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Protein

Genome polyprotein

Gene
N/A
Organism
Human parechovirus 1 (strain Harris) (HPeV-1) (Echovirus 22)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Active sitei1550For protease 3C activitySequence analysis1
Active sitei1581For protease 3C activitySequence analysis1
Active sitei1670For protease 3C activitySequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi1185 – 1192ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHelicase, Hydrolase, Ion channel, Nucleotidyltransferase, Protease, RNA-binding, RNA-directed RNA polymerase, Thiol protease, Transferase, Viral ion channel
Biological processClathrin-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
LigandATP-binding, Nucleotide-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, EC:3.4.22.29)
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 stagePicornaviralesPicornaviridaeParechovirus
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 :
RNA-directed RNA polymerase 3D-POL :

GO - Cellular componenti

Keywords - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000397301 – 289Protein VP0Sequence analysisAdd BLAST289
ChainiPRO_0000039731290 – 542Protein VP3Sequence analysisAdd BLAST253
ChainiPRO_0000039732543 – 776Protein VP1Sequence analysisAdd BLAST234
ChainiPRO_0000039733777 – 923Protein 2ASequence analysisAdd BLAST147
ChainiPRO_0000039734924 – 1045Protein 2BSequence analysisAdd BLAST122
ChainiPRO_00000397351046 – 1374Protein 2CSequence analysisAdd BLAST329
ChainiPRO_00000397361375 – 1491Protein 3ASequence analysisAdd BLAST117
ChainiPRO_00000397371492 – 1511Protein 3BSequence analysisAdd BLAST20
ChainiPRO_00000397381512 – 1711Protease 3CSequence analysisAdd BLAST200
ChainiPRO_00000397391712 – 2180RNA-directed RNA polymerase 3D-POLSequence analysisAdd BLAST469

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1494O-(5'-phospho-RNA)-tyrosineBy similarity1

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)DescriptionActionsGraphical viewLength
Sitei776 – 777Cleavage; by protease 2ASequence analysis2

Keywords - PTMi

Covalent protein-RNA linkage, Lipoprotein, Myristate, Phosphoprotein

Proteomic databases

PRIDEiQ66578

Interactioni

Protein-protein interaction databases

ELMiQ66578

Structurei

Secondary structure

12180
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ66578
SMRiQ66578
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1160 – 1318SF3 helicasePROSITE-ProRule annotationAdd BLAST159
Domaini1945 – 2059RdRp catalyticPROSITE-ProRule annotationAdd BLAST115

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi764 – 766Cell attachment siteSequence analysis3

Sequence similaritiesi

Belongs to the picornaviruses polyprotein family.Curated

Phylogenomic databases

OrthoDBiVOG090000PJ

Family and domain databases

CDDicd00205 rhv_like, 2 hits
Gene3Di2.60.120.20, 3 hits
InterProiView protein in InterPro
IPR004004 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
PfamiView protein in Pfam
PF06344 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
PRINTSiPR00918 CALICVIRUSNS
SUPFAMiSSF50494 SSF50494, 1 hit
SSF52540 SSF52540, 1 hit
PROSITEiView protein in PROSITE
PS50507 RDRP_SSRNA_POS, 1 hit
PS51218 SF3_HELICASE_2, 1 hit

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

Similar proteinsi

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
PDB 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[»]
5MJVX-ray3.09A543-776[»]
B290-542[»]
C1-289[»]
ProteinModelPortaliQ66578
SMRiQ66578
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

ELMiQ66578

Protein family/group databases

MEROPSiC03.023

Proteomic databases

PRIDEiQ66578

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

OrthoDBiVOG090000PJ

Family and domain databases

CDDicd00205 rhv_like, 2 hits
Gene3Di2.60.120.20, 3 hits
InterProiView protein in InterPro
IPR004004 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
PfamiView protein in Pfam
PF06344 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
PRINTSiPR00918 CALICVIRUSNS
SUPFAMiSSF50494 SSF50494, 1 hit
SSF52540 SSF52540, 1 hit
PROSITEiView protein in PROSITE
PS50507 RDRP_SSRNA_POS, 1 hit
PS51218 SF3_HELICASE_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPOLG_HPE1H
AccessioniPrimary (citable) accession number: Q66578
Secondary accession number(s): Q90062
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: November 1, 1996
Last modified: May 23, 2018
This is version 137 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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