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P0C6Y5

- R1AB_CVPPU

UniProt

P0C6Y5 - R1AB_CVPPU

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Protein

Replicase polyprotein 1ab

Gene
rep, 1a-1b
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.1 Publication
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.1 Publication
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.1 Publication
Nsp9 is a ssRNA-binding protein By similarity.1 Publication
NendoU is a Mn2+-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond By similarity.1 Publication

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-PRO By similarity
Sitei879 – 8802Cleavage; by PL1-PRO By similarity
Active sitei1093 – 10931For PL1-PRO activity By similarity
Active sitei1244 – 12441For PL1-PRO activity By similarity
Active sitei1588 – 15881For PL2-PRO activity By similarity
Active sitei1741 – 17411For PL2-PRO activity By similarity
Sitei2388 – 23892Cleavage; by PL2-PRO By similarity
Sitei2878 – 28792Cleavage; by 3CL-PRO By similarity
Active sitei2919 – 29191For 3CL-PRO activity By similarity
Active sitei3022 – 30221For 3CL-PRO activity By similarity
Sitei3180 – 31812Cleavage; by 3CL-PRO By similarity
Sitei3474 – 34752Cleavage; by 3CL-PRO By similarity
Sitei3557 – 35582Cleavage; by 3CL-PRO By similarity
Sitei3752 – 37532Cleavage; by 3CL-PRO By similarity
Sitei3863 – 38642Cleavage; by 3CL-PRO By similarity
Sitei3998 – 39992Cleavage; by 3CL-PRO By similarity
Sitei4927 – 49282Cleavage; by 3CL-PRO By similarity
Sitei5526 – 55272Cleavage; by 3CL-PRO By similarity
Sitei6045 – 60462Cleavage; by 3CL-PRO By similarity
Sitei6384 – 63852Cleavage; by 3CL-PRO By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1164 – 119532C4-typeAdd
BLAST
Zinc fingeri3937 – 395317 By similarityAdd
BLAST
Zinc fingeri3979 – 399214 By similarityAdd
BLAST
Nucleotide bindingi5210 – 52178ATP By 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.
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.
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.
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.
Chain Helicase : Host endoplasmic reticulum-Golgi intermediate compartment Reviewed prediction
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 – 191621Helical; Reviewed predictionAdd
BLAST
Transmembranei1995 – 201521Helical; Reviewed predictionAdd
BLAST
Transmembranei2033 – 205321Helical; Reviewed predictionAdd
BLAST
Transmembranei2401 – 242121Helical; Reviewed predictionAdd
BLAST
Transmembranei2467 – 248721Helical; Reviewed predictionAdd
BLAST
Transmembranei2497 – 251721Helical; Reviewed predictionAdd
BLAST
Transmembranei2538 – 255821Helical; Reviewed predictionAdd
BLAST
Transmembranei2666 – 268621Helical; Reviewed predictionAdd
BLAST
Transmembranei2695 – 271521Helical; Reviewed predictionAdd
BLAST
Transmembranei2721 – 274121Helical; Reviewed predictionAdd
BLAST
Transmembranei2746 – 276621Helical; Reviewed predictionAdd
BLAST
Transmembranei3187 – 320721Helical; Reviewed predictionAdd
BLAST
Transmembranei3217 – 323721Helical; Reviewed predictionAdd
BLAST
Transmembranei3242 – 326221Helical; Reviewed predictionAdd
BLAST
Transmembranei3280 – 330021Helical; Reviewed predictionAdd
BLAST
Transmembranei3313 – 333321Helical; Reviewed predictionAdd
BLAST
Transmembranei3347 – 336721Helical; Reviewed predictionAdd
BLAST
Transmembranei3371 – 339121Helical; Reviewed predictionAdd
BLAST
Transmembranei3394 – 341421Helical; Reviewed predictionAdd
BLAST

GO - Cellular componenti

  1. host cell endoplasmic reticulum-Golgi intermediate compartment Source: UniProtKB-SubCell
  2. host cell membrane Source: UniProtKB-SubCell
  3. host cell perinuclear region of cytoplasm Source: UniProtKB-SubCell
  4. 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 1 By similarityPRO_0000037386Add
BLAST
Chaini111 – 879769Non-structural protein 2 By similarityPRO_0000037387Add
BLAST
Chaini880 – 23881509Non-structural protein 3 By similarityPRO_0000037388Add
BLAST
Chaini2389 – 2878490Non-structural protein 4 By similarityPRO_0000037389Add
BLAST
Chaini2879 – 31803023C-like proteinasePRO_0000037390Add
BLAST
Chaini3181 – 3474294Non-structural protein 6 By similarityPRO_0000037391Add
BLAST
Chaini3475 – 355783Non-structural protein 7 By similarityPRO_0000037392Add
BLAST
Chaini3558 – 3752195Non-structural protein 8 By similarityPRO_0000037393Add
BLAST
Chaini3753 – 3863111Non-structural protein 9PRO_0000037394Add
BLAST
Chaini3864 – 3998135Non-structural protein 10 By similarityPRO_0000037395Add
BLAST
Chaini3999 – 4927929RNA-directed RNA polymerase By similarityPRO_0000037396Add
BLAST
Chaini4928 – 5526599Helicase By similarityPRO_0000037397Add
BLAST
Chaini5527 – 6045519Exoribonuclease By similarityPRO_0000037398Add
BLAST
Chaini6046 – 6384339Uridylate-specific endoribonuclease By similarityPRO_0000037399Add
BLAST
Chaini6385 – 6684300Putative 2'-O-methyl transferase By similarityPRO_0000037400Add
BLAST

Post-translational modificationi

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

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.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiP0C6Y5.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1055 – 1299245Peptidase C16 1Add
BLAST
Domaini1318 – 1489172MacroAdd
BLAST
Domaini1550 – 1803254Peptidase C16 2Add
BLAST
Domaini2879 – 3180302Peptidase C30Add
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.

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

MSSKQFKILV NEDYQVNVPS LPIRDVLQEI KYCYRNGFEG YVFVPEYCRD     50
LVDCDRKDHY VIGVLGNGVS DLKPVLLTEP SVMLQGFIVR ANCNGVLEDF 100
DLKIARTGRG AIYVDQYMCG ADGKPVIEGD FKDYFGDEDI IEFEGEEYHC 150
AWTTVRDEKP LNQQTLFTIQ EIQYNLDIPH KLPNCATRHV APPVKKNSKI 200
VLSEDYKKLY DIFGSPFMGN GDCLSKCFDT LHFIAATLRC PCGSESSGVG 250
DWTGFKTACC GLSGKVKGVT LGDIKPGDAV VTSMSAGKGV KFFANCVLQY 300
AGDVEGVSIW KVIKTFTVDE TVCTPGFEGE LNDFIKPESK SLVACSVKRA 350
FITGDIDDAV HDCIITGKLD LSTNLFGNVG LLFKKTPWFV QKCGALFVDA 400
WKVVEELCGS LTLTYKQIYE VVASLCTSAF TIVNYKPTFV VPDNRVKDLV 450
DKCVKVLVKA FDVFTQIITI AGIEAKCFVL GAKYLLFNNA LVKLVSVKIL 500
GKKQKGLECA FFATSLVGAT VNVTPKRTET ATISLNKVDD VVAPGEGYIV 550
IVGDMAFYKS GEYYFMMSSP NFVLTNNVFK AVKVPSYDIV YDVDNDTKSK 600
MIAKLGSSFE YDGDIDAAIV KVNELLIEFR QQSLCFRAFK DDKSIFVEAY 650
FKKYKMPACL AKHIGLWNII KKDSCKRGFL NLFNHLNELE DIKETNIQAI 700
KNILCPDPLL DLDYGAIWYN CMPGCSDPSV LGSVQLLIGN GVKVVCDGCK 750
GFANQLSKGY NKLCNAARND IEIGGIPFST FKTPTNTFIE MTDAIYSVIE 800
QGKALSFRDA DVPVVDNGTI STADWSEPIL LEPAEYVKPK NNGNVIVIAG 850
YTFYKDEDEH FYPYGFGKIV QRMYNKMGGG DKTVSFSEEV DVQEIAPVTR 900
VKLEFEFDNE IVTGVLERAI GTRYKFTGTT WEEFEESISE ELDAIFDTLA 950
NQGVELEGYF IYDTCGGFDI KNPDGIMISQ YDINITADEK SEVSASSEEE 1000
EVESVEEDPE NEIVEASEGA EGTSSQEEVE TVEVADITST EEDVDIVEVS 1050
AKDDPWAAAV DVQEAEQFNP SLPPFKTTNL NGKIILKQGD NNCWINACCY 1100
QLQAFDFFNN EAWEKFKKGD VMDFVNLCYA ATTLARGHSG DAEYLLELML 1150
NDYSTAKIVL AAKCGCGEKE IVLERAVFKL TPLKESFNYG VCGDCMQVNT 1200
CRFLSVEGSG VFVHDILSKQ TPEAMFVVKP VMHAVYTGTT QNGHYMVDDI 1250
EHGYCVDGMG IKPLKKRCYT STLFINANVM TRAEKPKQEF KVEKVEQQPI 1300
VEENKSSIEK EEIQSPKNDD LILPFYKAGK LSFYQGALDV LINFLEPDVI 1350
VNAANGDLKH MGGVARAIDV FTGGKLTERS KDYLKKNKSI APGNAVFFEN 1400
VIEHLSVLNA VGPRNGDSRV EAKLCNVYKA IAKCEGKILT PLISVGIFNV 1450
RLETSLQCLL KTVNDRGLNV FVYTDQERQT IENFFSCSIP VNVTEDNVNH 1500
ERVSVSFDKT YGEQLKGTVV IKDKDVTNQL PSAFDVGQKV IKAIDIDWQA 1550
HYGFRDAAAF SASSHDAYKF EVVTHSNFIV HKQTDNNCWI NAICLALQRL 1600
KPQWKFPGVR GLWNEFLERK TQGFVHMLYH ISGVKKGEPG DAELMLHKLG 1650
DLMDNDCEII VTHTTACDKC AKVEKFVGPV VAAPLAIHGT DETCVHGVSV 1700
NVKVTQIKGT VAITSLIGPI IGEVLEATGY ICYSGSNRNG HYTYYDNRNG 1750
LVVDAEKAYH FNRDLLQVTT AIASNFVVKK PQAEERPKNC AFNKVAASPK 1800
IVQEQKLLAI ESGANYALTE FGRYADMFFM AGDKILRLLL EVFKYLLVLF 1850
MCLRSTKMPK VKVKPPLAFK DFGAKVRTLN YMRQLNKPSV WRYAKLVLLL 1900
IAIYNFFYLF VSIPVVHKLT CNGAVQAYKN SSFIKSAVCG NSILCKACLA 1950
SYDELADFQH LQVTWDFKSD PLWNRLVQLS YFAFLAVFGN NYVRCFLMYF 2000
VSQYLNLWLS YFGYVEYSWF LHVVNFESIS AEFVIVVIVV KAVLALKHIV 2050
FACSNPSCKT CSRTARQTRI PIQVVVNGSM KTVYVHANGT GKFCKKHNFY 2100
CKNCDSYGFE NTFICDEIVR DLSNSVKQTV YATDRSHQEV TKVECSDGFY 2150
RFYVGDEFTS YDYDVKHKKY SSQEVLKSML LLDDFIVYSP SGSALANVRN 2200
ACVYFSQLIG KPIKIVNSDL LEDLSVDFKG ALFNAKKNVI KNSFNVDVSE 2250
CKNLDECYRA CNLNVSFSTF EMAVNNAHRF GILITDRSFN NFWPSKVKPG 2300
SSGVSAMDIG KCMTSDAKIV NAKVLTQRGK SVVWLSQDFA ALSSTAQKVL 2350
VKTFVEEGVN FSLTFNAVGS DDDLPYERFT ESVSPKSGSG FFDVITQLKQ 2400
IVILVFVFIF ICGLCSVYSV ATQSYIESAE GYDYMVIKNG IVQPFDDTIS 2450
CVHNTYKGFG DWFKAKYGFI PTFGKSCPIV VGTVFDLENM RPIPDVPAYV 2500
SIVGRSLVFA INAAFGVTNM CYDHTGNAVS KDSYFDTCVF NTACTTLTGL 2550
GGTIVYCAKQ GLVEGAKLYS DLMPDYYYEH ASGNMVKLPA IIRGLGLRFV 2600
KTQATTYCRV GECIDSKAGF CFGGDNWFVY DNEFGNGYIC GNSVLGFFKN 2650
VFKLFNSNMS VVATSGAMLV NIIIACLAIA MCYGVLKFKK IFGDCTFLIV 2700
MIIVTLVVNN VSYFVTQNTF FMIIYAIVYY FITRKLAYPG ILDAGFIIAY 2750
INMAPWYVIT AYILVFLYDS LPSLFKLKVS TNLFEGDKFV GNFESAAMGT 2800
FVIDMRSYET IVNSTSIARI KSYANSFNKY KYYTGSMGEA DYRMACYAHL 2850
GKALMDYSVN RTDMLYTPPT VSVNSTLQSG LRKMAQPSGL VEPCIVRVSY 2900
GNNVLNGLWL GDEVICPRHV IASDTTRVIN YENEMSSVRL HNFSVSKNNV 2950
FLGVVSARYK GVNLVLKVNQ VNPNTPEHKF KSIKAGESFN ILACYEGCPG 3000
SVYGVNMRSQ GTIKGSFIAG TCGSVGYVLE NGILYFVYMH HLELGNGSHV 3050
GSNFEGEMYG GYEDQPSMQL EGTNVMSSDN VVAFLYAALI NGERWFVTNT 3100
SMSLESYNTW AKTNSFTELS STDAFSMLAA KTGQSVEKLL DSIVRLNKGF 3150
GGRTILSYGS LCDEFTPTEV IRQMYGVNLQ AGKVKSFFYP IMTAMTILFA 3200
FWLEFFMYTP FTWINPTFVS IVLAVTTLIS TVFVSGIKHK MLFFMSFVLP 3250
SVILVTAHNL FWDFSYYESL QSIVENTNTM FLPVDMQGVM LTVFCFIVFV 3300
TYSVRFFTCK QSWFSLAVTT ILVIFNMVKI FGTSDEPWTE NQIAFCFVNM 3350
LTMIVSLTTK DWMVVIASYR IAYYIVVCVM PSAFVSDFGF MKCISIVYMA 3400
CGYLFCCYYG ILYWVNRFTC MTCGVYQFTV SAAELKYMTA NNLSAPKNAY 3450
DAMILSAKLI GVGGKRNIKI STVQSKLTEM KCTNVVLLGL LSKMHVESNS 3500
KEWNYCVGLH NEINLCDDPE IVLEKLLALI AFFLSKHNTC DLSELIESYF 3550
ENTTILQSVA SAYAALPSWI ALEKARADLE EAKKNDVSPQ ILKQLTKAFN 3600
IAKSDFEREA SVQKKLDKMA EQAAASMYKE ARAVDRKSKI VSAMHSLLFG 3650
MLKKLDMSSV NTIIDQARNG VLPLSIIPAA SATRLVVITP SLEVFSKIRQ 3700
ENNVHYAGAI WTIVEVKDAN GSHVHLKEVT AANELNLTWP LSITCERTTK 3750
LQNNEIMPGK LKERAVRASA TLDGEAFGSG KALMASESGK SFMYAFIASD 3800
NNLKYVKWES NNDIIPIELE APLRFYVDGA NGPEVKYLYF VKNLNTLRRG 3850
AVLGYIGATV RLQAGKPTEH PSNSSLLTLC AFSPDPAKAY VDAVKRGMQP 3900
VNNCVKMLSN GAGNGMAVTN GVEANTQQDS YGGASVCIYC RCHVEHPAID 3950
GLCRYKGKFV QIPTGTQDPI RFCIENEVCV VCGCWLNNGC MCDRTSMQSF 4000
TVDQSYLNRV RGSSAARLEP CNGTDPDHVS RAFDIYNKDV ACIGKFLKTN 4050
CSRFRNLDKH DAYYIVKRCT KTVMDHEQVC YNDLKDSGAV AEHDFFTYKE 4100
GRCEFGNVAR RNLTKYTMMD LCYAIRNFDE KNCEVLKEIL VTVGACTEEF 4150
FENKDWFDPV ENEAIHEVYA KLGPIVANAM LKCVAFCDAI VEKGYIGVIT 4200
LDNQDLNGNF YDFGDFVKTA PGFGCACVTS YYSYMMPLMG MTSCLESENF 4250
VKSDIYGSDY KQYDLLAYDF TEHKEYLFQK YFKYWDRTYH PNCSDCTSDE 4300
CIIHCANFNT LFSMTIPMTA FGPLVRKVHI DGVPVVVTAG YHFKQLGIVW 4350
NLDVKLDTMK LSMTDLLRFV TDPTLLVASS PALLDQRTVC FSIAALSTGI 4400
TYQTVKPGHF NKDFYDFITE RGFFEEGSEL TLKHFFFAQG GEAAMTDFNY 4450
YRYNRVTVLD ICQAQFVYKI VGKYFECYDG GCINAREVVV TNYDKSAGYP 4500
LNKFGKARLY YETLSYEEQD ALFALTKRNV LPTMTQMNLK YAISGKARAR 4550
TVGGVSLLST MTTRQYHQKH LKSIAATRNA TVVIGSTKFY GGWDNMLKNL 4600
MRDVDNGCLM GWDYPKCDRA LPNMIRMASA MILGSKHVGC CTHNDRFYRL 4650
SNELAQVLTE VVHCTGGFYF KPGGTTSGDG TTAYANSAFN IFQAVSANVN 4700
KLLGVDSNAC NNVTVKSIQR KIYDNCYRSS SIDEEFVVEY FSYLRKHFSM 4750
MILSDDGVVC YNKDYADLGY VADINAFKAT LYYQNNVFMS TSKCWVEPDL 4800
SVGPHEFCSQ HTLQIVGPDG DYYLPYPDPS RILSAGVFVD DIVKTDNVIM 4850
LERYVSLAID AYPLTKHPKP AYQKVFYTLL DWVKHLQKNL NAGVLDSFSV 4900
TMLEEGQDKF WSEEFYASLY EKSTVLQAAG MCVVCGSQTV LRCGDCLRRP 4950
LLCTKCAYDH VMGTKHKFIM SITPYVCSFN GCNVNDVTKL FLGGLSYYCM 5000
NHKPQLSFPL CANGNVFGLY KSSAVGSEAV EDFNKLAVSD WTNVEDYKLA 5050
NNVKESLKIF AAETVKAKEE SVKSEYAYAV LKEVIGPKEI VLQWEASKTK 5100
PPLNRNSVFT CFQISKDTKI QLGEFVFEQS EYGSDSVYYK STSTYKLTPG 5150
MIFVLTSHNV SPLKAPILVN QEKYNTISKL YPVFNIAEAY NTLVPYYQMI 5200
GKQKFTTIQG PPGSGKSHCV IGLGLYYPQA RIVYTACSHA AVDALCEKAA 5250
KNFNVDRCSR IIPQRIRVDC YTGFKPNNTN AQYLFCTVNA LPEASCDIVV 5300
VDEVSMCTNY DLSVINSRLS YKHIVYVGDP QQLPAPRTLI NKGVLQPQDY 5350
NVVTKRMCTL GPDVFLHKCY RCPAEIVKTV SALVYENKFV PVNPESKQCF 5400
KMFVKGQVQI ESNSSINNKQ LEVVKAFLAH NPKWRKAVFI SPYNSQNYVA 5450
RRLLGLQTQT VDSAQGSEYD YVIYTQTSDT QHATNVNRFN VAITRAKVGI 5500
LCIMCDRTMY ENLDFYELKD SKIGLQAKPE TCGLFKDCSK SEQYIPPAYA 5550
TTYMSLSDNF KTSDGLAVNI GTKDVKYANV ISYMGFRFEA NIPGYHTLFC 5600
TRDFAMRNVR AWLGFDVEGA HVCGDNVGTN VPLQLGFSNG VDFVVQTEGC 5650
VITEKGNSIE VVKARAPPGE QFAHLIPLMR KGQPWHIVRR RIVQMVCDYF 5700
DGLSDILIFV LWAGGLELTT MRYFVKIGRP QKCECGKSAT CYSSSQSVYA 5750
CFKHALGCDY LYNPYCIDIQ QWGYTGSLSM NHHEVCNIHR NEHVASGDAI 5800
MTRCLAIHDC FVKRVDWSIV YPFIDNEEKI NKAGRIVQSH VMKAALKIFN 5850
PAAIHDVGNP KGIRCATTPI PWFCYDRDPI NNNVRCLDYD YMVHGQMNGL 5900
MLFWNCNVDM YPEFSIVCRF DTRTRSKLSL EGCNGGALYV NNHAFHTPAY 5950
DRRAFAKLKP MPFFYYDDSN CELVDGQPNY VPLKSNVCIT KCNIGGAVCK 6000
KHAALYRAYV EDYNIFMQAG FTIWCPQNFD TYMLWHGFVN SKALQSLENV 6050
AFNVVKKGAF TGLKGDLPTA VIADKIMVRD GPTDKCIFTN KTSLPTNVAF 6100
ELYAKRKLGL TPPLTILRNL GVVATYKFVL WDYEAERPFS NFTKQVCSYT 6150
DLDSEVVTCF DNSIAGSFER FTTTRDAVLI SNNAVKGLSA IKLQYGLLND 6200
LPVSTVGNKP VTWYIYVRKN GEYVEQIDSY YTQGRTFETF KPRSTMEEDF 6250
LSMDTTLFIQ KYGLEDYGFE HVVFGDVSKT TIGGMHLLIS QVRLAKMGLF 6300
SVQEFMNNSD STLKSCCITY ADDPSSKNVC TYMDILLDDF VTIIKSLDLN 6350
VVSKVVDVIV DCKAWRWMLW CENSHIKTFY PQLQSAEWNP GYSMPTLYKI 6400
QRMCLERCNL YNYGAQVKLP DGITTNVVKY TQLCQYLNTT TLCVPHKMRV 6450
LHLGAAGASG VAPGSTVLRR WLPDDAILVD NDLRDYVSDA DFSVTGDCTS 6500
LYIEDKFDLL VSDLYDGSTK SIDGENTSKD GFFTYINGFI KEKLSLGGSV 6550
AIKITEFSWN KDLYELIQRF EYWTVFCTSV NTSSSEGFLI GINYLGPYCD 6600
KAIVDGNIMH ANYIFWRNST IMALSHNSVL DTPKFKCRCN NALIVNLKEK 6650
ELNEMVIGLL RKGKLLIRNN GKLLNFGNHF VNTP 6684

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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
Z34093 mRNA. No translation available.
AJ271965 Genomic RNA. Translation: CAB91143.1 . Sequence problems.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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: June 11, 2014
This is version 52 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

Similar proteinsi