
FT REGION 3555..3738
FT /note="HD3"
FT ACT_SITE 3304
FT /note="Charge relay system; for 3C-like serine proteinase
FT activity"
FT /evidence="ECO:0000255"
FT ACT_SITE 3347
FT /note="Charge relay system; for 3C-like serine proteinase
FT activity"
FT /evidence="ECO:0000255"
FT ACT_SITE 3416
FT /note="Charge relay system; for 3C-like serine proteinase
FT activity"
FT /evidence="ECO:0000255"
FT SITE 2873..2874
FT /note="Cleavage; by 3C-like serine proteinase"
FT /evidence="ECO:0000255"
FT SITE 3251..3252
FT /note="Cleavage; by 3C-like serine proteinase"
FT SITE 3543..3544
FT /note="Cleavage; by 3C-like serine proteinase"
FT SITE 3802..3803
FT /note="Cleavage; by 3C-like serine proteinase"
FT /evidence="ECO:0000255"
FT SITE 3979..3980
FT /note="Cleavage; by 3C-like serine proteinase"
FT /evidence="ECO:0000255"
FT SITE 4161..4162
FT /note="Cleavage; by 3C-like serine proteinase"
FT /evidence="ECO:0000255"
FT SITE 4246..4247
FT /note="Cleavage; by 3C-like serine proteinase"
FT /evidence="ECO:0000255"
FT SITE 4399..4400
FT /note="Cleavage; by 3C-like serine proteinase"
FT /evidence="ECO:0000255"
FT CONFLICT 251..252
FT /note="RR -> KK (in Ref. 2; CAA39493)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 4569 AA; 523793 MW; 753D2EA1FEF31AEA CRC64;
MSTSSSILDI PSKMFRILKN NTRETEQHLS SSTLDLISKS QLLAQCFDTQ EIMASLSKTV
RSILESQNLE HKSTLTPYNS SQSLQLLVMN TSCTQFKWTT GSTSSVKALL EKELCRGLVP
LNDITPKSNY VELSLLTPSI LIGNETSTTT TLPEIPLDME QSIISCVENT LLKEVQALSG
QESCQEYFLS ANYQSLIPPQ VLLNLMKMSS VVDLSPLTLP NTRLWLKLSP FHGGTSVSYA
TQIKGYANCA RREEKCLKNR LTKKQKNQEK GSFDARSVIT LGGKMYRYKV VVLRCEDQSD
NLSELQFEPQ VEYTMDMVPH CWKELVKKRL IRAKGTWDLS CVEDLDLDHV EVRGDSLLHR
SSVVHDLTSI VDDTLQEKLF SRTWLRQSLK YSGNILQRLS SLFATEGLKK ITLVNSDITP
VQVGDKWLNF VDFGKSTVFF VKTLNNIHLA MTRQRESCNY IHEKFGRVRW LGAKPEQGAI
VKVFAWCLNK KEFKFRDNQL KQYVCRQGVI KHEPCEYLNV EVLDEFVALN NDLNCVQKIK
TYLAAYFGLK KVKLTQKNFM TPLITKKQEL VFQPCNCPNH QFYVAQFDKH VTLGLGRKDG
ILFAEQVPSY AIILAVGFGT VETQLVTHYY SEMRRVYHPL DFQSNTFVFD HQGVMLEDIS
PADYNDVGEE DYQLEYSGGF DQPFQNYHSD DEDQAFPDFE DERHPDEENW ARPIISSGES
SVVSSRPSSP LVYSSLVPVA SPFGYMNGIR VFDICLADDL DFLQIHGQCP CARCKGLYFY
QPIRPRGFTI FENVVEFFSF VEKCEVFEEI GPFFKMIEYS MLYNEYNIFY GLGKKIYQSD
LVLPVKHLDQ LWKRAQLDID VVSEFENFKN SLQNINNVVY IAPYFNDQGE WNDIFDGYEF
NLNDNQFWFQ AKPVYDLVCY IYQGFFSDSR PLEKLYQKLC LDYHTSAMLH TQTHLKYCYV
ALLHSERAFQ MSINLDSLDN EQLHFLATMG MGDASLVGPT YLSEYHSNFN WYSIMSKACH
YVKLEQLVGL TYQEKRLMIL SRVQEFYEQQ HRGPIQLILS PLKVVNLPPI TCTEGYCYQP
VTRLFDTCVM PDIMKKLSRK RTSVSDVFGI LADYFKRTLS YRCFKVHEFC GIERQQEFSD
MTTLKLVTDW CQDTYYFYNE YATMTDVEPK VQVSSDYYLK IPSEVVEHIR QFLPHNVNVG
LMNYVSSNCD FDQCKFEFCL SGKGYVLGNM FFNRCAIQYV KTNLFIVLFK SRPLLYITQE
SIYLSDFNVL QAQCLTGEFC LDFEPVQGKT LFGVYFTNGQ RYGQQWETLP RFSLKPLNSP
RKRVPTQPFE ELAEVCIFKQ KLKLTQLHND CSVTPRVCSI PQTITATFQP YYCLENFYGV
KAPKVIVSGH LATHYVKLTH KISKCVLVTK LAVARAFYFT PTSMGSHYHL DPMEGISFGK
RATVQFEPVG LIKDVNLLVY QFGSHVSIQF FPEAPCIVAD GHYPSKYSGV WLGYLPSVEE
CKIAQVNHRV YVPTILRTSK SAPFHIIQNG DMGRGPITVT YHYAKNFDNK SLTPMFKMFQ
QVFEKSKDDI FKAFNTMSLE QKKVLSHFCG EFDEAYTLQT MSDEISFESS AYPDVVACSL
AYILGYEMCL TVKVNAKNEK LDIGSQCERV FVDYDVKKNE WTLSPEEGED SDDNLDLPFE
QYYEFKIGQT NVVLVQDDFK SVFEFLKSEQ GVDYVVNPAN SQLKHGGGIA KVISCMCGPK
LQAWSNNYIT KNKTVPVTKA IKSPGFQLGK KVNIIHAVGP RVSDGDVFQK LDQAWRSVFD
LCEDQHTILT SMLSTGIFGC TVNDSFNTFL SNVARLDKSL VVFVVTNMVE QYNQAFAVIK
MYQQYHGLPN FGNTCWFNAL YQLLKSFSEK EQCVNDLLNC FDDFYDCPTS QCVEWVCEQL
GVQFGQQQDA VEMLMKVFDV FKCDVRVGFD CLSRLQQVNC GFCVEVPAQA VLMFSGKDQC
GHWTAARKIV DKWYTFDDNH VVQKDPVWQN VVLVLRDRGI FRSADFERKP ARRRRVSHRV
PRDTLSQDAI TYIEDLRFSS GTCLSRYFVE SVESFVSGDN VSEVSDEQTC VEVAIEESDG
HVEQICQSSV DCVGMPESFQ FTFSMPLQTF VQECDQKCED DFSQEHVECD QQFEPVEQVG
QGGQQDGQVD QQIKESEQVV EPSAPSGQES PQALLQQVVD EVVYQIEQVK CDQKQDQDSV
QCDEIEEINS RGEQTVQQQL QPILGHDLNE NEGPTLSVGA GKLVRCRSLA VTESNLSTSN
TIFVWSEVLT HQYIGFKTDL MGLTYNIKFK LICYVLFLWF GVLCCTSHNT PFYMRLCIYL
VLLWLSLMIW NASQINVKTG WNELYVLKLL TSIKLPNIVK FRCELVQWFV LKCLFVSFYV
YDYVVKVCVS IFQMPQLRPF TWPFIKLGFV DTFLSHHILA FPEKVANQST LPTCGDKRYY
VYVPSWCRAS FTSLVMRARE LTSTGRSKTL DNWHYQCCSK TAKPLSCFNV REFVFDQDCK
HEAYGFLSSL CVYLLFYSGF LTFWLPLFCY YYVLFMCTFK NLPVDITKPI KWTVLQQVVN
DVLSLVTKPL FGRPVCPPLT TYLTSTTADE AVKVSRSLLG RFCTPLGFQQ PVMNVENGVT
VSNFGFFNPL MWPLFVVVLL DNRFIWFFNV LSYVMMPVFV IILFYFYLKK ICGCINFKGL
SKCCTKHFNQ FSKPLVAAGV HGNRTNFTYQ PMQEHWCDRH SWYCPKEEHY MTPDMAVYIK
NYYNLACAPT ADLVWCDYTK SAPTMTWSNF KYSSYKAKET VLCAPSSHAD SMLMAWYALL
HNVRFTVNPN VVDLPPAVNT IYVSSDSEDS VQDKSQPDVK LRPKKPKGNF KKQSVAYFSR
EPVDIWYYTT LVIVMGVLFM FMYSCLMVGQ YVVMPRDKFF GVNPTGYSYV NAPPYLHAAP
PVLQNSDGMI LATQLKVPSI TYSVYRLLSG HLYFTKLIVS DNECTPPFGA ARLSNEFSCN
GFTYVLPAHL RFFNRYVMLI HPDQLHMLPF EVEYGSHTRV CYTTGSNSVE CLPTFEIISP
YVFVFIVVIF TVIFLILIRL YIVMYSYFKV FTYVVFKLLF VNIIMVLFVV CLPPLVPGVV
FVLALWLCDS VMFLLYLAFL SLFILPWFYV LFFLFMVGGF VFWWMMRSAD VVHLTTDGLT
FNGTFEQISK CVFPLNPLIV NRMLLDCQMS HSDLVEKSKL KTTEGKLANE MMKVFMTGET
SYYQPSNFSF QSVFSKATSP FTLHARPPMP MFKLYVHFTG SCVGSTSTGT GFAIDDNTIV
TAKHLFEYDD LKPTHVSVEI VTRSHSARSA SIIWKEPDVK GWTFKGENAY IQVENLKDFY
IEDFKYLPFQ QIEKDFYKRM EPVTIYSVKY GSEFATQAWQ TVNGHFVCYN TEGGDSGAPL
VCNGRIVGVH QGLCDNFKTT LASDFEGKMM TEVKGHHVDP PVYYKPIIIS AAYNKFVAGE
DSSVGDGKNY HKFENEDFAC MCKELESVTF GDQLRRYCYN LPQFLEPLQY FHVPSFWQPF
KKQSVSNNVS WVVEHLHFIF SIYFLICDFV AYWWLDDPFS VVLPLFFIVQ LLSTVFLKNV
LFWTTSYLIT LAVTFYIHSE VAESMFLLGF LSDRVVNRMS LIIVVAIMCL FVVVRVVVNV
KRAIFVFVVS VVLIFVHICL GIVQFNSFVN VVLFDVYAVF TALLTPQPVV AIIMLLLFDT
KMLMSFAFIV IVLSFRVFKD YKFVKVLHNF CNFDFVLSQV SLFRYRHRNQ GNDPTHYEAL
WLFLKELYYG IQDAKYEVFS PQAGSYNVKF LTDMTEQDQL EAVEQVQRRL QRFNIVQDKA
SPRLVLYSKT IEFIKDQIQQ QRAVGANPFI ITTLTSNDIG LDNVEVHNPA NFKPEDLQAH
MWFFSKSPVF IGQVPIPTNV QTAAVLDTTY NCQDLTADEK NNVAATLQIQ NAAITLSLFE
KCTQFLESEL GEVPTLMWQA EDVADIKHLE SQIENLRKVL DGMQFGTTEY KATRKQLNIC
QSQLDQAKAF ERKLAKFLEK VDQQQAITNE TAKQLSAFKN LVKQVYESYM SSLKVKVLEA
NDASCLLTST DLPRKLVLMR PITGVDGIKI VEKANGCEIT AFGTTFNTGH GSNLAGLAYS
TTQPLSAYPF IFNLEGIFKQ QANIGYKTVE CNMSSHNGSV LYKGKVVAVP SDDNPDFVVC
GKGYKLDCGI NVLMIPSIVR YITLNLTDHL QKQSLKPRRR LQYRQQGVRL GGVNLGEHQA
FSNELISTVG YTTWVSSTVC RDNTHKHPWF VQIPVNEKDP EWFMHNTQLK DNQWVVDLKP
THWLVNADTG EQLFALSLTD EQALKAEAIL QKWSPITQDV ECWFKDLKGY YTVSGFQPLW
PVCPVNICNV RLDPVFKPQS IVYADDPTHF LSLPVVNKNF LAAFYDLQEG FPGKKQVAPH
ISLTMLKLSD EDIEKVEDIL DEMVLPNSWV TITNPHMMGK HYVCDVEGLD SLHDEVVSVL
REHGIACDQK RLWKPHLTIG ELNDVSFDKF KDFAISCKLE DCDFVKLGAP KANARYEFIT
TLPLGDLNC
