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P0C6Y5

- R1AB_CVPPU

UniProt

P0C6Y5 - R1AB_CVPPU

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Protein

Replicase polyprotein 1ab

Gene

rep

Organism
Porcine transmissible gastroenteritis coronavirus (strain Purdue) (TGEV)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.1 Publication
Non-structural protein 1 inhibits host translation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.1 Publication
The papain-like proteinase 1 (PLP1) and papain-like proteinase 2 (PLP2) 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. PLP2 also antagonizes innate immune induction of type I interferon by blocking the nuclear translocation of host IRF-3 (By similarity).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-|-[SAGC]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK.1 Publication
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).1 Publication
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 activityi

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).
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
ATP + H2O = ADP + phosphate.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei110 – 1112Cleavage; by PL1-PROBy similarity
Sitei879 – 8802Cleavage; by PL1-PROBy similarity
Active sitei1093 – 10931For PL1-PRO activityPROSITE-ProRule annotation
Active sitei1244 – 12441For PL1-PRO activityPROSITE-ProRule annotation
Active sitei1588 – 15881For PL2-PRO activityPROSITE-ProRule annotation
Active sitei1741 – 17411For PL2-PRO activityPROSITE-ProRule annotation
Sitei2388 – 23892Cleavage; by PL2-PROBy similarity
Sitei2878 – 28792Cleavage; by 3CL-PROBy similarity
Active sitei2919 – 29191For 3CL-PRO activityPROSITE-ProRule annotation
Active sitei3022 – 30221For 3CL-PRO activityPROSITE-ProRule annotation
Sitei3180 – 31812Cleavage; by 3CL-PROBy similarity
Sitei3474 – 34752Cleavage; by 3CL-PROBy similarity
Sitei3557 – 35582Cleavage; by 3CL-PROBy similarity
Sitei3752 – 37532Cleavage; by 3CL-PROBy similarity
Sitei3863 – 38642Cleavage; by 3CL-PROBy similarity
Sitei3998 – 39992Cleavage; by 3CL-PROBy similarity
Sitei4927 – 49282Cleavage; by 3CL-PROBy similarity
Sitei5526 – 55272Cleavage; by 3CL-PROBy similarity
Sitei6045 – 60462Cleavage; by 3CL-PROBy similarity
Sitei6384 – 63852Cleavage; by 3CL-PROBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1164 – 119532C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri3937 – 395317By similarityAdd
BLAST
Zinc fingeri3979 – 399214By similarityAdd
BLAST
Nucleotide bindingi5210 – 52178ATPBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. cysteine-type endopeptidase activity Source: InterPro
  3. endonuclease activity Source: UniProtKB-KW
  4. exoribonuclease activity, producing 5'-phosphomonoesters Source: InterPro
  5. helicase activity Source: UniProtKB-KW
  6. methyltransferase activity Source: InterPro
  7. omega peptidase activity Source: InterPro
  8. RNA binding Source: UniProtKB-KW
  9. RNA-directed RNA polymerase activity Source: UniProtKB-KW
  10. zinc ion binding Source: InterPro

GO - Biological processi

  1. induction by virus of host autophagy Source: UniProtKB-KW
  2. modulation by virus of host protein ubiquitination Source: UniProtKB-KW
  3. suppression by virus of host IRF3 activity Source: UniProtKB-KW
  4. transcription, DNA-templated Source: InterPro
  5. viral genome replication Source: InterPro
  6. viral protein processing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Helicase, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase

Keywords - Biological processi

Activation of host autophagy by virus, Host-virus interaction, Inhibition of host innate immune response by virus, Inhibition of host IRF3 by virus, Inhibition of host RLR pathway by virus, Modulation of host ubiquitin pathway by viral deubiquitinase, Modulation of host ubiquitin pathway by virus, Ubl conjugation pathway, Viral immunoevasion, Viral RNA replication

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Replicase polyprotein 1ab
Short name:
pp1ab
Alternative name(s):
ORF1ab polyprotein
Cleaved into the following 15 chains:
Non-structural protein 1
Short name:
nsp1
Alternative name(s):
p9
Non-structural protein 2
Short name:
nsp2
Alternative name(s):
p87
Alternative name(s):
PL1-PRO/PL2-PRO
PLP1/PLP2
Papain-like proteinases 1/2
p195
Non-structural protein 4
Short name:
nsp4
Alternative name(s):
Peptide HD2
3C-like proteinase (EC:3.4.22.-)
Short name:
3CL-PRO
Short name:
3CLp
Alternative name(s):
M-PRO
nsp5
p34
Non-structural protein 6
Short name:
nsp6
Non-structural protein 7
Short name:
nsp7
Alternative name(s):
p5
Non-structural protein 8
Short name:
nsp8
Alternative name(s):
p23
Non-structural protein 9
Short name:
nsp9
Alternative name(s):
p12
Non-structural protein 10
Short name:
nsp10
Alternative name(s):
Growth factor-like peptide
Short name:
GFL
p14
RNA-directed RNA polymerase (EC:2.7.7.48)
Short name:
Pol
Short name:
RdRp
Alternative name(s):
nsp12
p100
Helicase (EC:3.6.4.12, EC:3.6.4.13)
Short name:
Hel
Alternative name(s):
nsp13
p66
p66-HEL
Exoribonuclease (EC:3.1.13.-)
Short name:
ExoN
Alternative name(s):
nsp14
Alternative name(s):
NendoU
nsp15
p41
Alternative name(s):
nsp16
Gene namesi
Name:rep
ORF Names:1a-1b
OrganismiPorcine transmissible gastroenteritis coronavirus (strain Purdue) (TGEV)
Taxonomic identifieri11151 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageNidoviralesCoronaviridaeCoronavirinaeAlphacoronavirus
Virus hostiSus scrofa (Pig) [TaxID: 9823]
ProteomesiUP000001440: Genome

Subcellular locationi

Chain Non-structural protein 7 : Host cytoplasmhost perinuclear region By similarity
Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity).By similarity
Chain Non-structural protein 8 : Host cytoplasmhost perinuclear region By similarity
Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity).By similarity
Chain Non-structural protein 9 : Host cytoplasmhost perinuclear region By similarity
Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity).By similarity
Chain Non-structural protein 10 : Host cytoplasmhost perinuclear region By similarity
Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes (By similarity).By similarity
Chain Helicase : Host endoplasmic reticulum-Golgi intermediate compartment Curated
Note: The helicase interacts with the N protein in membranous complexes and colocalizes with sites of synthesis of new viral RNA.By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei1896 – 191621HelicalSequence AnalysisAdd
BLAST
Transmembranei1995 – 201521HelicalSequence AnalysisAdd
BLAST
Transmembranei2033 – 205321HelicalSequence AnalysisAdd
BLAST
Transmembranei2401 – 242121HelicalSequence AnalysisAdd
BLAST
Transmembranei2467 – 248721HelicalSequence AnalysisAdd
BLAST
Transmembranei2497 – 251721HelicalSequence AnalysisAdd
BLAST
Transmembranei2538 – 255821HelicalSequence AnalysisAdd
BLAST
Transmembranei2666 – 268621HelicalSequence AnalysisAdd
BLAST
Transmembranei2695 – 271521HelicalSequence AnalysisAdd
BLAST
Transmembranei2721 – 274121HelicalSequence AnalysisAdd
BLAST
Transmembranei2746 – 276621HelicalSequence AnalysisAdd
BLAST
Transmembranei3187 – 320721HelicalSequence AnalysisAdd
BLAST
Transmembranei3217 – 323721HelicalSequence AnalysisAdd
BLAST
Transmembranei3242 – 326221HelicalSequence AnalysisAdd
BLAST
Transmembranei3280 – 330021HelicalSequence AnalysisAdd
BLAST
Transmembranei3313 – 333321HelicalSequence AnalysisAdd
BLAST
Transmembranei3347 – 336721HelicalSequence AnalysisAdd
BLAST
Transmembranei3371 – 339121HelicalSequence AnalysisAdd
BLAST
Transmembranei3394 – 341421HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-KW
  2. host cell membrane Source: UniProtKB-KW
  3. integral component of membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Host cytoplasm, Host membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 110110Non-structural protein 1By similarityPRO_0000037386Add
BLAST
Chaini111 – 879769Non-structural protein 2By similarityPRO_0000037387Add
BLAST
Chaini880 – 23881509Non-structural protein 3By similarityPRO_0000037388Add
BLAST
Chaini2389 – 2878490Non-structural protein 4By similarityPRO_0000037389Add
BLAST
Chaini2879 – 31803023C-like proteinasePRO_0000037390Add
BLAST
Chaini3181 – 3474294Non-structural protein 6By similarityPRO_0000037391Add
BLAST
Chaini3475 – 355783Non-structural protein 7By similarityPRO_0000037392Add
BLAST
Chaini3558 – 3752195Non-structural protein 8By similarityPRO_0000037393Add
BLAST
Chaini3753 – 3863111Non-structural protein 9PRO_0000037394Add
BLAST
Chaini3864 – 3998135Non-structural protein 10By similarityPRO_0000037395Add
BLAST
Chaini3999 – 4927929RNA-directed RNA polymeraseBy similarityPRO_0000037396Add
BLAST
Chaini4928 – 5526599HelicaseBy similarityPRO_0000037397Add
BLAST
Chaini5527 – 6045519ExoribonucleaseBy similarityPRO_0000037398Add
BLAST
Chaini6046 – 6384339Uridylate-specific endoribonucleaseBy similarityPRO_0000037399Add
BLAST
Chaini6385 – 6684300Putative 2'-O-methyl transferaseBy similarityPRO_0000037400Add
BLAST

Post-translational modificationi

Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO is autocatalytically processed.1 Publication

Interactioni

Subunit structurei

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).By similarity

Structurei

Secondary structure

1
6684
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni2889 – 28913Combined sources
Helixi2892 – 28943Combined sources
Beta strandi2895 – 29006Combined sources
Beta strandi2903 – 29108Combined sources
Beta strandi2913 – 29175Combined sources
Helixi2918 – 29214Combined sources
Helixi2931 – 29366Combined sources
Helixi2940 – 29423Combined sources
Beta strandi2944 – 29474Combined sources
Beta strandi2950 – 29523Combined sources
Beta strandi2954 – 29607Combined sources
Beta strandi2963 – 29708Combined sources
Beta strandi2978 – 29803Combined sources
Beta strandi2988 – 29958Combined sources
Beta strandi2998 – 30069Combined sources
Beta strandi3025 – 30306Combined sources
Beta strandi3033 – 304311Combined sources
Beta strandi3049 – 30524Combined sources
Helixi3059 – 30613Combined sources
Beta strandi3064 – 30663Combined sources
Helixi3078 – 309013Combined sources
Helixi3104 – 31118Combined sources
Turni3112 – 31154Combined sources
Helixi3123 – 31253Combined sources
Helixi3126 – 31327Combined sources
Helixi3136 – 314611Combined sources
Beta strandi3158 – 31603Combined sources
Helixi3167 – 31737Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LVOX-ray1.96A/B/C/D/E/F2879-3180[»]
1P9UX-ray2.37A/B/C/D/E/F2879-3180[»]
2AMPX-ray2.70A/B2879-3180[»]
ProteinModelPortaliP0C6Y5.
SMRiP0C6Y5. Positions 2879-3179, 3869-3994.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C6Y5.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1055 – 1299245Peptidase C16 1PROSITE-ProRule annotationAdd
BLAST
Domaini1318 – 1489172MacroPROSITE-ProRule annotationAdd
BLAST
Domaini1550 – 1803254Peptidase C16 2PROSITE-ProRule annotationAdd
BLAST
Domaini2879 – 3180302Peptidase C30PROSITE-ProRule annotationAdd
BLAST
Domaini4607 – 4769163RdRp catalyticAdd
BLAST
Domaini4928 – 501184CV MBDAdd
BLAST
Domaini5175 – 5366192(+)RNA virus helicase ATP-bindingAdd
BLAST
Domaini5367 – 5536170(+)RNA virus helicase C-terminalAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1896 – 2053158HD1Add
BLAST
Regioni2401 – 2766366HD2Add
BLAST
Regioni3187 – 3414228HD3Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi932 – 1042111Glu-richAdd
BLAST

Domaini

The hydrophobic domains (HD) could mediate the membrane association of the replication complex and thereby alter the architecture of the host cell membrane.

Sequence similaritiesi

Contains 1 Macro domain.PROSITE-ProRule annotation
Contains 2 peptidase C16 domains.PROSITE-ProRule annotation
Contains 1 peptidase C30 domain.PROSITE-ProRule annotation
Contains 1 RdRp catalytic domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1164 – 119532C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri3937 – 395317By similarityAdd
BLAST
Zinc fingeri3979 – 399214By similarityAdd
BLAST

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix, Zinc-finger

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027351. (+)RNA_virus_helicase_core_dom.
IPR009461. Coronavirus_NSP16.
IPR027352. CV_MBD_dom.
IPR002589. Macro_dom.
IPR009466. NSP11.
IPR014828. NSP7.
IPR014829. NSP8.
IPR014822. NSP9.
IPR027417. P-loop_NTPase.
IPR008740. Peptidase_C30.
IPR013016. Peptidase_C30/C16.
IPR009469. RNA_pol_N_coronovir.
IPR018995. RNA_synth_NSP10_coronavirus.
IPR029063. SAM-dependent_MTases-like.
IPR009003. Trypsin-like_Pept_dom.
IPR014827. Viral_protease.
[Graphical view]
PfamiPF06478. Corona_RPol_N. 1 hit.
PF01661. Macro. 1 hit.
PF09401. NSP10. 2 hits.
PF06471. NSP11. 1 hit.
PF06460. NSP13. 1 hit.
PF08716. nsp7. 1 hit.
PF08717. nsp8. 1 hit.
PF08710. nsp9. 1 hit.
PF05409. Peptidase_C30. 1 hit.
PF01443. Viral_helicase1. 1 hit.
PF08715. Viral_protease. 2 hits.
[Graphical view]
SMARTiSM00506. A1pp. 1 hit.
[Graphical view]
SUPFAMiSSF101816. SSF101816. 1 hit.
SSF144246. SSF144246. 2 hits.
SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF53335. SSF53335. 1 hit.
PROSITEiPS51653. CV_MBD. 1 hit.
PS51442. M_PRO. 1 hit.
PS51154. MACRO. 1 hit.
PS51124. PEPTIDASE_C16. 2 hits.
PS51657. PSRV_HELICASE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. Align

Isoform Replicase polyprotein 1ab (identifier: P0C6Y5-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MSSKQFKILV NEDYQVNVPS LPIRDVLQEI KYCYRNGFEG YVFVPEYCRD
60 70 80 90 100
LVDCDRKDHY VIGVLGNGVS DLKPVLLTEP SVMLQGFIVR ANCNGVLEDF
110 120 130 140 150
DLKIARTGRG AIYVDQYMCG ADGKPVIEGD FKDYFGDEDI IEFEGEEYHC
160 170 180 190 200
AWTTVRDEKP LNQQTLFTIQ EIQYNLDIPH KLPNCATRHV APPVKKNSKI
210 220 230 240 250
VLSEDYKKLY DIFGSPFMGN GDCLSKCFDT LHFIAATLRC PCGSESSGVG
260 270 280 290 300
DWTGFKTACC GLSGKVKGVT LGDIKPGDAV VTSMSAGKGV KFFANCVLQY
310 320 330 340 350
AGDVEGVSIW KVIKTFTVDE TVCTPGFEGE LNDFIKPESK SLVACSVKRA
360 370 380 390 400
FITGDIDDAV HDCIITGKLD LSTNLFGNVG LLFKKTPWFV QKCGALFVDA
410 420 430 440 450
WKVVEELCGS LTLTYKQIYE VVASLCTSAF TIVNYKPTFV VPDNRVKDLV
460 470 480 490 500
DKCVKVLVKA FDVFTQIITI AGIEAKCFVL GAKYLLFNNA LVKLVSVKIL
510 520 530 540 550
GKKQKGLECA FFATSLVGAT VNVTPKRTET ATISLNKVDD VVAPGEGYIV
560 570 580 590 600
IVGDMAFYKS GEYYFMMSSP NFVLTNNVFK AVKVPSYDIV YDVDNDTKSK
610 620 630 640 650
MIAKLGSSFE YDGDIDAAIV KVNELLIEFR QQSLCFRAFK DDKSIFVEAY
660 670 680 690 700
FKKYKMPACL AKHIGLWNII KKDSCKRGFL NLFNHLNELE DIKETNIQAI
710 720 730 740 750
KNILCPDPLL DLDYGAIWYN CMPGCSDPSV LGSVQLLIGN GVKVVCDGCK
760 770 780 790 800
GFANQLSKGY NKLCNAARND IEIGGIPFST FKTPTNTFIE MTDAIYSVIE
810 820 830 840 850
QGKALSFRDA DVPVVDNGTI STADWSEPIL LEPAEYVKPK NNGNVIVIAG
860 870 880 890 900
YTFYKDEDEH FYPYGFGKIV QRMYNKMGGG DKTVSFSEEV DVQEIAPVTR
910 920 930 940 950
VKLEFEFDNE IVTGVLERAI GTRYKFTGTT WEEFEESISE ELDAIFDTLA
960 970 980 990 1000
NQGVELEGYF IYDTCGGFDI KNPDGIMISQ YDINITADEK SEVSASSEEE
1010 1020 1030 1040 1050
EVESVEEDPE NEIVEASEGA EGTSSQEEVE TVEVADITST EEDVDIVEVS
1060 1070 1080 1090 1100
AKDDPWAAAV DVQEAEQFNP SLPPFKTTNL NGKIILKQGD NNCWINACCY
1110 1120 1130 1140 1150
QLQAFDFFNN EAWEKFKKGD VMDFVNLCYA ATTLARGHSG DAEYLLELML
1160 1170 1180 1190 1200
NDYSTAKIVL AAKCGCGEKE IVLERAVFKL TPLKESFNYG VCGDCMQVNT
1210 1220 1230 1240 1250
CRFLSVEGSG VFVHDILSKQ TPEAMFVVKP VMHAVYTGTT QNGHYMVDDI
1260 1270 1280 1290 1300
EHGYCVDGMG IKPLKKRCYT STLFINANVM TRAEKPKQEF KVEKVEQQPI
1310 1320 1330 1340 1350
VEENKSSIEK EEIQSPKNDD LILPFYKAGK LSFYQGALDV LINFLEPDVI
1360 1370 1380 1390 1400
VNAANGDLKH MGGVARAIDV FTGGKLTERS KDYLKKNKSI APGNAVFFEN
1410 1420 1430 1440 1450
VIEHLSVLNA VGPRNGDSRV EAKLCNVYKA IAKCEGKILT PLISVGIFNV
1460 1470 1480 1490 1500
RLETSLQCLL KTVNDRGLNV FVYTDQERQT IENFFSCSIP VNVTEDNVNH
1510 1520 1530 1540 1550
ERVSVSFDKT YGEQLKGTVV IKDKDVTNQL PSAFDVGQKV IKAIDIDWQA
1560 1570 1580 1590 1600
HYGFRDAAAF SASSHDAYKF EVVTHSNFIV HKQTDNNCWI NAICLALQRL
1610 1620 1630 1640 1650
KPQWKFPGVR GLWNEFLERK TQGFVHMLYH ISGVKKGEPG DAELMLHKLG
1660 1670 1680 1690 1700
DLMDNDCEII VTHTTACDKC AKVEKFVGPV VAAPLAIHGT DETCVHGVSV
1710 1720 1730 1740 1750
NVKVTQIKGT VAITSLIGPI IGEVLEATGY ICYSGSNRNG HYTYYDNRNG
1760 1770 1780 1790 1800
LVVDAEKAYH FNRDLLQVTT AIASNFVVKK PQAEERPKNC AFNKVAASPK
1810 1820 1830 1840 1850
IVQEQKLLAI ESGANYALTE FGRYADMFFM AGDKILRLLL EVFKYLLVLF
1860 1870 1880 1890 1900
MCLRSTKMPK VKVKPPLAFK DFGAKVRTLN YMRQLNKPSV WRYAKLVLLL
1910 1920 1930 1940 1950
IAIYNFFYLF VSIPVVHKLT CNGAVQAYKN SSFIKSAVCG NSILCKACLA
1960 1970 1980 1990 2000
SYDELADFQH LQVTWDFKSD PLWNRLVQLS YFAFLAVFGN NYVRCFLMYF
2010 2020 2030 2040 2050
VSQYLNLWLS YFGYVEYSWF LHVVNFESIS AEFVIVVIVV KAVLALKHIV
2060 2070 2080 2090 2100
FACSNPSCKT CSRTARQTRI PIQVVVNGSM KTVYVHANGT GKFCKKHNFY
2110 2120 2130 2140 2150
CKNCDSYGFE NTFICDEIVR DLSNSVKQTV YATDRSHQEV TKVECSDGFY
2160 2170 2180 2190 2200
RFYVGDEFTS YDYDVKHKKY SSQEVLKSML LLDDFIVYSP SGSALANVRN
2210 2220 2230 2240 2250
ACVYFSQLIG KPIKIVNSDL LEDLSVDFKG ALFNAKKNVI KNSFNVDVSE
2260 2270 2280 2290 2300
CKNLDECYRA CNLNVSFSTF EMAVNNAHRF GILITDRSFN NFWPSKVKPG
2310 2320 2330 2340 2350
SSGVSAMDIG KCMTSDAKIV NAKVLTQRGK SVVWLSQDFA ALSSTAQKVL
2360 2370 2380 2390 2400
VKTFVEEGVN FSLTFNAVGS DDDLPYERFT ESVSPKSGSG FFDVITQLKQ
2410 2420 2430 2440 2450
IVILVFVFIF ICGLCSVYSV ATQSYIESAE GYDYMVIKNG IVQPFDDTIS
2460 2470 2480 2490 2500
CVHNTYKGFG DWFKAKYGFI PTFGKSCPIV VGTVFDLENM RPIPDVPAYV
2510 2520 2530 2540 2550
SIVGRSLVFA INAAFGVTNM CYDHTGNAVS KDSYFDTCVF NTACTTLTGL
2560 2570 2580 2590 2600
GGTIVYCAKQ GLVEGAKLYS DLMPDYYYEH ASGNMVKLPA IIRGLGLRFV
2610 2620 2630 2640 2650
KTQATTYCRV GECIDSKAGF CFGGDNWFVY DNEFGNGYIC GNSVLGFFKN
2660 2670 2680 2690 2700
VFKLFNSNMS VVATSGAMLV NIIIACLAIA MCYGVLKFKK IFGDCTFLIV
2710 2720 2730 2740 2750
MIIVTLVVNN VSYFVTQNTF FMIIYAIVYY FITRKLAYPG ILDAGFIIAY
2760 2770 2780 2790 2800
INMAPWYVIT AYILVFLYDS LPSLFKLKVS TNLFEGDKFV GNFESAAMGT
2810 2820 2830 2840 2850
FVIDMRSYET IVNSTSIARI KSYANSFNKY KYYTGSMGEA DYRMACYAHL
2860 2870 2880 2890 2900
GKALMDYSVN RTDMLYTPPT VSVNSTLQSG LRKMAQPSGL VEPCIVRVSY
2910 2920 2930 2940 2950
GNNVLNGLWL GDEVICPRHV IASDTTRVIN YENEMSSVRL HNFSVSKNNV
2960 2970 2980 2990 3000
FLGVVSARYK GVNLVLKVNQ VNPNTPEHKF KSIKAGESFN ILACYEGCPG
3010 3020 3030 3040 3050
SVYGVNMRSQ GTIKGSFIAG TCGSVGYVLE NGILYFVYMH HLELGNGSHV
3060 3070 3080 3090 3100
GSNFEGEMYG GYEDQPSMQL EGTNVMSSDN VVAFLYAALI NGERWFVTNT
3110 3120 3130 3140 3150
SMSLESYNTW AKTNSFTELS STDAFSMLAA KTGQSVEKLL DSIVRLNKGF
3160 3170 3180 3190 3200
GGRTILSYGS LCDEFTPTEV IRQMYGVNLQ AGKVKSFFYP IMTAMTILFA
3210 3220 3230 3240 3250
FWLEFFMYTP FTWINPTFVS IVLAVTTLIS TVFVSGIKHK MLFFMSFVLP
3260 3270 3280 3290 3300
SVILVTAHNL FWDFSYYESL QSIVENTNTM FLPVDMQGVM LTVFCFIVFV
3310 3320 3330 3340 3350
TYSVRFFTCK QSWFSLAVTT ILVIFNMVKI FGTSDEPWTE NQIAFCFVNM
3360 3370 3380 3390 3400
LTMIVSLTTK DWMVVIASYR IAYYIVVCVM PSAFVSDFGF MKCISIVYMA
3410 3420 3430 3440 3450
CGYLFCCYYG ILYWVNRFTC MTCGVYQFTV SAAELKYMTA NNLSAPKNAY
3460 3470 3480 3490 3500
DAMILSAKLI GVGGKRNIKI STVQSKLTEM KCTNVVLLGL LSKMHVESNS
3510 3520 3530 3540 3550
KEWNYCVGLH NEINLCDDPE IVLEKLLALI AFFLSKHNTC DLSELIESYF
3560 3570 3580 3590 3600
ENTTILQSVA SAYAALPSWI ALEKARADLE EAKKNDVSPQ ILKQLTKAFN
3610 3620 3630 3640 3650
IAKSDFEREA SVQKKLDKMA EQAAASMYKE ARAVDRKSKI VSAMHSLLFG
3660 3670 3680 3690 3700
MLKKLDMSSV NTIIDQARNG VLPLSIIPAA SATRLVVITP SLEVFSKIRQ
3710 3720 3730 3740 3750
ENNVHYAGAI WTIVEVKDAN GSHVHLKEVT AANELNLTWP LSITCERTTK
3760 3770 3780 3790 3800
LQNNEIMPGK LKERAVRASA TLDGEAFGSG KALMASESGK SFMYAFIASD
3810 3820 3830 3840 3850
NNLKYVKWES NNDIIPIELE APLRFYVDGA NGPEVKYLYF VKNLNTLRRG
3860 3870 3880 3890 3900
AVLGYIGATV RLQAGKPTEH PSNSSLLTLC AFSPDPAKAY VDAVKRGMQP
3910 3920 3930 3940 3950
VNNCVKMLSN GAGNGMAVTN GVEANTQQDS YGGASVCIYC RCHVEHPAID
3960 3970 3980 3990 4000
GLCRYKGKFV QIPTGTQDPI RFCIENEVCV VCGCWLNNGC MCDRTSMQSF
4010 4020 4030 4040 4050
TVDQSYLNRV RGSSAARLEP CNGTDPDHVS RAFDIYNKDV ACIGKFLKTN
4060 4070 4080 4090 4100
CSRFRNLDKH DAYYIVKRCT KTVMDHEQVC YNDLKDSGAV AEHDFFTYKE
4110 4120 4130 4140 4150
GRCEFGNVAR RNLTKYTMMD LCYAIRNFDE KNCEVLKEIL VTVGACTEEF
4160 4170 4180 4190 4200
FENKDWFDPV ENEAIHEVYA KLGPIVANAM LKCVAFCDAI VEKGYIGVIT
4210 4220 4230 4240 4250
LDNQDLNGNF YDFGDFVKTA PGFGCACVTS YYSYMMPLMG MTSCLESENF
4260 4270 4280 4290 4300
VKSDIYGSDY KQYDLLAYDF TEHKEYLFQK YFKYWDRTYH PNCSDCTSDE
4310 4320 4330 4340 4350
CIIHCANFNT LFSMTIPMTA FGPLVRKVHI DGVPVVVTAG YHFKQLGIVW
4360 4370 4380 4390 4400
NLDVKLDTMK LSMTDLLRFV TDPTLLVASS PALLDQRTVC FSIAALSTGI
4410 4420 4430 4440 4450
TYQTVKPGHF NKDFYDFITE RGFFEEGSEL TLKHFFFAQG GEAAMTDFNY
4460 4470 4480 4490 4500
YRYNRVTVLD ICQAQFVYKI VGKYFECYDG GCINAREVVV TNYDKSAGYP
4510 4520 4530 4540 4550
LNKFGKARLY YETLSYEEQD ALFALTKRNV LPTMTQMNLK YAISGKARAR
4560 4570 4580 4590 4600
TVGGVSLLST MTTRQYHQKH LKSIAATRNA TVVIGSTKFY GGWDNMLKNL
4610 4620 4630 4640 4650
MRDVDNGCLM GWDYPKCDRA LPNMIRMASA MILGSKHVGC CTHNDRFYRL
4660 4670 4680 4690 4700
SNELAQVLTE VVHCTGGFYF KPGGTTSGDG TTAYANSAFN IFQAVSANVN
4710 4720 4730 4740 4750
KLLGVDSNAC NNVTVKSIQR KIYDNCYRSS SIDEEFVVEY FSYLRKHFSM
4760 4770 4780 4790 4800
MILSDDGVVC YNKDYADLGY VADINAFKAT LYYQNNVFMS TSKCWVEPDL
4810 4820 4830 4840 4850
SVGPHEFCSQ HTLQIVGPDG DYYLPYPDPS RILSAGVFVD DIVKTDNVIM
4860 4870 4880 4890 4900
LERYVSLAID AYPLTKHPKP AYQKVFYTLL DWVKHLQKNL NAGVLDSFSV
4910 4920 4930 4940 4950
TMLEEGQDKF WSEEFYASLY EKSTVLQAAG MCVVCGSQTV LRCGDCLRRP
4960 4970 4980 4990 5000
LLCTKCAYDH VMGTKHKFIM SITPYVCSFN GCNVNDVTKL FLGGLSYYCM
5010 5020 5030 5040 5050
NHKPQLSFPL CANGNVFGLY KSSAVGSEAV EDFNKLAVSD WTNVEDYKLA
5060 5070 5080 5090 5100
NNVKESLKIF AAETVKAKEE SVKSEYAYAV LKEVIGPKEI VLQWEASKTK
5110 5120 5130 5140 5150
PPLNRNSVFT CFQISKDTKI QLGEFVFEQS EYGSDSVYYK STSTYKLTPG
5160 5170 5180 5190 5200
MIFVLTSHNV SPLKAPILVN QEKYNTISKL YPVFNIAEAY NTLVPYYQMI
5210 5220 5230 5240 5250
GKQKFTTIQG PPGSGKSHCV IGLGLYYPQA RIVYTACSHA AVDALCEKAA
5260 5270 5280 5290 5300
KNFNVDRCSR IIPQRIRVDC YTGFKPNNTN AQYLFCTVNA LPEASCDIVV
5310 5320 5330 5340 5350
VDEVSMCTNY DLSVINSRLS YKHIVYVGDP QQLPAPRTLI NKGVLQPQDY
5360 5370 5380 5390 5400
NVVTKRMCTL GPDVFLHKCY RCPAEIVKTV SALVYENKFV PVNPESKQCF
5410 5420 5430 5440 5450
KMFVKGQVQI ESNSSINNKQ LEVVKAFLAH NPKWRKAVFI SPYNSQNYVA
5460 5470 5480 5490 5500
RRLLGLQTQT VDSAQGSEYD YVIYTQTSDT QHATNVNRFN VAITRAKVGI
5510 5520 5530 5540 5550
LCIMCDRTMY ENLDFYELKD SKIGLQAKPE TCGLFKDCSK SEQYIPPAYA
5560 5570 5580 5590 5600
TTYMSLSDNF KTSDGLAVNI GTKDVKYANV ISYMGFRFEA NIPGYHTLFC
5610 5620 5630 5640 5650
TRDFAMRNVR AWLGFDVEGA HVCGDNVGTN VPLQLGFSNG VDFVVQTEGC
5660 5670 5680 5690 5700
VITEKGNSIE VVKARAPPGE QFAHLIPLMR KGQPWHIVRR RIVQMVCDYF
5710 5720 5730 5740 5750
DGLSDILIFV LWAGGLELTT MRYFVKIGRP QKCECGKSAT CYSSSQSVYA
5760 5770 5780 5790 5800
CFKHALGCDY LYNPYCIDIQ QWGYTGSLSM NHHEVCNIHR NEHVASGDAI
5810 5820 5830 5840 5850
MTRCLAIHDC FVKRVDWSIV YPFIDNEEKI NKAGRIVQSH VMKAALKIFN
5860 5870 5880 5890 5900
PAAIHDVGNP KGIRCATTPI PWFCYDRDPI NNNVRCLDYD YMVHGQMNGL
5910 5920 5930 5940 5950
MLFWNCNVDM YPEFSIVCRF DTRTRSKLSL EGCNGGALYV NNHAFHTPAY
5960 5970 5980 5990 6000
DRRAFAKLKP MPFFYYDDSN CELVDGQPNY VPLKSNVCIT KCNIGGAVCK
6010 6020 6030 6040 6050
KHAALYRAYV EDYNIFMQAG FTIWCPQNFD TYMLWHGFVN SKALQSLENV
6060 6070 6080 6090 6100
AFNVVKKGAF TGLKGDLPTA VIADKIMVRD GPTDKCIFTN KTSLPTNVAF
6110 6120 6130 6140 6150
ELYAKRKLGL TPPLTILRNL GVVATYKFVL WDYEAERPFS NFTKQVCSYT
6160 6170 6180 6190 6200
DLDSEVVTCF DNSIAGSFER FTTTRDAVLI SNNAVKGLSA IKLQYGLLND
6210 6220 6230 6240 6250
LPVSTVGNKP VTWYIYVRKN GEYVEQIDSY YTQGRTFETF KPRSTMEEDF
6260 6270 6280 6290 6300
LSMDTTLFIQ KYGLEDYGFE HVVFGDVSKT TIGGMHLLIS QVRLAKMGLF
6310 6320 6330 6340 6350
SVQEFMNNSD STLKSCCITY ADDPSSKNVC TYMDILLDDF VTIIKSLDLN
6360 6370 6380 6390 6400
VVSKVVDVIV DCKAWRWMLW CENSHIKTFY PQLQSAEWNP GYSMPTLYKI
6410 6420 6430 6440 6450
QRMCLERCNL YNYGAQVKLP DGITTNVVKY TQLCQYLNTT TLCVPHKMRV
6460 6470 6480 6490 6500
LHLGAAGASG VAPGSTVLRR WLPDDAILVD NDLRDYVSDA DFSVTGDCTS
6510 6520 6530 6540 6550
LYIEDKFDLL VSDLYDGSTK SIDGENTSKD GFFTYINGFI KEKLSLGGSV
6560 6570 6580 6590 6600
AIKITEFSWN KDLYELIQRF EYWTVFCTSV NTSSSEGFLI GINYLGPYCD
6610 6620 6630 6640 6650
KAIVDGNIMH ANYIFWRNST IMALSHNSVL DTPKFKCRCN NALIVNLKEK
6660 6670 6680
ELNEMVIGLL RKGKLLIRNN GKLLNFGNHF VNTP

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

Length:6,684
Mass (Da):748,912
Last modified:June 10, 2008 - v1
Checksum:i88468A64F84E35A2
GO
Isoform Replicase polyprotein 1a (identifier: P0C6V2-1) [UniParc]FASTAAdd to Basket

Also known as: pp1a, ORF1a polyprotein

The sequence of this isoform can be found in the external entry P0C6V2.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:4,017
Mass (Da):447,352
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti572 – 5721F → S in strain: Isolate Purdue-115.
Natural varianti1041 – 10411E → D in strain: Isolate Purdue-115.
Natural varianti2375 – 23751P → T in strain: Isolate Purdue-115.
Natural varianti2381 – 23811E → Q in strain: Isolate Purdue-115.
Natural varianti5276 – 52761P → A in strain: Isolate Purdue-115.
Natural varianti6054 – 60541V → I in strain: Isolate Purdue-115.
Natural varianti6421 – 64211D → V in strain: Isolate Purdue-115.
Natural varianti6426 – 64272NV → KF in strain: Isolate Purdue-115.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z34093 mRNA. No translation available.
AJ271965 Genomic RNA. Translation: CAB91143.1. Sequence problems.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z34093 mRNA. No translation available.
AJ271965 Genomic RNA. Translation: CAB91143.1 . Sequence problems.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1LVO X-ray 1.96 A/B/C/D/E/F 2879-3180 [» ]
1P9U X-ray 2.37 A/B/C/D/E/F 2879-3180 [» ]
2AMP X-ray 2.70 A/B 2879-3180 [» ]
ProteinModelPortali P0C6Y5.
SMRi P0C6Y5. Positions 2879-3179, 3869-3994.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P0C6Y5.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR027351. (+)RNA_virus_helicase_core_dom.
IPR009461. Coronavirus_NSP16.
IPR027352. CV_MBD_dom.
IPR002589. Macro_dom.
IPR009466. NSP11.
IPR014828. NSP7.
IPR014829. NSP8.
IPR014822. NSP9.
IPR027417. P-loop_NTPase.
IPR008740. Peptidase_C30.
IPR013016. Peptidase_C30/C16.
IPR009469. RNA_pol_N_coronovir.
IPR018995. RNA_synth_NSP10_coronavirus.
IPR029063. SAM-dependent_MTases-like.
IPR009003. Trypsin-like_Pept_dom.
IPR014827. Viral_protease.
[Graphical view ]
Pfami PF06478. Corona_RPol_N. 1 hit.
PF01661. Macro. 1 hit.
PF09401. NSP10. 2 hits.
PF06471. NSP11. 1 hit.
PF06460. NSP13. 1 hit.
PF08716. nsp7. 1 hit.
PF08717. nsp8. 1 hit.
PF08710. nsp9. 1 hit.
PF05409. Peptidase_C30. 1 hit.
PF01443. Viral_helicase1. 1 hit.
PF08715. Viral_protease. 2 hits.
[Graphical view ]
SMARTi SM00506. A1pp. 1 hit.
[Graphical view ]
SUPFAMi SSF101816. SSF101816. 1 hit.
SSF144246. SSF144246. 2 hits.
SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF53335. SSF53335. 1 hit.
PROSITEi PS51653. CV_MBD. 1 hit.
PS51442. M_PRO. 1 hit.
PS51154. MACRO. 1 hit.
PS51124. PEPTIDASE_C16. 2 hits.
PS51657. PSRV_HELICASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete sequence (20 kilobases) of the polyprotein-encoding gene 1 of transmissible gastroenteritis virus."
    Eleouet J., Rasschaert D., Lambert P., Levy L., Vende P., Laude H.
    Virology 206:817-822(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ORF1A).
    Strain: Isolate Purdue-115.
  2. "Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome."
    Almazan F., Gonzalez J.M., Penzes Z., Izeta A., Calvo E., Plana-Duran J., Enjuanes L.
    Proc. Natl. Acad. Sci. U.S.A. 97:5516-5521(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Isolate PUR46-MAD.
  3. "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.
    Strain: Isolate Purdue-115.
  4. "Alphacoronavirus transmissible gastroenteritis virus nsp1 protein suppresses protein translation in mammalian cells and in cell-free HeLa cell extracts but not in rabbit reticulocyte lysate."
    Huang C., Lokugamage K.G., Rozovics J.M., Narayanan K., Semler B.L., Makino S.
    J. Virol. 85:638-643(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF NSP1.
  5. "Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain."
    Anand K., Palm G.J., Mesters J.R., Siddell S.G., Ziebuhr J., Hilgenfeld R.
    EMBO J. 21:3213-3224(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF 2879-3180.
  6. "Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs."
    Anand K., Ziebuhr J., Wadhwani P., Mesters J.R., Hilgenfeld R.
    Science 300:1763-1767(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) OF 2879-3180 COMPLEXED WITH THE SUBSTRATE-ANALOG HEXAPEPTIDYL CMK.

Entry informationi

Entry nameiR1AB_CVPPU
AccessioniPrimary (citable) accession number: P0C6Y5
Secondary accession number(s): Q88508, Q9IW05, Q9IW06
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: June 10, 2008
Last modified: November 26, 2014
This is version 55 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3