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Q98VG9

- R1AB_FIPV

UniProt

Q98VG9 - R1AB_FIPV

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Protein

Replicase polyprotein 1ab

Gene
rep, 1a-1b
Organism
Feline coronavirus (strain FIPV WSU-79/1146) (FCoV)
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.
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.
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 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 sitei1117 – 11171For PL1-PRO activity By similarity
Active sitei1268 – 12681For PL1-PRO activity By similarity
Active sitei1599 – 15991For PL2-PRO activity By similarity
Active sitei1752 – 17521For PL2-PRO activity By similarity
Sitei2413 – 24142Cleavage; by PL2-PRO By similarity
Sitei2903 – 29042Cleavage; by 3CL-PRO By similarity
Active sitei2944 – 29441For 3CL-PRO activity
Active sitei3047 – 30471For 3CL-PRO activity
Sitei3053 – 30531Important for substrate recognition
Sitei3205 – 32062Cleavage; by 3CL-PRO By similarity
Sitei3499 – 35002Cleavage; by 3CL-PRO By similarity
Sitei3582 – 35832Cleavage; by 3CL-PRO By similarity
Sitei3777 – 37782Cleavage; by 3CL-PRO By similarity
Sitei3888 – 38892Cleavage; by 3CL-PRO By similarity
Sitei4023 – 40242Cleavage; by 3CL-PRO By similarity
Sitei4952 – 49532Cleavage; by 3CL-PRO By similarity
Sitei5551 – 55522Cleavage; by 3CL-PRO By similarity
Sitei6070 – 60712Cleavage; by 3CL-PRO By similarity
Sitei6409 – 64102Cleavage; by 3CL-PRO By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1188 – 121932C4-type 1 By similarityAdd
BLAST
Zinc fingeri1678 – 170730C4-type 2; atypical By similarityAdd
BLAST
Zinc fingeri3962 – 397817 By similarityAdd
BLAST
Zinc fingeri4004 – 401714 By similarityAdd
BLAST
Nucleotide bindingi5235 – 52428ATP 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

Protein family/group databases

MEROPSiC30.004.

Names & Taxonomyi

Protein namesi
Recommended name:
Replicase polyprotein 1ab
Short name:
pp1ab
Alternative name(s):
ORF1ab polyprotein
Cleaved into the following 16 chains:
Non-structural protein 1
Short name:
nsp1
Non-structural protein 2
Short name:
nsp2
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
Non-structural protein 6
Short name:
nsp6
Non-structural protein 7
Short name:
nsp7
Non-structural protein 8
Short name:
nsp8
Non-structural protein 9
Short name:
nsp9
Non-structural protein 10
Short name:
nsp10
Non-structural protein 11
Short name:
nsp11
RNA-directed RNA polymerase (EC:2.7.7.48)
Short name:
Pol
Short name:
RdRp
Alternative name(s):
nsp12
Helicase (EC:3.6.4.12, EC:3.6.4.13)
Short name:
Hel
Alternative name(s):
nsp13
Exoribonuclease (EC:3.1.13.-)
Short name:
ExoN
Alternative name(s):
nsp14
Alternative name(s):
NendoU
nsp15
Alternative name(s):
nsp16
Gene namesi
Name:rep
ORF Names:1a-1b
OrganismiFeline coronavirus (strain FIPV WSU-79/1146) (FCoV)
Taxonomic identifieri33734 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageNidoviralesCoronaviridaeCoronavirinaeAlphacoronavirus
Virus hostiFelidae (cat family) [TaxID: 9681]
ProteomesiUP000000835: 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
Transmembranei1860 – 187819Helical; Reviewed predictionAdd
BLAST
Transmembranei1921 – 194121Helical; Reviewed predictionAdd
BLAST
Transmembranei2006 – 202621Helical; Reviewed predictionAdd
BLAST
Transmembranei2043 – 206523Helical; Reviewed predictionAdd
BLAST
Transmembranei2426 – 244621Helical; Reviewed predictionAdd
BLAST
Transmembranei2691 – 271121Helical; Reviewed predictionAdd
BLAST
Transmembranei2720 – 274021Helical; Reviewed predictionAdd
BLAST
Transmembranei2771 – 279121Helical; Reviewed predictionAdd
BLAST
Transmembranei3212 – 323221Helical; Reviewed predictionAdd
BLAST
Transmembranei3242 – 326221Helical; Reviewed predictionAdd
BLAST
Transmembranei3267 – 328721Helical; Reviewed predictionAdd
BLAST
Transmembranei3306 – 332621Helical; Reviewed predictionAdd
BLAST
Transmembranei3339 – 335921Helical; Reviewed predictionAdd
BLAST
Transmembranei3396 – 341621Helical; Reviewed predictionAdd
BLAST
Transmembranei3419 – 343921Helical; 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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi2944 – 29441H → Y or R: Complete loss of 3CL-PRO activity. 1 Publication
Mutagenesisi2967 – 29671N → A or D: Increase of 3CL-PRO activity. 1 Publication
Mutagenesisi2986 – 29861G → A: 5% loss of 3CL-PRO activity. 1 Publication
Mutagenesisi2986 – 29861G → D: Increase of 3CL-PRO activity. 1 Publication
Mutagenesisi2986 – 29861G → E: 50% loss of 3CL-PRO activity. 1 Publication
Mutagenesisi2986 – 29861G → P or V: 95% loss of 3CL-PRO activity. 1 Publication
Mutagenesisi2986 – 29861G → R, T or W: 70% loss of 3CL-PRO activity. 1 Publication
Mutagenesisi3041 – 30411S → A: 80% loss of 3CL-PRO activity. 1 Publication
Mutagenesisi3041 – 30411S → T: 40% loss of 3CL-PRO activity. 1 Publication
Mutagenesisi3047 – 30471C → A or S: Complete loss of 3CL-PRO activity. 1 Publication
Mutagenesisi3063 – 30631Y → A, F, G or T: Almost complete loss of 3CL-PRO activity. 1 Publication
Mutagenesisi3064 – 30641M → A: Increase of 3CL-PRO activity. 1 Publication
Mutagenesisi3065 – 30651H → A: Complete loss of 3CL-PRO activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 67096709Replicase polyprotein 1abPRO_0000283825Add
BLAST
Chaini1 – 110110Non-structural protein 1 By similarityPRO_5000140208Add
BLAST
Chaini111 – 879769Non-structural protein 2 By similarityPRO_5000140209Add
BLAST
Chaini880 – 24131534Non-structural protein 3 By similarityPRO_5000140210Add
BLAST
Chaini2414 – 2903490Non-structural protein 4 By similarityPRO_5000140211Add
BLAST
Chaini2904 – 32053023C-like proteinase By similarityPRO_5000140212Add
BLAST
Chaini3206 – 3499294Non-structural protein 6 By similarityPRO_5000140213Add
BLAST
Chaini3500 – 358283Non-structural protein 7 By similarityPRO_5000140214Add
BLAST
Chaini3583 – 3777195Non-structural protein 8 By similarityPRO_5000140215Add
BLAST
Chaini3778 – 3888111Non-structural protein 9 By similarityPRO_5000140216Add
BLAST
Chaini3889 – 4023135Non-structural protein 10 By similarityPRO_5000140217Add
BLAST
Chaini4024 – 4952929RNA-directed RNA polymerase By similarityPRO_5000140219Add
BLAST
Chaini4024 – 404219Non-structural protein 11 By similarityPRO_5000140218Add
BLAST
Chaini4953 – 5551599Helicase By similarityPRO_5000140220Add
BLAST
Chaini5552 – 6070519Exoribonuclease Reviewed predictionPRO_5000140221Add
BLAST
Chaini6071 – 6409339Uridylate-specific endoribonuclease Reviewed predictionPRO_5000140222Add
BLAST
Chaini6410 – 6709300Putative 2'-O-methyl transferase Reviewed predictionPRO_5000140223Add
BLAST

Post-translational modificationi

Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed By similarity.

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
6709
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1336 – 13394
Beta strandi1342 – 13476
Helixi1349 – 13568
Beta strandi1359 – 13657
Helixi1376 – 13827
Turni1383 – 13853
Helixi1386 – 139510
Beta strandi1405 – 14139
Beta strandi1416 – 14227
Helixi1431 – 144313
Beta strandi1449 – 14513
Helixi1463 – 147311
Beta strandi1479 – 14835
Helixi1486 – 149712
Helixi2818 – 28236
Beta strandi2826 – 28283
Helixi2830 – 28378
Turni2838 – 28403
Helixi2842 – 28509
Helixi2852 – 28565
Helixi2864 – 288421
Beta strandi2889 – 28913
Beta strandi2895 – 28995
Helixi3510 – 35189
Helixi3521 – 35233
Helixi3525 – 354016
Helixi3544 – 356118
Helixi3568 – 357710
Helixi3579 – 35813
Beta strandi3583 – 35853
Helixi3587 – 360923
Helixi3614 – 365239
Helixi3663 – 368018
Helixi3683 – 369311
Beta strandi3697 – 37026
Beta strandi3709 – 37146
Helixi3717 – 37237
Beta strandi3728 – 37314
Beta strandi3734 – 37429
Helixi3751 – 37533
Helixi3756 – 37616
Beta strandi3766 – 37727

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3ETIX-ray2.20A/B/C/D/E/F/G/H1331-1498[»]
3EW5X-ray3.10A/B/C1331-1498[»]
3GZFX-ray2.76A/B/C/D/E2808-2902[»]
3JZTX-ray3.91A/B/C/D/E/F/G/H1331-1498[»]
3UB0X-ray2.60A/D3583-3777[»]
B/C/E/F3500-3582[»]
ProteinModelPortaliQ98VG9.
SMRiQ98VG9. Positions 2904-3204, 3894-4019.

Miscellaneous databases

EvolutionaryTraceiQ98VG9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1079 – 1330252Peptidase C16 1Add
BLAST
Domaini1329 – 1500172MacroAdd
BLAST
Domaini1561 – 1814254Peptidase C16 2Add
BLAST
Domaini2904 – 3205302Peptidase C30Add
BLAST
Domaini4632 – 4794163RdRp catalyticAdd
BLAST
Domaini4953 – 503684CV MBDAdd
BLAST
Domaini5200 – 5391192(+)RNA virus helicase ATP-bindingAdd
BLAST
Domaini5392 – 5561170(+)RNA virus helicase C-terminalAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1860 – 2065206HD1 By similarityAdd
BLAST
Regioni2426 – 2791366HD2 By similarityAdd
BLAST
Regioni3212 – 3439228HD3 By similarityAdd
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 By similarity.

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: Q98VG9-1) [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.

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MSSKQFKILV NEDYQVNVPS LPFRDALQEI KYCYRNGFDG YVFVPEYRRD     50
LVDCNRKDHY VIGVLGNGIS DLKPVLLTEP SVMLQGFIVR ANCNGVLEDF 100
DLKFARTGNG AIYVDQYMCG ADGKPVIEGE FKDYFGDEDV IIYEGEEYHC 150
AWLTVRDEKP LWQQTLLTIR EIQYNLDIPH KLPNCAIREV APPVKKNSKV 200
VLSEEYRKLY DIFGSPFMGN GDSLNTCFDS LHFIAATLKC PCGAESSGVG 250
DWTGFKTACC GLHGKVKGVT LGAVKPGDAI VTSMSAGKGV KFFANSVLQY 300
AGDVENVSVW KVIKTFTVNE TVCTTDFEGE LNDFIRPEST SPVSCSIKRA 350
FITGEVDDAV HDCIIAGKLD LSTNLFGSAN LLFKKMPWFV QKCGAIFADA 400
WKVVEELLCS LKLTYKQIYD VVASLCTSAF TIMDYKPVFV VSSNSVKDLV 450
DKCVKILVKA FDVFTQTITI AGVEAKCFVL GSKYLLFNNA LVKLVSVKIL 500
GKRQKGLDSA FFATNLIGAT VNVTPQRTES AYISLNKVDD VVTPGGGHIV 550
IIGDMAFYKS EEYYFMMASP DSVLVNNVFK AARVPSYNIV YDVNDDTKSK 600
MVVKIGTSFD FDGDLDAAIA KVNDLLIEFR QEKLCFRALK DGENILVEAY 650
LKKYKMPVCL KNHVGLWDII RQDSGKKGFL DTFNHLNELE DVKDIKIQTI 700
KNIICPDLLL ELDFGAIWYR CMPACSDKSI LGNVKIMLGN GVKVVCDGCH 750
SFANRLTINY NKLCDTARKD IEIGGIPFST FKTPSSSFID MKDAIYSVVE 800
YGEALSFKTA SVPVTNSGII TTDDWSDPIL LEPADYVEPK DNGDVIVIAG 850
YTFYKDEDDH FYPYGSGMVV QKMYNKMGGG DKSVSFSDNV NVREIEPVTR 900
VRLEFEFDNE VVTQVLEKVI GTKYKFIGTT WEEFEDSISE KLDKIFDTLA 950
EQGVELEGYF IYDTCGGFDI NNPDGVMISQ YDLNTAADDK SDSDASVEDI 1000
SLISDNEDVE QIEEDNTSTD DAEDVSSVEG ETVSVVDVED FVEQVSLVEE 1050
NNVLTPAVNP DEQLSSVEKK DEVSAKNDPW AAAVDEQEAE QPKPSLTPFK 1100
TTNLNGKIIL KQQDNNCWIN ACCYQLQAFD FFNHDLWDGF KKDDVMPFVD 1150
FCYAALTLKQ GDSGDAEYLL ETMLNDYSTA KVTLSAKCGC GVKEIVLERT 1200
VFKLTPLRNE FKYGVCGDCK QINMCKFASV EGSGVFVHDR IEKQTPVSQF 1250
IVTPTMHAVY TGTTQSGHYM IEDCIHDYCV DGMGIKPRKH KFYTSTLFLN 1300
ANVMTAKSKT MVEPPVPVED KCVEDCQSPK DLILPFYKAG KVSFYQGDLD 1350
VLINFLEPDV LVNAANGDLR HVGGVARAID VFTGGKLTKR SKEYLKSSKA 1400
IAPGNAVLFE NVLEHLSVLN AVGPRNGDSR VEGKLCNVYK AIAKCDGKIL 1450
TPLISVGIFK VKLEVSLQCL LKTVTDRDLN VFVYTDQERV TIENFFNGTI 1500
PIKVTEDTVN QKRVSVALDK TYGEQLKGTV VIKDKDVTNQ LPSVSDVGEK 1550
VVKALDVDWN AYYGFPNAAA FSASSHDAYE FDVVTHNNFI VHKQTDNNCW 1600
VNAICLALQR LKPTWKFPGV KSLWDAFLTR KTAGFVHMLY HISGLTKGQP 1650
GDAELTLHKL VDLMSSDSAV TVTHTTACDK CAKVETFTGP VVAAPLLVCG 1700
TDEICVHGVH VNVKVTSIRG TVAITSLIGP VVGDVIDATG YICYTGLNSR 1750
GHYTYYDNRN GLMVDADKAY HFEKNLLQVT TAIASNFVAN TPKKEIMPKT 1800
QAKESKAKES NTARVFSEVE ENPKNIVRKE KLLAIESGVD YTITTLGKYA 1850
DVFFMAGDKI LRFLLEVFKY LLVVFMCLRK SKMPKVKVKP PHVFRNLGAK 1900
VRTLNYVRQL NKPALWRYIK LVLLLIALYH FFYLFVSIPV VHKLACSGSV 1950
QAYSNSSFVK SEVCGNSILC KACLASYDEL ADFDHLQVSW DYKSDPLWNR 2000
VIQLSYFIFL AVFGNNYVRC LLMYFVSQYL NLWLSYFGYV KYSWFLHVVN 2050
FESISVEFVI IVVVFKAVLA LKHIFLPCNN PSCKTCSKIA RQTRIPIQVV 2100
VNGSMKTVYV HANGTGKLCK KHNFYCKNCD SYGFDHTFIC DEIVRDLSNS 2150
IKQTVYATDR SYQEVTKVEC TDGFYRFYVG EEFTAYDYDV KHKKYSSQEV 2200
LKTMFLLDDF IVYNPSGSSL ASVRNVCVYF SQLIGRPIKI VNSELLEDLS 2250
VDFKGALFNA KKNVIKNSFN VDVSECKNLE ECYKLCNLDV TFSTFEMAIN 2300
NAHRFGILIT DRSFNNFWPS KIKPGSSGVS AMDIGKCMTF DAKIVNAKVL 2350
TQRGKSVVWL SQDFSTLSST AQKVLVKTFV EEGVNFSLTF NAVGSDEDLP 2400
YERFTESVSA KSGSGFFDVL KQLKQLFWCL VLFITLYGLC SVYSVATQSY 2450
IDSAEGYDYM VIKNGVVQSF DDSINCVHNT YKGFAVWFKA KHGFVPTFDK 2500
SCPIVLGTVF DLGNMRPIPD VPAYVALVGR SLVFAINAAF GVTNVCYDHT 2550
GAAVSKNSYF DTCVFNSACT TLTGIGGTVV YCAKQGLVEG AKLYSELLPD 2600
YYYEHASGNM VKIPAIIRSF GLRFVKTQAT TYCRVGECTE SQAGFCFGGD 2650
NWFVYDKEFG DGYICGSSTL GFFKNVFALF NSNMSVVATS GAMLANIVIA 2700
CLAIAVCYGV LKFKKIFGDC TLLVVMIIVT LVVNNVSYFV TQNTFFMIVY 2750
AIIYYFTTRK LAYPGVLDAG FIIAYLNMAP WYVLVLYIMV FLYDSLPSLF 2800
KLKVTTNLFE GDKFVGSFES AAMGTFVIDM RSYETLVNST SLDRIKSYAN 2850
SFNKYKYYTG SMGEADYRMA CYAHLGKALM DYSVSRNDML YTPPTVSVNS 2900
TLQSGLRKMA QPSGVVEPCI VRVAYGNNVL NGLWLGDEVI CPRHVIASDT 2950
SRVINYENEL SSVRLHNFSI AKNNAFLGVV SAKYKGVNLV LKVNQVNPNT 3000
PEHKFKSVRP GESFNILACY EGCPGSVYGV NMRSQGTIKG SFIAGTCGSV 3050
GYVLENGTLY FVYMHHLELG NGSHVGSNLE GEMYGGYEDQ PSMQLEGTNV 3100
MSSDNVVAFL YAALINGERW FVTNTSMTLE SYNAWAKTNS FTEIVSTDAF 3150
NMLAAKTGYS VEKLLECIVR LNKGFGGRTI LSYGSLCDEF TPTEVIRQMY 3200
GVNLQSGKVK SIFYPMMTAI AILFAFWLEF FMYTPFTWIN PTFVSVVLAI 3250
TTLVSVLLVA GIKHKMLFFM SFVMPSVILA TAHNVVWDMT YYESLQVLVE 3300
NVNTTFLPVD MQGVMLALFC VVVFVICTIR FFTCKQSWFS LFATTIFVMF 3350
NIVKLLGMIG EPWTDDHFLL CLVNMLTMLI SLTTKDWFVV FASYKVAYYI 3400
VVYVMQPAFV QDFGFVKCVS IIYMACGYLF CCYYGILYWV NRFTCMTCGV 3450
YQFTVSPAEL KYMTANNLSA PKTAYDAMIL SFKLMGIGGG RNIKISTVQS 3500
KLTEMKCTNV VLLGLLSKMH VESNSKEWNY CVGLHNEINL CDDPDAVLEK 3550
LLALIAFFLS KHNTCDLSDL IESYFENTTI LQSVASAYAA LPSWIAYEKA 3600
RADLEEAKKN DVSPQLLKQL TKACNIAKSE FEREASVQKK LDKMAEQAAA 3650
SMYKEARAVD RKSKIVSAMH SLLFGMLKKL DMSSVNTIIE QARNGVLPLS 3700
IIPAASATRL IVVTPNLEVL SKVRQENNVH YAGAIWSIVE VKDANGAQVH 3750
LKEVTAANEL NITWPLSITC ERTTKLQNNE ILPGKLKEKA VKASATIDGD 3800
AYGSGKALMA SEGGKSFIYA FIASDSNLKY VKWESNNDVI PIELEAPLRF 3850
YVDGVNGPEV KYLYFVKSLN TLRRGAVLGY IGATVRLQAG KPTEHPSNSG 3900
LLTLCAFAPD PAKAYVDAVK RGMQPVTNCV KMLSNGAGNG MAITNGVESN 3950
TQQDSYGGAS VCIYCRCHVE HPAIDGLCRF KGKFVQVPTG TQDPIRFCIE 4000
NEVCVVCGCW LTNGCMCDRT SIQGTTIDQS YLNECGVLVQ LDLEPCNGTD 4050
PDHVSRAFDI YNKDVACIGK FLKTNCSRFR NLDKHDAYYV VKRCTKSVMD 4100
HEQVCYNDLK DSGVVAEHDF FLYKEGRCEF GNVARKDLTK YTMMDLCYAI 4150
RNFDEKNCEV LKEILVTLGA CNESFFENKD WFDPVENEAI HEVYARLGPI 4200
VANAMLKCVA FCDAIVEKGY IGIITLDNQD LNGNFYDFGD FVKTTPGFGC 4250
ACVTSYYSYM MPLMGMTSCL ESENFVKSDI YGADYKQYDL LAYDFTDHKE 4300
KLFHKYFKHW DRTYHPNCSD CTSDECIIHC ANFNTLFSMT IPSTAFGPLV 4350
RKVHIDGVPV VVTAGYHFKQ LGIVWNLDVK LDTMKLSMTD LLRFVTDPTL 4400
LVASSPALLD QRTVCFSIAA LSTGVTYQTV KPGHFNKDFY DFITERGFFE 4450
EGSELTLKHF FFAQGGEAAM TDFNYYRYNR VTVLDICQAQ FVYKIVGKYF 4500
ECYDGGCINA REVVVTNYDK SAGYPLNKFG KARLYYETLS YEEQDALFAL 4550
TKRNVLPTMT QMNLKYAISG KARARTVGGV SLLSTMTTRQ YHQKHLKSIA 4600
ATRNATVVIG STKFYGGWDN MLKNLMRDVD NGCLMGWDYP KCDRALPNMI 4650
RMASAMILGS KHVGCCTHSD RFYRLSNELA QVLTEVVHCT GGFYFKPGGT 4700
TSGDGTTAYA NSAFNIFQAV SANVNKLLGV DSNACNNVTV KSIQRKIYDN 4750
CYRSSSIDEE FVVEYFSYLR KHFSMMILSD DGVVCYNKDY ADLGYVADIN 4800
AFKATLYYQN NVFMSTSKCW VEPDLSVGPH EFCSQHTLQI VGPDGDYYLP 4850
YPDPSRILSA GVFVDDIVKT DNVIMLERYV SLAIDAYPLT KHPKPAYQKV 4900
FYTLLDWVKH LQKNLNAGVL DSFSVTMLEE GQDKFWSEEF YASLYEKSTV 4950
LQAAGMCVVC GSQTVLRCGD CLRRPLLCTK CAYDHVMGTK HKFIMSITPY 5000
VCSFNGCNVN DVTKLFLGGL SYYCMDHKPQ LSFPLCANGN VFGLYKSSAV 5050
GSEDVEDFNK LAVSDWTNVE DYKLANNVKE SLKIFAAETV KAKEESVKSE 5100
YAYAILKEVI GPKEIVLQWE ASKTKPPLNR NSVFTCFQIS KDTKIQLGEF 5150
VFEQSEYGSD SVYYKSTSTY KLTPGMIFVL TSHNVSPLKA TILVNQEKYN 5200
TISKLYPVFN IAEAYNTLVP YYQMIGKQKF TTIQGPPGSG KSHCVIGLGL 5250
YYPQARIVYT ACSHAAVDAL CEKAAKNFNV DRCSRIIPQR IRVDCYTGFK 5300
PNNTNAQYLF CTVNALPEAS CDIVVVDEVS MCTNYDLSVI NSRLSYKHIV 5350
YVGDPQQLPA PRTLINKGVL QPQDYNVVTQ RVCTLGPDVF LHKCYRCPAE 5400
IVKTVSALVY ENKFVPVNPE SKQCFKMFVK GQVQIESNSS INNKQLEVVK 5450
AFLAHNPKWR KAVFISPYNS QNYVARRLLG LQTQTVDSAQ GSEYDYVIYT 5500
QTSDTQHATN VNRFNVAITR AKVGILCIMC DRTMYENLDF YELKDSKIGL 5550
QAKPETCGLF KDCSKSEQYI PPAYATTYMS LSDNFKTSDG LAVNIGTKDV 5600
KYANVISYMG FRFEANIPGY HTLFCTRDFA MRNVRAWLGF DVEGAHVCGD 5650
NVGTNVPLQL GFSNGVDFVV QTEGCVVTEK GNSIEVVKAR APPGEQFAHL 5700
IPLMRKGQPW HIVRRRIVQM VCDYFDGLSD ILIFVLWAGG LELTTMRYFV 5750
KIGRPQKCEC GKSATCYSSS QCVYACFKHA LGCDYLYNPY CIDIQQWGYT 5800
GSLSMNHHEV CNIHRNEHVA SGDAIMTRCL AIHDCFVKRV DWSIVYPFID 5850
NEEKINKAGR IVQSHVMKAA LKIFNPAAIH DVGNPKGIRC ATTPIPWFCY 5900
DRDPINNNVR CLEYDYMVHG QMNGLMLFWN CNVDMYPEFS IVCRFDTRTR 5950
SKLSLEGCNG GALYVNNHAF HTPAYDRRAF AKLKPMPFFY YDDSNCELVD 6000
GQPNYVPLKS NVCITKCNIG GAVCKKHAAL YRAYVEDYNM FMQAGFTIWC 6050
PQNFDTYMLW HGFVNSKALQ SLENVAFNVV KKGAFTGLKG DLPTAVIADK 6100
IMVRDGPTDK CIFTNKTSLP TNVAFELYAK RKLGLTPPLT ILRNLGVVAT 6150
YKFVLWDYEA ECPFSNFTKQ VCSYTDLDSE VVTCFDNSIA GSFERFTTTK 6200
DAVLISNNAV KGLSAIKLQY GFLNDLPVST VGNKPVTWYI YVRKNGEYVE 6250
QIDSYYTHGR TFETFKPRST MEEDFLSMDT TLFIQKYGLE DYGFEHVVFG 6300
DVSKTTIGGM HLLISQVRLA KMGLFSVQEF MTNSDSTLKS CCITYADDPS 6350
SKNVCTYMDI LLDDFVTIIK SLDLNVVSKV VDVIVDCKAW RWMLWCENSQ 6400
IKTFYPQLQS AEWNPGYSMP TLYKIQRMCL ERCNLYNYGA QVRLPDGITT 6450
NVVKYTQLCQ YLNTTTVCVP HKMRVLHLGA AGASGVAPGS TVLRRWLPDD 6500
AILVDNDLRD YVSDADFSVT GDCTSLYIED KFDLLISDLY DGSTKSIDGE 6550
NTSKDGFFTY INGFIKEKLS LGGSAAIKIT EFSWNKDLYE LIQRFEYWTV 6600
FCTSVNTSSS EGFLIGINYL GPYCDKAIVD GNIMHANYIF WRNSTIMALS 6650
HNSVLDTPKF KCRCNNALIV NLKEKELNEM VVGLLRKGKL LIRNNGKLLN 6700
FGNHLVNVP 6709

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

Length:6,709
Mass (Da):751,196
Last modified:April 17, 2007 - v2
Checksum:iF26AC0FFF5FE27F9
GO
Isoform Replicase polyprotein 1a (identifier: Q98VG9-2) [UniParc]FASTAAdd to Basket

Also known as: pp1a, ORF1a polyprotein

The sequence of this isoform differs from the canonical sequence as follows:
     4043-6709: Missing.

Note: Produced by conventional translation.

Show »
Length:4,042
Mass (Da):449,790
Checksum:i34663B2576D09550
GO

Sequence cautioni

The sequence AAY16374.1 differs from that shown. Reason: Frameshift at position 4033.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti162 – 1621W → C.
Natural varianti177 – 1771D → G.
Natural varianti388 – 3881W → C.
Natural varianti808 – 8081K → T.
Natural varianti1784 – 17841A → V.
Natural varianti2889 – 28891M → K.
Natural varianti3280 – 32801A → V.
Natural varianti3992 – 39921Q → R.
Natural varianti4304 – 43041H → Q.
Natural varianti5846 – 58461Y → H.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei4043 – 67092667Missing in isoform Replicase polyprotein 1a. VSP_032885Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1016 – 109277Missing in AAY32594. 1 PublicationAdd
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
DQ010921 Genomic RNA. Translation: AAY32594.1.
DQ010921 Genomic RNA. Translation: AAY32595.1.
AY994055 Genomic RNA. Translation: AAY16374.1. Frameshift.
AF326575 Genomic RNA. Translation: AAK09095.1.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
DQ010921 Genomic RNA. Translation: AAY32594.1 .
DQ010921 Genomic RNA. Translation: AAY32595.1 .
AY994055 Genomic RNA. Translation: AAY16374.1 . Frameshift.
AF326575 Genomic RNA. Translation: AAK09095.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3ETI X-ray 2.20 A/B/C/D/E/F/G/H 1331-1498 [» ]
3EW5 X-ray 3.10 A/B/C 1331-1498 [» ]
3GZF X-ray 2.76 A/B/C/D/E 2808-2902 [» ]
3JZT X-ray 3.91 A/B/C/D/E/F/G/H 1331-1498 [» ]
3UB0 X-ray 2.60 A/D 3583-3777 [» ]
B/C/E/F 3500-3582 [» ]
ProteinModelPortali Q98VG9.
SMRi Q98VG9. Positions 2904-3204, 3894-4019.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi C30.004.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei Q98VG9.

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. "Genomic RNA sequence of Feline coronavirus strain FIPV WSU-79/1146."
    Dye C., Siddell S.G.
    J. Gen. Virol. 86:2249-2253(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. Haijema B.J., de Groot-Mijnes J.D.F., Vennema H., Raamsman M.J., Rottier P.J.M., de Groot R.J.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  3. "Mutational analysis of the active centre of coronavirus 3C-like proteases."
    Hegyi A., Friebe A., Gorbalenya A.E., Ziebuhr J.
    J. Gen. Virol. 83:581-593(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 2894-3215, MUTAGENESIS OF HIS-2944; ASN-2967; GLY-2986; SER-3041; CYS-3047; TYR-3063; MET-3064 AND HIS-3065.

Entry informationi

Entry nameiR1AB_FIPV
AccessioniPrimary (citable) accession number: Q98VG9
Secondary accession number(s): Q4U5G1, Q4U5G2, Q52PA4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: April 17, 2007
Last modified: June 11, 2014
This is version 93 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference 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