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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)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

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)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

Structurei

Secondary structure

12180
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni36 – 41Combined sources6
Helixi42 – 47Combined sources6
Beta strandi70 – 74Combined sources5
Beta strandi77 – 83Combined sources7
Helixi110 – 113Combined sources4
Helixi114 – 116Combined sources3
Beta strandi119 – 126Combined sources8
Beta strandi135 – 137Combined sources3
Helixi143 – 146Combined sources4
Helixi154 – 157Combined sources4
Beta strandi160 – 163Combined sources4
Beta strandi166 – 173Combined sources8
Beta strandi180 – 188Combined sources9
Helixi190 – 194Combined sources5
Helixi204 – 206Combined sources3
Beta strandi207 – 213Combined sources7
Turni214 – 216Combined sources3
Beta strandi218 – 224Combined sources7
Beta strandi229 – 234Combined sources6
Beta strandi242 – 252Combined sources11
Beta strandi255 – 257Combined sources3
Beta strandi261 – 271Combined sources11
Helixi329 – 332Combined sources4
Beta strandi335 – 337Combined sources3
Helixi350 – 352Combined sources3
Helixi362 – 365Combined sources4
Turni379 – 382Combined sources4
Beta strandi387 – 392Combined sources6
Beta strandi397 – 406Combined sources10
Helixi408 – 410Combined sources3
Helixi412 – 418Combined sources7
Beta strandi421 – 426Combined sources6
Beta strandi428 – 435Combined sources8
Beta strandi441 – 450Combined sources10
Beta strandi463 – 469Combined sources7
Beta strandi475 – 480Combined sources6
Beta strandi485 – 494Combined sources10
Beta strandi497 – 508Combined sources12
Beta strandi515 – 525Combined sources11
Helixi570 – 573Combined sources4
Helixi578 – 580Combined sources3
Beta strandi602 – 605Combined sources4
Beta strandi607 – 609Combined sources3
Helixi610 – 613Combined sources4
Beta strandi618 – 628Combined sources11
Beta strandi631 – 633Combined sources3
Beta strandi639 – 641Combined sources3
Helixi642 – 648Combined sources7
Beta strandi650 – 652Combined sources3
Beta strandi656 – 663Combined sources8
Beta strandi665 – 674Combined sources10
Beta strandi679 – 684Combined sources6
Beta strandi691 – 694Combined sources4
Beta strandi698 – 703Combined sources6
Beta strandi708 – 716Combined sources9
Beta strandi722 – 729Combined sources8
Beta strandi735 – 742Combined sources8
Beta strandi744 – 746Combined sources3

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[»]
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
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
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[»]
ProteinModelPortaliQ66578.
SMRiQ66578.
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: November 30, 2016
This is version 127 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.