P0C6Y0 (R1AB_CVMJH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Replicase polyprotein 1ab
Short name=pp1ab

Alternative name(s):
ORF1ab polyprotein

Cleaved into the following 15 chains:

1. Non-structural protein 1
   Short name=nsp1
   Alternative name(s):
   p28
2. Non-structural protein 2
   Short name=nsp2
   Alternative name(s):
   p65
3. Non-structural protein 3
   Short name=nsp3
   EC=3.4.19.12
   EC=3.4.22.69
   Alternative name(s):
   PL1-PRO/PL2-PRO
   PL1/PL2
   Papain-like proteinases 1/2
   p210
4. Non-structural protein 4
   Short name=nsp4
   Alternative name(s):
   Peptide HD2
   p44
5. 3C-like proteinase
   Short name=3CL-PRO
   Short name=3CLp
   EC=3.4.22.-
   Alternative name(s):
   M-PRO
   nsp5
   p27
6. Non-structural protein 6
   Short name=nsp6
7. Non-structural protein 7
   Short name=nsp7
   Alternative name(s):
   p10
8. Non-structural protein 8
   Short name=nsp8
   Alternative name(s):
   p22
9. Non-structural protein 9
   Short name=nsp9
   Alternative name(s):
   p12
10. Non-structural protein 10
    Short name=nsp10
    Alternative name(s):
    Growth factor-like peptide
    Short name=GFL
    p15
11. RNA-directed RNA polymerase
    Short name=Pol
    Short name=RdRp
    EC=2.7.7.48
    Alternative name(s):
    nsp12
    p100
12. Helicase
    Short name=Hel
    EC=3.6.4.12
    EC=3.6.4.13
    Alternative name(s):
    nsp13
    p67
13. Exoribonuclease
    Short name=ExoN
    EC=3.1.13.-
    Alternative name(s):
    nsp14
14. Uridylate-specific endoribonuclease
    EC=3.1.-.-
    Alternative name(s):
    NendoU
    nsp15
    p35
15. Putative 2'-O-methyl transferase
    EC=2.1.1.-
    Alternative name(s):
    nsp16

Gene names

Name:	rep
ORF Names:	1a-1b

Organism

Murine coronavirus (strain JHM) (MHV-JHM) (Murine hepatitis virus) [Complete proteome]

Taxonomic identifier

11144 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Nidovirales › Coronaviridae › Coronavirinae › Betacoronavirus › Murine coronavirus › Murine hepatitis virus

Virus host

Mus musculus (Mouse) [TaxID: 10090]

Protein attributes

Sequence length	7180 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products. The papain-like proteinase 1 (PL1-PRO) and papain-like proteinase 2 (PL2-PRO) are responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PLP2 possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3 By similarity. The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function By similarity. The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G) By similarity. The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction By similarity. Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter By similarity. Nsp9 is a ssRNA-binding protein By similarity. NendoU is a Mn2+-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond By similarity.
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). ATP + H2O = ADP + phosphate. TSAVLQ-|-SGFRK-NH2 and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position. Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Subunit structure	3CL-PRO exists as monomer and homodimer. Eight copies of nsp7 and eight copies of nsp8 assemble to form a heterohexadecamer. Nsp9 is a dimer. Nsp10 forms a dodecamer By similarity.
Subcellular location	Non-structural protein 3: Host membrane; Multi-pass membrane protein Potential Ref.6. Non-structural protein 4: Host membrane; Multi-pass membrane protein Potential Ref.6. Non-structural protein 6: Host membrane; Multi-pass membrane protein Potential Ref.6. Non-structural protein 7: Host cytoplasm › host perinuclear region By similarity Ref.6. Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes By similarity. Ref.6 Non-structural protein 8: Host cytoplasm › host perinuclear region By similarity Ref.6. Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes By similarity. Ref.6 Non-structural protein 9: Host cytoplasm › host perinuclear region By similarity Ref.6. Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes By similarity. Ref.6 Non-structural protein 10: Host cytoplasm › host perinuclear region By similarity Ref.6. Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes By similarity. Ref.6 Helicase: Host endoplasmic reticulum-Golgi intermediate compartment Potential. Note: The helicase interacts with the N protein in membranous complexes and colocalizes with sites of synthesis of new viral RNA By similarity. Ref.6 Uridylate-specific endoribonuclease: Host cytoplasm › host perinuclear region By similarity Ref.6.
Domain	The hydrophobic domains (HD) could mediate the membrane association of the replication complex and thereby alter the architecture of the host cell membrane.
Post-translational modification	Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed By similarity.
Sequence similarities	Belongs to the coronaviruses polyprotein 1ab family. Contains 1 (+)RNA virus helicase ATP-binding domain. Contains 1 (+)RNA virus helicase C-terminal domain. Contains 1 CV MBD (coronavirus metal-binding) domain. Contains 1 Macro domain. Contains 2 peptidase C16 domains. Contains 1 peptidase C30 domain. Contains 1 RdRp catalytic domain.
Sequence caution	The sequence AAA46457.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence AAA46457.1 differs from that shown. Reason: Frameshift at positions 690, 915, 1529, 2069 and 3316. The sequence AAA46458.2 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Activation of host autophagy by virus Host-virus interaction Inhibition of host ISG15 by virus Inhibition of host innate immune response by virus Inhibition of host interferon signaling pathway by virus Modulation of host ubiquitin pathway by viral deubiquitinase Modulation of host ubiquitin pathway by virus Ubl conjugation pathway Viral RNA replication Viral immunoevasion
Cellular component	Host cytoplasm Host membrane Membrane
Coding sequence diversity	Ribosomal frameshifting
Domain	Repeat Transmembrane Transmembrane helix Zinc-finger
Ligand	ATP-binding Metal-binding Nucleotide-binding RNA-binding Zinc
Molecular function	Endonuclease Exonuclease Helicase Hydrolase Nuclease Nucleotidyltransferase Protease RNA-directed RNA polymerase Thiol protease Transferase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	induction by virus of host autophagy Inferred from electronic annotation. Source: UniProtKB-KW methylation Inferred from electronic annotation. Source: GOC modulation by virus of host protein ubiquitination Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC proteolysis Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host ISG15 activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host type I interferon-mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral genome replication Inferred from electronic annotation. Source: InterPro viral protein processing Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell endoplasmic reticulum-Golgi intermediate compartment Inferred from electronic annotation. Source: UniProtKB-SubCell host cell membrane Inferred from electronic annotation. Source: UniProtKB-SubCell host cell perinuclear region of cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW viral replication complex Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW exoribonuclease activity, producing 5'-phosphomonoesters Inferred from electronic annotation. Source: InterPro helicase activity Inferred from electronic annotation. Source: UniProtKB-KW methyltransferase activity Inferred from electronic annotation. Source: InterPro omega peptidase activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

Isoform Replicase polyprotein 1ab (identifier: P0C6Y0-1)

Also known as: pp1ab;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: Produced by -1 ribosomal frameshifting at the 1a-1b genes boundary.

Isoform Replicase polyprotein 1a (identifier: P0C6V1-1)

Also known as: pp1a; ORF1a polyprotein;

The sequence of this isoform can be found in the external entry P0C6V1.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 247	247	Non-structural protein 1 Probable		PRO_0000037354
	Chain	248 – 832	585	Non-structural protein 2 Probable		PRO_0000037355
	Chain	833 – 2840	2008	Non-structural protein 3 Probable		PRO_0000037356
	Chain	2841 – 3336	496	Non-structural protein 4 Probable		PRO_0000037357
	Chain	3337 – 3639	303	3C-like proteinase Probable		PRO_0000037358
	Chain	3640 – 3927	288	Non-structural protein 6 Probable		PRO_0000037359
	Chain	3928 – 4019	92	Non-structural protein 7 Probable		PRO_0000037360
	Chain	4020 – 4213	194	Non-structural protein 8		PRO_0000037361
	Chain	4214 – 4323	110	Non-structural protein 9 Probable		PRO_0000037362
	Chain	4324 – 4460	137	Non-structural protein 10 Probable		PRO_0000037363
	Chain	4461 – 5388	928	RNA-directed RNA polymerase Probable		PRO_0000037364
	Chain	5389 – 5988	600	Helicase Probable		PRO_0000037365
	Chain	5989 – 6507	519	Exoribonuclease By similarity		PRO_0000037366
	Chain	6508 – 6881	374	Uridylate-specific endoribonuclease By similarity		PRO_0000037367
	Chain	6882 – 7180	299	Putative 2'-O-methyl transferase By similarity		PRO_0000037368
Regions
	Transmembrane	2228 – 2248	21	Helical; Potential
	Transmembrane	2289 – 2309	21	Helical; Potential
	Transmembrane	2320 – 2340	21	Helical; Potential
	Transmembrane	2403 – 2423	21	Helical; Potential
	Transmembrane	2445 – 2465	21	Helical; Potential
	Transmembrane	2846 – 2866	21	Helical; Potential
	Transmembrane	3099 – 3119	21	Helical; Potential
	Transmembrane	3121 – 3141	21	Helical; Potential
	Transmembrane	3153 – 3173	21	Helical; Potential
	Transmembrane	3180 – 3200	21	Helical; Potential
	Transmembrane	3205 – 3225	21	Helical; Potential
	Transmembrane	3648 – 3668	21	Helical; Potential
	Transmembrane	3678 – 3698	21	Helical; Potential
	Transmembrane	3705 – 3725	21	Helical; Potential
	Transmembrane	3748 – 3768	21	Helical; Potential
	Transmembrane	3775 – 3795	21	Helical; Potential
	Transmembrane	3802 – 3822	21	Helical; Potential
	Transmembrane	3846 – 3866	21	Helical; Potential
	Domain	1083 – 1320	238	Peptidase C16 1
	Domain	1321 – 1481	161	Macro
	Domain	1677 – 1936	260	Peptidase C16 2
	Domain	3337 – 3639	303	Peptidase C30
	Domain	5068 – 5230	163	RdRp catalytic
	Domain	5389 – 5472	84	CV MBD
	Domain	5644 – 5825	182	(+)RNA virus helicase ATP-binding
	Domain	5826 – 6003	178	(+)RNA virus helicase C-terminal
	Zinc finger	1197 – 1225	29	C4-type 1
	Zinc finger	1793 – 1829	37	C4-type 2
	Zinc finger	4397 – 4413	17	By similarity
	Zinc finger	4439 – 4452	14	By similarity
	Nucleotide binding	5669 – 5676	8	ATP By similarity
	Region	2228 – 2465	238	HD1
	Region	2846 – 3225	380	HD2
	Region	3648 – 3866	219	HD3
Sites
	Active site	1120	1	For PL1-PRO activity By similarity
	Active site	1271	1	For PL1-PRO activity By similarity
	Active site	1715	1	For PL2-PRO activity By similarity
	Active site	1872	1	For PL2-PRO activity By similarity
	Active site	3377	1	For 3CL-PRO activity By similarity
	Active site	3481	1	For 3CL-PRO activity By similarity
	Site	247 – 248	2	Cleavage; by PL1-PRO Probable
	Site	832 – 833	2	Cleavage; by PL1-PRO Probable
	Site	2840 – 2841	2	Cleavage; by PL2-PRO Probable
	Site	3336 – 3337	2	Cleavage; by 3CL-PRO Probable
	Site	3639 – 3640	2	Cleavage; by 3CL-PRO Probable
	Site	3927 – 3928	2	Cleavage; by 3CL-PRO Probable
	Site	4019 – 4020	2	Cleavage; by 3CL-PRO Probable
	Site	4213 – 4214	2	Cleavage; by 3CL-PRO Probable
	Site	4323 – 4324	2	Cleavage; by 3CL-PRO Probable
	Site	4460 – 4461	2	Cleavage; by 3CL-PRO Probable
	Site	5388 – 5389	2	Cleavage; by 3CL-PRO Probable
	Site	5988 – 5989	2	Cleavage; by 3CL-PRO Probable
	Site	6507 – 6508	2	Cleavage; by 3CL-PRO Probable
	Site	6881 – 6882	2	Cleavage; by 3CL-PRO Probable
Experimental info
	Mutagenesis	2835	1	F → A: No processing between p210 and peptide HD2. Ref.5
	Mutagenesis	2836	1	S → A: No effect. Ref.5
	Mutagenesis	2837	1	L → A: No effect. Ref.5
	Mutagenesis	2838	1	K → A: No effect. Ref.5
	Mutagenesis	2838	1	K → N: No effect. Ref.5
	Mutagenesis	2839	1	G → A: Partial processing between p210 and peptide HD2. Ref.5
	Mutagenesis	2839	1	G → N: No processing between p210 and peptide HD2. Ref.5
	Mutagenesis	2839	1	G → V: No processing between p210 and peptide HD2. Ref.5
	Mutagenesis	2840	1	G → A: No processing between p210 and peptide HD2. Ref.5
	Mutagenesis	2840	1	G → N: No processing between p210 and peptide HD2. Ref.5
	Mutagenesis	2840	1	G → V: No processing between p210 and peptide HD2. Ref.5
	Mutagenesis	2841	1	A → N: No effect. Ref.5
	Mutagenesis	2842	1	V → N or M: No effect. Ref.5
	Mutagenesis	2846	1	V → M: No effect. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Isoform Replicase polyprotein 1ab (pp1ab) [UniParc]. Last modified June 10, 2008. Version 1. Checksum: 313A78E1CC87B347	FASTA	7,180	803,440
	10 20 30 40 50 60 MAKMGKYGLG FKWAPEFPWM LPNASEKLGN PERSEEDGFC PSAAQEPKVK GKTLVNHVRV 70 80 90 100 110 120 DCSRLPALEC CVQSAIIRDI FVDEDPQKVE ASTMMALQFG SAVLVKPSKR LSVQAWAKLG 130 140 150 160 170 180 VLPKTPAMGL FKRFCLCNTR ECVCDAHVAF QLFTVQPDGV CLGNGRFIGW FVPVTAIPEY 190 200 210 220 230 240 AKQWLQPWSI LLRKGGNKGS VTSGHFRRAV TMPVYDFNVE DACEEVHLNP RGKYSCKAYA 250 260 270 280 290 300 LLRGYRGVKP ILFVDQYGCD YTGCLAKGLE DYGDLTLSEM KELSPVWRDS LDNEVVVAWH 310 320 330 340 350 360 VDRDPRAVMR LQTLATVRSI EYVGQPIEDM VDGDVVMREP AHLLAPNAIV KRLPRLVETM 370 380 390 400 410 420 LYTDSSVTEF CYKTKLCDCG FITQFGYVDC CGDTCGFRGW VPGNMMDGFP CPGCCKSYMP 430 440 450 460 470 480 WELEAQSSGV IPEGGVLFTQ STDTVNRESF KLYGHAVVPF GGAAYWSPYP GMWLPVIWSS 490 500 510 520 530 540 VKSYSYLTYT GVVGCKAIVQ ETDAICRFLY MDYVQHKCGN LEQRAILGLD DVYHRQLLVN 550 560 570 580 590 600 RGDYSLLLEN VDLFVKRRAE FACKFATCGD GLVPLLLDGL VPRSYYLIKS GQAFTSLMVN 610 620 630 640 650 660 FSREVVDMCM DMALLFMHDV KVATKYVKKV TGKVAVRFKA LGIAVVRKIT EWFDLAVDTA 670 680 690 700 710 720 ASAAGWLCYQ LVNGLFAVAN GVITFIQEVP ELVKNFVDKF KTFFKVLIDS MSVSILSGLT 730 740 750 760 770 780 VVKTASNRVC LAGSKVYEVV QKSLPAYIMP VGCSEATCLV GEIEPAVFED DVVDVVKAPL 790 800 810 820 830 840 TYQGCCKPPS SFEKICIVDK LYMAKCGDQF YPVVVDNDTV GVLDQCWRFP CAGKKVVFND 850 860 870 880 890 900 KPKVKEVPST RKIKIIFALD ATFDSVLSKA CSEFEVDKDV TLDELLDVVL DAVESTLSPC 910 920 930 940 950 960 KEHGVIGTKV CALLERLVDD YVYLFDEGGE EVIASRMYCS FSAPDEDCVA TDVVYADENQ 970 980 990 1000 1010 1020 DDDADDPVVL VADTQEEDGV AREQVDSADS EICVAHTGGQ EMTEPDVVGS QTPIASAEET 1030 1040 1050 1060 1070 1080 EVGEACDREG IAEVKATVCA DALDACPDQV EAFDIEKVED SILSELQTEL NAPADKTYED 1090 1100 1110 1120 1130 1140 VLAFDAIYSE TLSAFYAVPS DETHFKVCGF YSPAIERTNC WLRSTLIVMQ SLPLEFKDLG 1150 1160 1170 1180 1190 1200 MQKLWLSYKA GYDQCFVDKL VKSAPKSIIL PQGGYVADFA YFFLSQCSFK VHANWRCLKC 1210 1220 1230 1240 1250 1260 GMELKLQGLD AVFFYGDVVS HMCKCGNSMT LLSADIPYTF DFGVRDDKFC AFYTPRKVFR 1270 1280 1290 1300 1310 1320 AACAVDVNDC HSMAVVDGKQ IDGKVVTKFN GDKFDFMVGH GMTFSMSPFE IAQLYGSCIT 1330 1340 1350 1360 1370 1380 PNVCFVKGDV IKVLRRVGAE VIVNPANGRM AHGAGVAGAI AKAAGKAFIN ETADMVKAQG 1390 1400 1410 1420 1430 1440 VCQVGGCYES TGGKLCKKVL NIVGPDARGH GNECYSLLER AYQHINKCDN VVTTLISAGI 1450 1460 1470 1480 1490 1500 FSVPTDVSLT YLLGVVTKNV ILVSNNQDDF DVIEKCQVTS VAGTKALSFQ LAKNLCRDVK 1510 1520 1530 1540 1550 1560 FVTNACSSLF SESSFVSSYD VLQEVEALRH DIQLDDDARV FVQANMDCLP TDWRLVNKFD 1570 1580 1590 1600 1610 1620 SVDGVRTIKY FECPGEVFVS SQGKKFGYVQ NGSFKEASVS QIRALLANKV DVLCTVDGVN 1630 1640 1650 1660 1670 1680 FRSCCVAEGE VFGKTLGSVF CDGINVTKVR CSAIHKGKVF FQYSGLSAAD LAAVKDAFGF 1690 1700 1710 1720 1730 1740 DEPQLLQYYS MLGMCKWPVV VCGNYFAFKQ SNNNCYINVA CLMLQHLSLK FPKWQWRRPG 1750 1760 1770 1780 1790 1800 NEFRSGKPLR FVSLVLAKGS FKFNEPSDST DFIRVELREA DLSGATCDLE FICKCGVKQE 1810 1820 1830 1840 1850 1860 QRKGVDAVMH FGTLDKSGLV KGYNIACTCG DKLVHCTQFN VPFLICSNTP EGKKLPDDVV 1870 1880 1890 1900 1910 1920 AANIFTGGSV GHYTHVKCKP KYQLYDACNV SKVSEAKGNF TDCLYLKNLK QTFSSVLTTY 1930 1940 1950 1960 1970 1980 YLDDVKCVAY KPDLSQYYCE SGKYYTKPII KAQFRTFEKV EGVYTNFKLV GHDIAEKLNA 1990 2000 2010 2020 2030 2040 KLGFDCNSPF MEYKITEWPT ATGDVVLASD DLYVSRYSGG CVTFGKPVIW RGHEEASLKS 2050 2060 2070 2080 2090 2100 LTYFNRPSVV CENKFNVLPV DVSEPTDRRP VPSAVLVTGA ASGADASAIS TEPGTAKEQK 2110 2120 2130 2140 2150 2160 ACASDSVEDQ IVMEAQKKSS VTTVAVKEVK LNGVKKPVKW NCSVVVNDPT SETKVVKSLS 2170 2180 2190 2200 2210 2220 IVDVYDMFLT GCRYVVWTAN ELSRLINSPT VREYVKWGMS KLIIPANLLL LRDEKQEFVA 2230 2240 2250 2260 2270 2280 PKVVKAKAIA CYGAVKWFLL YCFSWIKFNT DNKVIYTTEV ASKLTFKLCC LAFKNALQTF 2290 2300 2310 2320 2330 2340 NWSVVSRGFF LVATVFLLWF NFLYANVILS DFYLPNIGPL PMFVGQIVAW VKTTFGVLTI 2350 2360 2370 2380 2390 2400 CDFYQVTDLG YRSSFCNGSM VCELCFSGFD MLDNYESINV VQHVVDRRVS FDYISLFKLV 2410 2420 2430 2440 2450 2460 VELVIGYSLY TVCFYPLFVL VGMQLLTTWL PEFFMLGTMH WSARLFVFVA NMLPAFTLLR 2470 2480 2490 2500 2510 2520 FYIVVTAMYK VYCLCRHVMY GCSKPGCLFC YKRNRSVRVK CSTVVGGSLR YYDVMANGGT 2530 2540 2550 2560 2570 2580 GFCTKHQWNC LNCNSWKPGN TFITHEAAAD LSKELKRPVN PTDSAYYSVI EVKQVGCSMR 2590 2600 2610 2620 2630 2640 LFYERDGQRV YDDVSASLFV DMNGLLHSKV KGVPETHVVV VENEADKAGF LNAAVFYAQS 2650 2660 2670 2680 2690 2700 LYRPMLMVEK KLITTANTGL SVSRTMFDLY VYSLLRHLDV DRKSLTSFVN AAHNSLKEGV 2710 2720 2730 2740 2750 2760 QLEQVMDTFV GCARRKCAID SDVETKSITK SVMAAVNAGV EVTDESCNNL VPTYVKSDTI 2770 2780 2790 2800 2810 2820 VAADLGVLIQ NNAKHVQSNV AKAANVACIW SVDAFNQLSA DLQHRLRKAC VKTGLKIKLT 2830 2840 2850 2860 2870 2880 YNKQEANVPI LTTPFSLKGG AVFSRVLQWL FVANLICFIV LWALMPTYAV HKSDMQLPLY 2890 2900 2910 2920 2930 2940 ASFKVIDNGV LRDVSVTDAC FANKFNQFDQ WYESTFGLVY YRNSKACPVV VAVIDQDIGH 2950 2960 2970 2980 2990 3000 TLFNVPTKVL RYGFHVLHFI THAFATDRVQ CYTPHMQIPY DNFYASGCVL SSLCTMLAHA 3010 3020 3030 3040 3050 3060 DGTPHPYCYT EGVMHNASLY SSLVPHVRYN LASSNGYIRF PEVVSEGIVR VVRTRSMTYC 3070 3080 3090 3100 3110 3120 RVGLCEEAEE GICFNFNSSW VLNNPYYRAM PGTFCGRNAF DLIHQVLGGL VQPIDFFALT 3130 3140 3150 3160 3170 3180 ASSVAGAILA IIVVLAFYYL IKLKRAFGDY TSVVVINVIV WCINFLMLFV FQVYPTLSCL 3190 3200 3210 3220 3230 3240 YACFYFYTTL YFPSEISVVM HLQWLVMYGA IMPLWFCITY VAVVVSNHAL WLFSYCRKIG 3250 3260 3270 3280 3290 3300 TDVRSDGTFE EMALTTFMIT KESYCKLKNS VSDVAFNRYL SLYNKYRYFS GKMDTATYRE 3310 3320 3330 3340 3350 3360 AACSQLAKAM ETFNHNNGND VLYQPPTASV TTSFLQSGIV KMVSPTSKVE PCVVSVTYGN 3370 3380 3390 3400 3410 3420 MTLNGLWLDD KVYCPRHVIC SSADMTDPDY PNLLCRVTSS DFCVMSDRMS LTVMSYQMQG 3430 3440 3450 3460 3470 3480 SLLVLTVTLQ NPNTPKYSFG VVKPGETFTV LAAYNGRPQG AFHVVMRSSH TIKGSFLCGS 3490 3500 3510 3520 3530 3540 CGSVGYVLTG DSVRFVYMHQ LELSTGCHTG TDFSGNFYGP YRDAQVVQLP VQDYTQTVNV 3550 3560 3570 3580 3590 3600 VAWLYAAILN RCNWFVQSDS CSLEEFNVWA MTNGFSSIKA DLVLDALASM TGVTVEQVLA 3610 3620 3630 3640 3650 3660 AIKRLHSGFQ GKQILGSCVL EDELTPSDVY QQLAGVKLQS KRTRVIKGTC CWILASTFLF 3670 3680 3690 3700 3710 3720 CSIISAFVKW TMFMYVTTHM LGVTLCALCF VIFAMLLIKH KHLYLTMYIM PVLCTLFYTN 3730 3740 3750 3760 3770 3780 YLVVGYKQSF RGLAYAWLSY FVPAVDYTYM DEVLYGVVLL VAMVFVTMRS INHDVFSTMF 3790 3800 3810 3820 3830 3840 LVGRLVSLVS MWYFGANLEE EVLLFLTSLF GTYTWTTMLS LATAKVIAKW LAVNVLYFTD 3850 3860 3870 3880 3890 3900 IPQIKLVLLS YLCIGYVCCC YWGVLSLLNS IFRMPLGVYN YKISVQELRY MNANGLRPPR 3910 3920 3930 3940 3950 3960 NSFEALMLNF KLLGIGGVPV IEVSQIQSRL TDVKCANVVL LNCLQHLHIA SNSKLWQYCS 3970 3980 3990 4000 4010 4020 TLHNEILATS DLSVAFDKLA QLLVVLFANP AAVDSKCLAS IEEVSDDYVR DNTVLQALQS 4030 4040 4050 4060 4070 4080 EFVNMASFVE YELAKKNLDE AKASGSANQQ QIKQLEKACN IAKSAYERDR AVARKLERMA 4090 4100 4110 4120 4130 4140 DLALTNMYKE ARINDKKSKV VSALQTMLFS MVRKLDNQAL NSILDNAVKG CVPLNAIPPL 4150 4160 4170 4180 4190 4200 TSNTLTIIVP DKQVFDQVVD NVYVTYAPNV WHIQSIQDAD GAVKQLNEID VNSTWPLVIS 4210 4220 4230 4240 4250 4260 ANRHNEVSTV VLQNNELMPQ KLRTQVVNSG SDMNCNIPTQ CYYNTTGTGK IVYAILSDCD 4270 4280 4290 4300 4310 4320 GLKYTKIVKE DGNCVVLELD PPCKFSVQDV KGLKIKYLYF VKGCNTLARG WVVGTLSSTV 4330 4340 4350 4360 4370 4380 RLQAGTATEY ASNSAILSLC AFSVDPKKTY LDYIQQGGVP VTNCVKMLCD HAGTGMAITI 4390 4400 4410 4420 4430 4440 KPEATTNQDS YGGASVCIYC RSRVEHPDVD GLCKLRGKFV QVPLGIKDPV SYVLTHDVCQ 4450 4460 4470 4480 4490 4500 VCGFWRDGSC SCVGTGSQFQ SKDTNFLNRV RGTSVNARLV PCASGLDTDV QLRAFDICNA 4510 4520 4530 4540 4550 4560 NRAGIGLYYK VNCFRFQRVD EEGNKLDKFF VVKRTNLEVY NKEKECYELT KDCGVVAEHE 4570 4580 4590 4600 4610 4620 FFTFDVEGSR VPHIVRKDLS KFTMLDLCYA LRHFDRNDCS TLKEILLTYA ECDESYFQKK 4630 4640 4650 4660 4670 4680 DWYDFVENPD IINVYKKLGP IFNRALLNTA NFADTLVEAG LVGVLTLDNQ DLYGQWYDFG 4690 4700 4710 4720 4730 4740 DFVKTVPCCG VAVADSYYSY MMPMLTMCHA LDSELFVNGT YREFDLVQYD FTDFKLELFN 4750 4760 4770 4780 4790 4800 KYFKHWSMTY HPNTSECEDD RCIIHCANFN ILFSMVLPKT CFGPLVRQIF VDGVPFVVSI 4810 4820 4830 4840 4850 4860 GYHYKELGVV MNMDVDTHRY RLSLKDLLLY AADPALHVAS ASALLDLRTC CFSVAAITSG 4870 4880 4890 4900 4910 4920 VKFQTVKPGN FNQDFYEFIL SKGLLKEGSS VDLKHFFFTQ DGNAAITDYN YYKYNLPTMV 4930 4940 4950 4960 4970 4980 DIKQLLFVVE VVNKYFEIYE GGCIPATQVI VNNYDKSAGY PFNKFGKARL YYEALSFEEQ 4990 5000 5010 5020 5030 5040 DEIYAYTKRN VLPTLTQMNL KYAISAKNRA RTVAGVSILS TMTGRMFHQK CLKSIAATRG 5050 5060 5070 5080 5090 5100 VPVVIGTTKF YGGWDDMLRR LIKDVDSPVL MGWDYPKCDR AMPNILRIVS SLVLARKHDS 5110 5120 5130 5140 5150 5160 CCSHTDRFYR LANECAQVLG EIVMCGGCYY VKPGGTSSGD ATTAFANSVF NICQAVSANV 5170 5180 5190 5200 5210 5220 CSLMACNGHK IEDLSIRELQ KRLYSNVYRA DHVDPAFVSE YYEFLNKHFS MIILSDDGVV 5230 5240 5250 5260 5270 5280 CYNSEFASKG YIANISDFQQ VLYYQNNVFM SEAKCWVETD IEKGPHEFCS QHTMLVKMDG 5290 5300 5310 5320 5330 5340 DEVYLPYPDP SRILGAGCFV DDLLKTDSVL LIERFVSLAI DAYPLVYHEN PEYQNVFRVY 5350 5360 5370 5380 5390 5400 LEYIKKLYND LGNQILDSIS VILSTCDGQK FTDETFYKNM YLRSAVMQSV GACVVCSSQT 5410 5420 5430 5440 5450 5460 SLRCGSCIRK PLLCCKCAYD HVMSTDHKYV LSVSPYVCNS PGCDVNDVTK LYLGGMSYYC 5470 5480 5490 5500 5510 5520 EAHKPQYSFK LVMNGMVFGL YKQSCTGSPY IEDFNKIASC KWTEVDDYVL ANECTERLKL 5530 5540 5550 5560 5570 5580 FAAETQKATE EAFKQCYASA TIREIVSDRE LILSWEIGKV RPPLNKNYVF TGYHFTNNGK 5590 5600 5610 5620 5630 5640 TVLGEYVFDK SELTNGVYYR ATTTYKLSVG DVFILTSHAV SSLSAPTLVP QENYTSVRFA 5650 5660 5670 5680 5690 5700 SAYSVPETFQ NNVPNYQHIG IKRYCTVQGP PGTGKSHLAI GHAVYYCTAR VVYTAASHAA 5710 5720 5730 5740 5750 5760 VDALCEKAHK FLNINDCARI VPAKLRVDCY DKFNVNDTTR KYVFTTINAL PELVTDIIVV 5770 5780 5790 5800 5810 5820 DEVSMLTNYE LSVINSRVRA KHYVYIGDPA QLPAPRVLLN KGTLEPRYFN SVTKLMCCLG 5830 5840 5850 5860 5870 5880 PDIFLGTCYR CPKEIVDTVS ALVYNNKLKA KNDNSAMCFK VYYKGQTTHE SSSAVNMQQI 5890 5900 5910 5920 5930 5940 HLISKLLKAN PSWSNAVFIS PYNSQNYVAK RVLGLQTQTA DSAQGSAYDF VIYSQTAQTA 5950 5960 5970 5980 5990 6000 HSVNVNRFNV AITRAKKGIL CVMSSMQLIG VFNFTTLTLD KINNPRLQCT TNLFKDCSKS 6010 6020 6030 6040 6050 6060 YVGIPPCAFL LAVDDKYKVS GNLAVCLNVA DSAVTYSRLI SLMGFKLDLT LDGYCKLFIT 6070 6080 6090 6100 6110 6120 RDEAIKRVRA WVGFDAEGAH ATRDSIGTNF PLQLGFSTGI DFVVEATGMF AERDGYVFKK 6130 6140 6150 6160 6170 6180 AAARAPPGEQ FKHLVPLMSR GQKWDVVRIR IVQMLSDHLV DLADSVVLVT WAASFELTCL 6190 6200 6210 6220 6230 6240 RYFAKVGKEV VCSVCNKRAT CFNSRTGYYG CWRHSYSCDY LYNPLIVDIQ QWGYTGSLTS 6250 6260 6270 6280 6290 6300 NHDPICSVHK GAHVASSDAI MTRCLAVHDC FCKSVNWNLE YPIISNEVSV NTSCRLLQRV 6310 6320 6330 6340 6350 6360 MFRAAMLCNR YDVCYDIGNP KGLACVKGYD FKFYDASPVV KSVKQFVYKY EAHKDQFLDG 6370 6380 6390 6400 6410 6420 LCMFWNCNVD KYPANAVVCR FDTRVLSKLN LPGCNGGSLY VNKHAFHTNP FTRAAFENLK 6430 6440 6450 6460 6470 6480 PMPFFYYSDT PCVYMEGMES KQVDYVPLRS ATCITRCNLG GAVCLKHAEE YREYLESYNT 6490 6500 6510 6520 6530 6540 ATTAGFTFWV YKTFDFYNLW NTFTRLQSLE NVVYNLVNAG HFDGRAGELP CAVIGEKVIA 6550 6560 6570 6580 6590 6600 KIQNEDVVVF KNNTPFPTNV AVELFAERSI RPHPELKLFR SSNIHVCWNH VLWDYAKDSV 6610 6620 6630 6640 6650 6660 FCSSTYKVCK YTDLQCIESL NVLFDGRDNG ALEAFKKCRN GVYINTTKIK SLSMIKGPQR 6670 6680 6690 6700 6710 6720 ADLNGVVVEK VGDSDVEFWF AMRRDGDDVI FSRTGSLEPS HYRSPQGNPG GNRVGDLSGN 6730 6740 6750 6760 6770 6780 EALARGTIFT QSRFLSSFSP RSEMEKDFMD LDEDVFIAKY SLQDYAFEHV VYGSFNQKII 6790 6800 6810 6820 6830 6840 GGLHLLIGLA RRPKKSNLVI QEFVPYDSSI HSYFITDENS GSSESVCTVI DLLLDDFVDI 6850 6860 6870 6880 6890 6900 VKSLNLKCVS KVVNVNVDFK DFQFMLWCNE EKVMTFYPRL QAAADWKPGY VMPVLYKYLE 6910 6920 6930 6940 6950 6960 SPMERVNLWN YGKPITLPTG CMMNVAKYTQ LCQYLSTTTL AVPANMRVLH LGAGSDKGVA 6970 6980 6990 7000 7010 7020 PGSAVLRQWL PSGSILVDND MNPFVSDSVA SYYGNCITLP FDCQWDLIIS DMYDPLTKNI 7030 7040 7050 7060 7070 7080 GEYNVSKDGF FTYLCHLIRD KLALGGSVAI KITEFSWNAE LYSLMGKFAF WTIFCTNVNA 7090 7100 7110 7120 7130 7140 SSSEGFLIGI NWLNRTRNEI DGKTMHANYL FWRNSTMWNG GAYSLFDMTK FPLKAAGTAV 7150 7160 7170 7180 VSLKPDQIND LVLSLIEKGK LLVRDTRKEV FVGDSLVNVK
	Isoform Replicase polyprotein 1a (pp1a) (ORF1a polyprotein) [UniParc]. See P0C6V1.		–	–

References

[1]	"The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase." Lee H.-J., Shieh C.-K., Gorbalenya A.E., Koonin E.V., la Monica N., Tuler J., Bagdzhardzhyan A., Lai M.M.C. Virology 180:567-582(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Sequence and translation of the murine coronavirus 5'-end genomic RNA reveals the N-terminal structure of the putative RNA polymerase." Soe L.H., Shieh C.-K., Baker S.C., Chang M.F., Lai M.M.C. J. Virol. 61:3968-3976(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1-595.
[3]	"Mouse hepatitis virus strain A59 RNA polymerase gene ORF 1a: heterogeneity among MHV strains." Bonilla P.J., Gorbalenya A.E., Weiss S.R. Virology 198:736-740(1994) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION.
[4]	"Murine coronavirus gene 1 polyprotein contains an autoproteolytic activity." Baker S.C., La Monica N., Shieh C.K., Lai M.M. Adv. Exp. Med. Biol. 276:283-289(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1021-1326.
[5]	"Identification of the murine coronavirus MP1 cleavage site recognized by papain-like proteinase 2." Kanjanahaluethai A., Jukneliene D., Baker S.C. J. Virol. 77:7376-7382(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN, MUTAGENESIS OF PHE-2835; SER-2836; LEU-2837; LYS-2838; GLY-2839; GLY-2840; ALA-2841; VAL-2842 AND VAL-2846.
[6]	"Processing of the coronavirus MHV-JHM polymerase polyprotein: identification of precursors and proteolytic products spanning 400 kilodaltons of ORF1a." Schiller J.J., Kanjanahaluethai A., Baker S.C. Virology 242:288-302(1998) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN, SUBCELLULAR LOCATION.
[7]	"Conservation of substrate specificities among coronavirus main proteases." Hegyi A., Ziebuhr J. J. Gen. Virol. 83:595-599(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M55148 Genomic RNA. Translation: AAA46457.1. Sequence problems. M55148 Genomic RNA. Translation: AAA46458.2. Sequence problems. M18040 Genomic RNA. Translation: AAA46466.1. S51684 Genomic RNA. Translation: AAB19566.1.
PIR	RRIHM2. A36815. VFIHJH. B36815.
3D structure databases
ProteinModelPortal	P0C6Y0.
SMR	P0C6Y0. Positions 4055-4205, 4329-4453, 6508-6876.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
InterPro	IPR027351. (+)RNA_virus_helicase_core_dom. IPR002589. A1pp. IPR022570. Coronavirus_NSP1. IPR009461. Coronavirus_NSP13. IPR027352. CV_MBD_dom. IPR009466. NSP11. IPR014828. NSP7. IPR014829. NSP8. IPR014822. NSP9. IPR002705. Pept_C30/C16_sub. IPR008740. Peptidase_C30. IPR013016. Peptidase_C30/C16. IPR001205. RNA-dir_pol_C. IPR007094. RNA-dir_pol_PSvirus. IPR009469. RNA_pol_N_coronovir. IPR018995. RNA_synth_NSP10_coronavirus. IPR009003. Trypsin-like_Pept_dom. IPR014827. Viral_protease. [Graphical view]
Pfam	PF06478. Corona_RPol_N. 1 hit. PF11963. DUF3477. 2 hits. PF01661. Macro. 1 hit. PF09401. NSP10. 1 hit. PF06471. NSP11. 1 hit. PF06460. NSP13. 1 hit. PF08716. nsp7. 1 hit. PF08717. nsp8. 1 hit. PF08710. nsp9. 1 hit. PF01831. Peptidase_C16. 1 hit. PF05409. Peptidase_C30. 1 hit. PF00680. RdRP_1. 1 hit. PF08715. Viral_protease. 1 hit. [Graphical view]
SMART	SM00506. A1pp. 1 hit. [Graphical view]
SUPFAM	SSF101816. Nsp9. 1 hit. SSF50494. Pept_Ser_Cys. 1 hit. SSF144246. SSF144246. 1 hit.
PROSITE	PS51653. CV_MBD. 1 hit. PS51442. M_PRO. 1 hit. PS51154. MACRO. 1 hit. PS51124. PEPTIDASE_C16. 2 hits. PS51657. PSRV_HELICASE. 1 hit. PS50507. RDRP_SSRNA_POS. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

R1AB_CVMJH

Accession

Primary (citable) accession number: P0C6Y0
Secondary accession number(s): P19751 , P29982, Q66194, Q90045

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
Last sequence update:	June 10, 2008
Last modified:	May 1, 2013
This is version 43 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program