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Protein

Genome polyprotein

Gene
N/A
Organism
Human parechovirus 1 (strain Harris) (HPeV-1) (Echovirus 22)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Capsid proteins VP0, VP2, VP3 form a closed capsid enclosing the viral positive strand RNA genome. Capsid proteins interact with host alpha-V/beta-3 integrin heterodimer to provide virion attachment target cell. This attachment induces virion internalization predominantly through clathrin-mediated endocytosis.1 Publication
Protein 2A: Is not a protease.By similarity
Protein 2B: Affects membrane integrity and cause an increase in membrane permeability.By similarity
Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).By similarity
Protein 3A, via its hydrophobic domain, serves as membrane anchor.By similarity
Protease 3C: cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease (By similarity).By similarity
RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals.PROSITE-ProRule annotation

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation
Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein.
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
NTP + H2O = NDP + phosphate.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei1550 – 15501For protease 3C activitySequence analysis
Active sitei1581 – 15811For protease 3C activitySequence analysis
Active sitei1670 – 16701For protease 3C activitySequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1185 – 11928ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Ion channel, Nucleotidyltransferase, Protease, RNA-directed RNA polymerase, Thiol protease, Transferase, Viral ion channel

Keywords - Biological processi

Clathrin-mediated endocytosis of virus by host, Host-virus interaction, Ion transport, Transport, Viral attachment to host cell, Viral penetration into host cytoplasm, Viral RNA replication, Virus endocytosis by host, Virus entry into host cell

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Protein family/group databases

MEROPSiC03.023.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 10 chains:
Alternative name(s):
P1AB
Virion protein 0
Alternative name(s):
P1C
Virion protein 3
Alternative name(s):
P1D
Virion protein 1
Protein 2A
Short name:
P2A
Protein 2B
Short name:
P2B
Protein 2C (EC:3.6.1.15)
Short name:
P2C
Protein 3A
Short name:
P3A
Protein 3B
Short name:
P3B
Alternative name(s):
VPg
Protease 3C (EC:3.4.22.28)
Short name:
P3C
Alternative name(s):
Picornain 3C
OrganismiHuman parechovirus 1 (strain Harris) (HPeV-1) (Echovirus 22)
Taxonomic identifieri103911 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stagePicornaviralesPicornaviridaeParechovirusunclassified Parechovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Macaca (macaques) [TaxID: 9539]
Proteomesi
  • UP000002496 Componenti: Genome

Subcellular locationi

Protein VP3 :
Protein VP1 :
Protein 2B :
Protein 2C :
Protein 3A :
Protein 3B :
RNA-directed RNA polymerase 3D-POL :

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, Host cytoplasmic vesicle, Host membrane, Membrane, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 289289Protein VP0Sequence analysisPRO_0000039730Add
BLAST
Chaini290 – 542253Protein VP3Sequence analysisPRO_0000039731Add
BLAST
Chaini543 – 776234Protein VP1Sequence analysisPRO_0000039732Add
BLAST
Chaini777 – 923147Protein 2ASequence analysisPRO_0000039733Add
BLAST
Chaini924 – 1045122Protein 2BSequence analysisPRO_0000039734Add
BLAST
Chaini1046 – 1374329Protein 2CSequence analysisPRO_0000039735Add
BLAST
Chaini1375 – 1491117Protein 3ASequence analysisPRO_0000039736Add
BLAST
Chaini1492 – 151120Protein 3BSequence analysisPRO_0000039737Add
BLAST
Chaini1512 – 1711200Protease 3CSequence analysisPRO_0000039738Add
BLAST
Chaini1712 – 2180469RNA-directed RNA polymerase 3D-POLSequence analysisPRO_0000039739Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1494 – 14941O-(5'-phospho-RNA)-tyrosineBy similarity

Post-translational modificationi

VPg is uridylylated by the polymerase and is covalently linked to the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-peptide primer for the polymerase (By similarity).By similarity
Specific enzymatic cleavages yield mature proteins. All cleavages are catalyzed by P3C.
The N-terminus of VP0 is blocked.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei776 – 7772Cleavage; by protease 2ASequence analysis

Keywords - PTMi

Covalent protein-RNA linkage, Lipoprotein, Myristate, Phosphoprotein

Structurei

Secondary structure

1
2180
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni36 – 416Combined sources
Helixi42 – 476Combined sources
Beta strandi70 – 745Combined sources
Beta strandi77 – 837Combined sources
Helixi110 – 1134Combined sources
Helixi114 – 1163Combined sources
Beta strandi119 – 1268Combined sources
Beta strandi135 – 1373Combined sources
Helixi143 – 1464Combined sources
Helixi154 – 1574Combined sources
Beta strandi160 – 1634Combined sources
Beta strandi166 – 1738Combined sources
Beta strandi180 – 1889Combined sources
Helixi190 – 1945Combined sources
Helixi204 – 2063Combined sources
Beta strandi207 – 2137Combined sources
Turni214 – 2163Combined sources
Beta strandi218 – 2247Combined sources
Beta strandi229 – 2346Combined sources
Beta strandi242 – 25211Combined sources
Beta strandi255 – 2573Combined sources
Beta strandi261 – 27111Combined sources
Helixi329 – 3324Combined sources
Beta strandi335 – 3373Combined sources
Helixi350 – 3523Combined sources
Helixi362 – 3654Combined sources
Turni379 – 3824Combined sources
Beta strandi387 – 3926Combined sources
Beta strandi397 – 40610Combined sources
Helixi408 – 4103Combined sources
Helixi412 – 4187Combined sources
Beta strandi421 – 4266Combined sources
Beta strandi428 – 4358Combined sources
Beta strandi441 – 45010Combined sources
Beta strandi463 – 4697Combined sources
Beta strandi475 – 4806Combined sources
Beta strandi485 – 49410Combined sources
Beta strandi497 – 50812Combined sources
Beta strandi515 – 52511Combined sources
Helixi570 – 5734Combined sources
Helixi578 – 5803Combined sources
Beta strandi602 – 6054Combined sources
Beta strandi607 – 6093Combined sources
Helixi610 – 6134Combined sources
Beta strandi618 – 62811Combined sources
Beta strandi631 – 6333Combined sources
Beta strandi639 – 6413Combined sources
Helixi642 – 6487Combined sources
Beta strandi650 – 6523Combined sources
Beta strandi656 – 6638Combined sources
Beta strandi665 – 67410Combined sources
Beta strandi679 – 6846Combined sources
Beta strandi691 – 6944Combined sources
Beta strandi698 – 7036Combined sources
Beta strandi708 – 7169Combined sources
Beta strandi722 – 7298Combined sources
Beta strandi735 – 7428Combined sources
Beta strandi744 – 7463Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4UDFelectron microscopy20.0012/16/1A/1E/1I/1M/1Q/1U/1Y/22/26/2A/2E/2I/2M/2Q/2U/2Y/32/36/3A/3E/3I/3M/3Q/3U/3Y/42/46/4A360-542[»]
13/17/1B/1F/1J/1N/1R/1V/1Z/23/27/2B/2F/2J/2N/2R/2V/2Z/33/37/3B/3F/3J/3N/3R/3V/3Z/43/47/4B61-289[»]
4Z92X-ray3.10A543-776[»]
B290-542[»]
C1-289[»]
ProteinModelPortaliQ66578.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1160 – 1318159SF3 helicasePROSITE-ProRule annotationAdd
BLAST
Domaini1945 – 2059115RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi764 – 7663Cell attachment siteSequence analysis

Sequence similaritiesi

Belongs to the picornaviruses polyprotein family.Curated
Contains 2 peptidase C3 domains.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation
Contains 1 SF3 helicase domain.PROSITE-ProRule annotation

Family and domain databases

CDDicd00205. rhv_like. 2 hits.
Gene3Di2.60.120.20. 3 hits.
3.40.50.300. 1 hit.
InterProiIPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR009003. Peptidase_S1_PA.
IPR001676. Picornavirus_capsid.
IPR033703. Rhv_like.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR029053. Viral_coat.
IPR009419. VPP_parechovir_P3A.
IPR009407. VPP_parechovir_P3B.
[Graphical view]
PfamiPF06344. Parecho_VpG. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF06363. Picorna_P3A. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00918. CALICVIRUSNS.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q66578-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
METIKSIADM ATGVVSSVDS TINAVNEKVE SVGNEIGGNL LTKVADDASN
60 70 80 90 100
ILGPNCFATT AEPENKNVVQ ATTTVNTTNL TQHPSAPTMP FSPDFSNVDN
110 120 130 140 150
FHSMAYDITT GDKNPSKLVR LETHEWTPSW ARGYQITHVE LPKVFWDHQD
160 170 180 190 200
KPAYGQSRYF AAVRCGFHFQ VQVNVNQGTA GSALVVYEPK PVVTYDSKLE
210 220 230 240 250
FGAFTNLPHV LMNLAETTQA DLCIPYVADT NYVKTDSSDL GQLKVYVWTP
260 270 280 290 300
LSIPTGSANQ VDVTILGSLL QLDFQNPRVF AQDVNIYDNA PNGKKKNWKK
310 320 330 340 350
IMTMSTKYKW TRTKIDIAEG PGSMNMANVL CTTGAQSVAL VGERAFYDPR
360 370 380 390 400
TAGSKSRFDD LVKIAQLFSV MADSTTPSEN HGVDAKGYFK WSATTAPQSI
410 420 430 440 450
VHRNIVYLRL FPNLNVFVNS YSYFRGSLVL RLSVYASTFN RGRLRMGFFP
460 470 480 490 500
NATTDSTSTL DNAIYTICDI GSDNSFEITI PYSFSTWMRK TNGHPIGLFQ
510 520 530 540 550
IEVLNRLTYN SSSPSEVYCI VQGKMGQDAR FFCPTGSVVT FQNSWGSQMD
560 570 580 590 600
LTDPLCIEDD TENCKQTMSP NELGLTSAQD DGPLGQEKPN YFLNFRSMNV
610 620 630 640 650
DIFTVSHTKV DNLFGRAWFF MEHTFTNEGQ WRVPLEFPKQ GHGSLSLLFA
660 670 680 690 700
YFTGELNIHV LFLSERGFLR VAHTYDTSND RVNFLSSNGV ITVPAGEQMT
710 720 730 740 750
LSAPYYSNKP LRTVRDNNSL GYLMCKPFLT GTSTGKIEVY LSLRCPNFFF
760 770 780 790 800
PLPAPKVTSS RALRGDMANL TNQSPYGQQP QNRMMKLAYL DRGFYKHYGI
810 820 830 840 850
IVGDHVYQLD SDDIFKTALT GKAKFTKTKL TSDWVIEEEC ELDYFRIKYL
860 870 880 890 900
ESAVDSEHIF SVDKNCETIA KDIFGTHTLS QHQAIGLVGT ILLTAGLMST
910 920 930 940 950
IKTPVNAVTI KEFFNHAIDG DEQGLSLLVQ KCTTFFSSAA TEILDNDLVK
960 970 980 990 1000
FIVKILVRIL CYMVLYCHKP NILTTACLST LLIMDVTSSS VLSPSCKALM
1010 1020 1030 1040 1050
QCLMDGDVKK LAEIVAESMS NTDDDEVKEQ ICDTVKYTKT ILSNQGPFKG
1060 1070 1080 1090 1100
FNEVSTAFRH IDWWIHTLLK IKDMVLSVFK PSIESKAIQW LERNKEHVCS
1110 1120 1130 1140 1150
ILDYASDIIV ESKDQSKMKT QDFYQRYSDC LAKFKPIMAI CFRSCHNSIS
1160 1170 1180 1190 1200
NTVYRLFQEL ARIPNRISTN NDLIRIEPIG IWIQGEPGQG KSFLTHTLSR
1210 1220 1230 1240 1250
QLQKSCKLNG VFTNPTASEF MDGYDNQDIH LIDDLGQTRK EKDIEMLCNC
1260 1270 1280 1290 1300
ISSVPFIVPM AHLEEKGKFY TSKLVVATTN KSDFSSTVLQ DSGALKRRFP
1310 1320 1330 1340 1350
YIMHIRAAKA YSKAGKLNVS QAMATMSTGE CWEVSKNGRD WETLKLKDLV
1360 1370 1380 1390 1400
DKITIDYNER VKNYNAWKQQ LENQTLDDLD DAVSYIKHNF PDAIPYVDEY
1410 1420 1430 1440 1450
LNIEMSTLIE QMEAFIEPKP SVFKCFANKI GSKISKASRE VVDWFSDKIK
1460 1470 1480 1490 1500
SMLSFVERNK AWLTVVSAVT SAISILLLVT KIFKKEESKD ERAYNPTLPV
1510 1520 1530 1540 1550
AKPKGTFPVS QREFKNEAPY DGQLEHIISQ MAYITGSTTG HMTHCAGYQH
1560 1570 1580 1590 1600
DEIILHGHSI KYLEQEDELT LHYKNKVFPI EQPSVTQVTL GGKPMDLAIL
1610 1620 1630 1640 1650
KCKLPFRFKK NSKYYTNKIG TESMLIWMTE QGIITKEVQR VHHSGGIKTR
1660 1670 1680 1690 1700
EGTESTKTIS YTVKSCKGMC GGLLISKVEG NFKILGMHIA GNGEMGVAIP
1710 1720 1730 1740 1750
FNFLKNDMSD QGIVTEITPI QPMYINTKTQ IHKSPVYGAV EVKMGPAVLS
1760 1770 1780 1790 1800
KSDTRLEEPV ECLIKKSASK YRVNKFQVNN ELWQGVKACV KSKFREIFGM
1810 1820 1830 1840 1850
NGIVDMKTAI LGTSHVNSMD LSTSAGYSFV KSGYKKKDLI CLEPFSVAPL
1860 1870 1880 1890 1900
LERLVQDKFH NLLKGNQITT TFNTCLKDEL RKLDKIASGK TRCIEACEVD
1910 1920 1930 1940 1950
YCIVYRMIMM EIYDKIYQTP CYYSGLAVGI NPYKDWHFMI NALNDYNYEM
1960 1970 1980 1990 2000
DYSQYDGSLS SMLLWEAVEV LAYCHDSPDL VMQLHKPVID SDHVVFNERW
2010 2020 2030 2040 2050
LIHGGMPSGS PCTTVLNSLC NLMMCIYTTN LISPGIDCLP IVYGDDVILS
2060 2070 2080 2090 2100
LDKEIEPEKL QSIMADSFGA EVTGSRKDEP PSLKPRMEVE FLKRKPGYFP
2110 2120 2130 2140 2150
ESTFIVGKLD TENMIQHLMW MKNFSTFKQQ LQSYLMELCL HGKDTYQHYI
2160 2170 2180
KILEPYLQEW NITVDDYDVV ITKLMPMVFD
Length:2,180
Mass (Da):245,844
Last modified:November 1, 1996 - v1
Checksum:i3A5F1DAC43C12DEE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L02971 Genomic RNA. Translation: AAA72291.1.
S45208 Genomic RNA. Translation: AAB23363.1.
PIRiA46182.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L02971 Genomic RNA. Translation: AAA72291.1.
S45208 Genomic RNA. Translation: AAB23363.1.
PIRiA46182.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4UDFelectron microscopy20.0012/16/1A/1E/1I/1M/1Q/1U/1Y/22/26/2A/2E/2I/2M/2Q/2U/2Y/32/36/3A/3E/3I/3M/3Q/3U/3Y/42/46/4A360-542[»]
13/17/1B/1F/1J/1N/1R/1V/1Z/23/27/2B/2F/2J/2N/2R/2V/2Z/33/37/3B/3F/3J/3N/3R/3V/3Z/43/47/4B61-289[»]
4Z92X-ray3.10A543-776[»]
B290-542[»]
C1-289[»]
ProteinModelPortaliQ66578.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiC03.023.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

CDDicd00205. rhv_like. 2 hits.
Gene3Di2.60.120.20. 3 hits.
3.40.50.300. 1 hit.
InterProiIPR004004. Helic/Pol/Pept_Calicivir-typ.
IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR014759. Helicase_SF3_ssRNA_vir.
IPR027417. P-loop_NTPase.
IPR000199. Peptidase_C3A/C3B_picornavir.
IPR009003. Peptidase_S1_PA.
IPR001676. Picornavirus_capsid.
IPR033703. Rhv_like.
IPR001205. RNA-dir_pol_C.
IPR007094. RNA-dir_pol_PSvirus.
IPR029053. Viral_coat.
IPR009419. VPP_parechovir_P3A.
IPR009407. VPP_parechovir_P3B.
[Graphical view]
PfamiPF06344. Parecho_VpG. 1 hit.
PF00548. Peptidase_C3. 1 hit.
PF06363. Picorna_P3A. 1 hit.
PF00680. RdRP_1. 1 hit.
PF00073. Rhv. 1 hit.
PF00910. RNA_helicase. 1 hit.
[Graphical view]
PRINTSiPR00918. CALICVIRUSNS.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50507. RDRP_SSRNA_POS. 1 hit.
PS51218. SF3_HELICASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_HPE1H
AccessioniPrimary (citable) accession number: Q66578
Secondary accession number(s): Q90062
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: November 1, 1996
Last modified: September 7, 2016
This is version 125 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, Direct protein sequencing

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.