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P04936

- POLG_HRV2

UniProt

P04936 - POLG_HRV2

Protein

Genome polyprotein

Gene
N/A
Organism
Human rhinovirus 2 (HRV-2)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 158 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Capsid protein VP1: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Capsid protein VP1 mainly forms the vertices of the capsid. Capsid protein VP1 interacts with host VLDLR to provide virion attachment to target host cells. This attachment induces virion internalization. Tyrosine kinases are probably involved in the entry process. After binding to its receptor, the capsid undergoes conformational changes. Capsid protein VP1 N-terminus (that contains an amphipathic alpha-helix) and capsid protein VP4 are externalized. Together, they shape a pore in the host membrane through which viral genome is translocated to host cell cytoplasm. After genome has been released, the channel shrinks By similarity.By similarity
    Capsid protein VP2: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome By similarity.By similarity
    Capsid protein VP3: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome By similarity.By similarity
    Capsid protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. Capsid protein VP4 is released, Capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm. After genome has been released, the channel shrinks By similarity.By similarity
    Capsid protein VP0: Component of immature procapsids, which is cleaved into capsid proteins VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step By similarity.By similarity
    Protein 2A: Cysteine protease that cleaves viral polyprotein and specific host proteins. It is responsible for the cleavage between the P1 and P2 regions, first cleavage occurring in the polyprotein. Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation. Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores By similarity.By similarity
    Protein 2B: Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cyctoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication By similarity.By similarity
    Protein 2C: Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3 By similarity.By similarity
    Protein 3AB: Localizes the viral replication complex to the surface of membranous vesicles. Together with protein 3CD binds the Cis-Active RNA Element (CRE) which is involved in RNA synthesis initiation. Acts as a cofactor to stimulate the activity of 3D polymerase, maybe through a nucleid acid chaperone activity By similarity.By similarity
    Protein 3A: Localizes the viral replication complex to the surface of membranous vesicles. It inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport and causes the dissassembly of the Golgi complex, possibly through GBF1 interaction. This would result in depletion of MHC, trail receptors and IFN receptors at the host cell surface By similarity.By similarity
    Viral protein genome-linked: acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU. The oriI viral genomic sequence may act as a template for this. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome. VPg may be removed in the cytoplasm by an unknown enzyme termed "unlinkase". VPg is not cleaved off virion genomes because replicated genomic RNA are encapsidated at the site of replication By similarity.By similarity
    Protein 3CD: Is involved in the viral replication complex and viral polypeptide maturation. It exhibits protease activity with a specificity and catalytic efficiency that is different from protease 3C. Protein 3CD lacks polymerase activity. The 3C domain in the context of protein 3CD may have an RNA binding activity By similarity.By similarity
    Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 By similarity.By similarity
    RNA-directed RNA polymerase: Replicates the viral genomic RNA on the surface of intracellular membranes. May form linear arrays of subunits that propagate along a strong head-to-tail interaction called interface-I. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss+RNA genomes are either translated, replicated or encapsidated By similarity.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.

    Enzyme regulationi

    RNA-directed RNA polymerase: replication or transcription is subject to high level of random mutations by the nucleotide analog ribavirin.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei330 – 3312Cleavage; by Protease 3CSequence Analysis
    Active sitei868 – 8681For Protease 2A activity
    Active sitei885 – 8851For Protease 2A activity
    Active sitei956 – 9561For Protease 2A activity
    Sitei992 – 9932Cleavage; by Protease 3CSequence Analysis
    Sitei1409 – 14102Cleavage; by Protease 3CSequence Analysis
    Sitei1486 – 14872Cleavage; by Protease 3CSequence Analysis
    Sitei1507 – 15082Cleavage; by Protease 3CSequence Analysis
    Active sitei1547 – 15471For Protease 3C activitySequence Analysis
    Active sitei1578 – 15781For Protease 3C activitySequence Analysis
    Active sitei1654 – 16541For Protease 3C activityCurated
    Sitei1690 – 16912Cleavage; by Protease 3CSequence Analysis
    Active sitei2017 – 20171For RdRp activityBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. cysteine-type endopeptidase activity Source: InterPro
    3. ion channel activity Source: UniProtKB-KW
    4. RNA binding Source: UniProtKB-KW
    5. RNA-directed RNA polymerase activity Source: UniProtKB-KW
    6. RNA helicase activity Source: InterPro
    7. structural molecule activity Source: InterPro

    GO - Biological processi

    1. DNA replication Source: UniProtKB-KW
    2. endocytosis involved in viral entry into host cell Source: UniProtKB-KW
    3. induction by virus of host autophagy Source: UniProtKB
    4. pore formation by virus in membrane of host cell Source: UniProtKB-KW
    5. pore-mediated entry of viral genome into host cell Source: UniProtKB-KW
    6. protein oligomerization Source: UniProtKB-KW
    7. RNA-protein covalent cross-linking Source: UniProtKB-KW
    8. suppression by virus of host gene expression Source: UniProtKB-KW
    9. suppression by virus of host mRNA export from nucleus Source: UniProtKB-KW
    10. suppression by virus of host RIG-I activity by RIG-I proteolysis Source: UniProtKB
    11. suppression by virus of host translation initiation factor activity Source: UniProtKB
    12. transcription, DNA-templated Source: InterPro
    13. viral RNA genome replication Source: InterPro
    14. virion attachment to host cell Source: UniProtKB-KW

    Keywords - Molecular functioni

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

    Keywords - Biological processi

    Activation of host autophagy by virus, DNA replication, Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host mRNA suppression by virus, Host-virus interaction, Inhibition of host innate immune response by virus, Inhibition of host mRNA nuclear export by virus, Inhibition of host RIG-I by virus, Inhibition of host RLR pathway by virus, Ion transport, Pore-mediated penetration of viral genome into host cell, Transport, Viral attachment to host cell, Viral immunoevasion, 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

    Enzyme and pathway databases

    SABIO-RKP04936.

    Protein family/group databases

    MEROPSiC03.007.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Genome polyprotein
    Cleaved into the following 17 chains:
    Alternative name(s):
    VP4-VP2
    Alternative name(s):
    P1A
    Virion protein 4
    Alternative name(s):
    P1B
    Virion protein 2
    Alternative name(s):
    P1C
    Virion protein 3
    Alternative name(s):
    P1D
    Virion protein 1
    Protease 2A (EC:3.4.22.29)
    Short name:
    P2A
    Alternative name(s):
    Picornain 2A
    Protein 2A
    Protein 2B
    Short name:
    P2B
    Protein 2C (EC:3.6.1.15)
    Short name:
    P2C
    Protein 3A
    Short name:
    P3A
    Alternative name(s):
    Protein 3B
    Short name:
    P3B
    Protease 3C (EC:3.4.22.28)
    Short name:
    P3C
    Alternative name(s):
    3D polymerase
    Short name:
    3Dpol
    Protein 3D
    Short name:
    3D
    OrganismiHuman rhinovirus 2 (HRV-2)
    Taxonomic identifieri12130 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stagePicornaviralesPicornaviridaeEnterovirusRhinovirus A
    Virus hostiHomo sapiens (Human) [TaxID: 9606]

    Subcellular locationi

    Chain Capsid protein VP0 : Virion By similarity. Host cytoplasm By similarity
    Chain Capsid protein VP2 : Virion By similarity. Host cytoplasm By similarity
    Chain Capsid protein VP3 : Virion By similarity. Host cytoplasm By similarity
    Chain Capsid protein VP1 : Virion By similarity. Host cytoplasm By similarity
    Chain Protein 2B : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
    Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum.
    Chain Protein 2C : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
    Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum.
    Chain Protein 3A : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
    Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum.
    Chain Protein 3AB : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
    Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum.
    Chain Protein 3CD : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
    Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum.
    Chain RNA-directed RNA polymerase : Host cytoplasmic vesicle membrane Curated; Peripheral membrane protein Curated; Cytoplasmic side Curated
    Note: Probably localizes to the surface of intracellular membrane vesicles that are induced after virus infection as the site for viral RNA replication. These vesicles are derived from the endoplasmic reticulum.

    GO - Cellular componenti

    1. host cell cytoplasmic vesicle membrane Source: UniProtKB-SubCell
    2. integral to membrane of host cell Source: UniProtKB-KW
    3. membrane Source: UniProtKB-KW
    4. T=pseudo3 icosahedral viral capsid Source: UniProtKB-KW

    Keywords - Cellular componenti

    Capsid protein, Host cytoplasm, Host cytoplasmic vesicle, Host membrane, Membrane, T=pseudo3 icosahedral capsid protein, Virion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed; by hostBy similarity
    Chaini2 – 21502149Genome polyproteinBy similarityPRO_0000426506Add
    BLAST
    Chaini2 – 844843P1By similarityPRO_0000426507Add
    BLAST
    Chaini2 – 330329Capsid protein VP0Sequence AnalysisPRO_0000426508Add
    BLAST
    Chaini2 – 6968Capsid protein VP4Sequence AnalysisPRO_0000426509Add
    BLAST
    Chaini70 – 330261Capsid protein VP2Sequence AnalysisPRO_0000426510Add
    BLAST
    Chaini331 – 565235Capsid protein VP3Sequence AnalysisPRO_0000426511Add
    BLAST
    Chaini565 – 844280Capsid protein VP1Sequence AnalysisPRO_0000426512Add
    BLAST
    Chaini845 – 1409565P2By similarityPRO_0000426513Add
    BLAST
    Chaini845 – 992148Protease 2ASequence AnalysisPRO_0000426514Add
    BLAST
    Chaini993 – 108795Protein 2BSequence AnalysisPRO_0000040015Add
    BLAST
    Chaini1088 – 1409322Protein 2CSequence AnalysisPRO_0000040016Add
    BLAST
    Chaini1410 – 2150741P3By similarityPRO_0000426515Add
    BLAST
    Chaini1410 – 150798Protein 3ABSequence AnalysisPRO_0000426516Add
    BLAST
    Chaini1410 – 148677Protein 3ASequence AnalysisPRO_0000040017Add
    BLAST
    Chaini1487 – 150721Viral protein genome-linkedSequence AnalysisPRO_0000426517Add
    BLAST
    Chaini1508 – 2150643Protein 3CDSequence AnalysisPRO_0000426518Add
    BLAST
    Chaini1508 – 1689182Protease 3CSequence AnalysisPRO_0000426519Add
    BLAST
    Chaini1690 – 2150461RNA-directed RNA polymeraseBy similarityPRO_0000426520Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi2 – 21N-myristoyl glycine; by hostBy similarity
    Modified residuei1489 – 14891O-(5'-phospho-RNA)-tyrosineBy similarity

    Post-translational modificationi

    Specific enzymatic cleavages in vivo by the viral proteases yield a variety of precursors and mature proteins. Polyprotein processing intermediates such as VP0 which is a VP4-VP2 precursor are produced. During virion maturation, non-infectious particles are rendered infectious following cleavage of VP0. This maturation cleavage is followed by a conformational change of the particle By similarity.By similarity
    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
    Myristoylation of VP4 is required during RNA encapsidation and formation of the mature virus particle.By similarity
    Capsid protein VP0: Myristoylation is required for the formation of pentamers during virus assembly. Further assembly of 12 pentamers and a molecule of genomic RNA generates the provirion By similarity.By similarity
    Genome polyprotein: Specific enzymatic cleavages in vivo by the viral proteases yield processing intermediates and the mature proteins.By similarity
    Capsid protein VP0: During virion maturation, immature virions are rendered infectious following cleavage of VP0 into VP4 and VP2. This maturation seems to be an autocatalytic event triggered by the presence of RNA in the capsid and it is followed by a conformational change infectious virion By similarity.By similarity
    Viral protein genome-linked: VPg is uridylylated by the polymerase into VPg-pUpU. This acts as a nucleotide-peptide primer for the genomic RNA replication By similarity.By similarity

    Keywords - PTMi

    Covalent protein-RNA linkage, Lipoprotein, Myristate, Phosphoprotein

    Interactioni

    Subunit structurei

    Capsid protein VP1: Interacts with capsid protein VP0, and capsid protein VP3 to form heterotrimeric protomers. Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid. Interacts with capsid protein VP4 in the mature capsid By similarity. Interact with host VLDLR. Capsid protein VP0: interacts with capsid protein VP1 and capsid protein VP3 to form heterotrimeric protomers. Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid. Capsid protein VP2: Interacts with capsid protein VP1 and capsid protein VP3 in the mature capsid By similarity. Capsid protein VP3: interacts with capsid protein VP0 and capsid protein VP1 to form heterotrimeric protomers. Five protomers subsequently associate to form pentamers which serve as building blocks for the capsid. Interacts with capsid protein VP4 in the mature capsid By similarity. Capsid protein VP4: Interacts with capsid protein VP1 and capsid protein VP3 By similarity. Protein 2C: interacts with capsid protein VP3; this interaction may be important for virion morphogenesis By similarity. Protein 3AB: interacts with protein 3CD By similarity. Viral protein genome-linked: interacts with RNA-directed RNA polymerase By similarity. Protein 3CD: interacts with protein 3AB and with RNA-directed RNA polymerase. RNA-directed RNA polymerase: interacts with viral protein genome-linked and with protein 3CD By similarity.By similarity

    Structurei

    Secondary structure

    1
    2150
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi33 – 353
    Helixi36 – 383
    Turni52 – 543
    Beta strandi83 – 864
    Beta strandi91 – 966
    Helixi103 – 1053
    Turni113 – 1153
    Beta strandi117 – 1193
    Helixi126 – 1283
    Beta strandi138 – 1403
    Beta strandi147 – 1515
    Helixi153 – 1553
    Helixi159 – 1679
    Beta strandi168 – 18013
    Beta strandi187 – 19711
    Beta strandi203 – 2086
    Helixi213 – 2164
    Helixi219 – 2213
    Helixi233 – 2353
    Helixi241 – 2433
    Turni244 – 2474
    Helixi253 – 2553
    Beta strandi256 – 2627
    Turni263 – 2653
    Beta strandi267 – 2737
    Beta strandi278 – 2825
    Turni284 – 2863
    Beta strandi290 – 30516
    Beta strandi309 – 32517
    Turni338 – 3414
    Beta strandi353 – 3553
    Beta strandi367 – 3726
    Helixi374 – 3774
    Turni389 – 3935
    Helixi395 – 3984
    Beta strandi399 – 4035
    Beta strandi411 – 4166
    Beta strandi418 – 4214
    Helixi424 – 4263
    Helixi428 – 4336
    Beta strandi436 – 4416
    Beta strandi443 – 4497
    Beta strandi456 – 4649
    Beta strandi466 – 4683
    Helixi474 – 4785
    Beta strandi480 – 48910
    Beta strandi492 – 4976
    Beta strandi502 – 5043
    Beta strandi506 – 5094
    Beta strandi517 – 5248
    Beta strandi530 – 5323
    Beta strandi534 – 54411
    Beta strandi549 – 5535
    Turni572 – 5798
    Beta strandi581 – 5833
    Beta strandi599 – 6024
    Helixi604 – 6063
    Helixi614 – 6174
    Helixi630 – 6323
    Helixi634 – 6385
    Beta strandi642 – 6509
    Turni654 – 6585
    Beta strandi661 – 6655
    Helixi672 – 6787
    Beta strandi681 – 69818
    Beta strandi707 – 7137
    Helixi726 – 7294
    Beta strandi731 – 7333
    Beta strandi735 – 7395
    Beta strandi746 – 7494
    Beta strandi754 – 7607
    Turni774 – 7774
    Beta strandi782 – 7876
    Beta strandi796 – 81419
    Beta strandi855 – 86612
    Helixi867 – 8693
    Helixi874 – 8763
    Beta strandi878 – 8814
    Helixi882 – 8843
    Beta strandi886 – 89611
    Beta strandi906 – 9116
    Turni912 – 9154
    Beta strandi916 – 9216
    Beta strandi923 – 9308
    Beta strandi938 – 94811
    Beta strandi959 – 9624
    Beta strandi965 – 9739
    Beta strandi975 – 9828
    Helixi983 – 9864
    Helixi1509 – 152113
    Beta strandi1522 – 15276
    Beta strandi1530 – 153910
    Beta strandi1541 – 15455
    Helixi1546 – 15483
    Beta strandi1552 – 15565
    Beta strandi1559 – 157012
    Beta strandi1576 – 15849
    Helixi1593 – 15964
    Beta strandi1604 – 16118
    Beta strandi1615 – 16173
    Beta strandi1619 – 162810
    Beta strandi1632 – 16343
    Beta strandi1637 – 16393
    Beta strandi1641 – 16455
    Helixi1651 – 16533
    Beta strandi1657 – 16604
    Beta strandi1663 – 16719
    Beta strandi1676 – 16805
    Helixi1683 – 16853

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1A3RX-ray2.10P225-239[»]
    1CQQX-ray1.85A1508-1687[»]
    1FPNX-ray2.601568-856[»]
    270-330[»]
    3331-567[»]
    42-69[»]
    1V9UX-ray3.601568-856[»]
    270-330[»]
    3331-567[»]
    42-69[»]
    2HRVX-ray1.95A/B851-992[»]
    2XYAX-ray2.40A1508-1687[»]
    3DPRX-ray3.50A568-856[»]
    B70-330[»]
    C331-567[»]
    D2-69[»]
    3TN9X-ray3.001568-856[»]
    270-330[»]
    3331-567[»]
    3VDDX-ray3.20A568-850[»]
    B70-330[»]
    C331-567[»]
    D1-69[»]
    4L3BX-ray6.50A568-856[»]
    B70-330[»]
    C331-567[»]
    ProteinModelPortaliP04936.
    SMRiP04936. Positions 2-68, 81-567, 582-989, 1508-1687, 1691-2150.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04936.

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini2 – 14631462CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini1480 – 2150671CytoplasmicSequence AnalysisAdd
    BLAST

    Intramembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Intramembranei1464 – 147916Sequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1181 – 1343163SF3 helicasePROSITE-ProRule annotationAdd
    BLAST
    Domaini1508 – 1673166Peptidase C3Add
    BLAST
    Domaini1918 – 2031114RdRp catalyticPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni565 – 58117Amphipatic alpha-helixSequence AnalysisAdd
    BLAST
    Regioni1410 – 142415DisorderedBy similarityAdd
    BLAST

    Sequence similaritiesi

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

    Keywords - Domaini

    Repeat

    Family and domain databases

    Gene3Di2.60.120.20. 3 hits.
    3.40.50.300. 1 hit.
    4.10.80.10. 2 hits.
    InterProiIPR003593. AAA+_ATPase.
    IPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR014759. Helicase_SF3_ssRNA_vir.
    IPR027417. P-loop_NTPase.
    IPR014838. P3A.
    IPR000081. Peptidase_C3.
    IPR000199. Peptidase_C3A/C3B_picornavir.
    IPR003138. Pico_P1A.
    IPR002527. Pico_P2B.
    IPR001676. Picornavirus_capsid.
    IPR001205. RNA-dir_pol_C.
    IPR007094. RNA-dir_pol_PSvirus.
    IPR009003. Trypsin-like_Pept_dom.
    IPR029053. Viral_coat.
    [Graphical view]
    PfamiPF08727. P3A. 1 hit.
    PF00548. Peptidase_C3. 1 hit.
    PF02226. Pico_P1A. 1 hit.
    PF00947. Pico_P2A. 1 hit.
    PF01552. Pico_P2B. 1 hit.
    PF00680. RdRP_1. 1 hit.
    PF00073. Rhv. 3 hits.
    PF00910. RNA_helicase. 1 hit.
    [Graphical view]
    ProDomiPD001306. Peptidase_C3. 1 hit.
    PD649346. Pico_P2B. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    SMARTiSM00382. AAA. 1 hit.
    [Graphical view]
    SUPFAMiSSF50494. SSF50494. 2 hits.
    SSF52540. SSF52540. 1 hit.
    SSF89043. SSF89043. 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.

    P04936-1 [UniParc]FASTAAdd to Basket

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    MGAQVSRQNV GTHSTQNSVS NGSSLNYFNI NYFKDAASNG ASKLEFTQDP     50
    SKFTDPVKDV LEKGIPTLQS PTVEACGYSD RIIQITRGDS TITSQDVANA 100
    IVAYGVWPHY LSSKDASAID KPSQPDTSSN RFYTLRSVTW SSSSKGWWWK 150
    LPDALKDMGI FGENMFYHYL GRSGYTIHVQ CNASKFHQGT LIVALIPEHQ 200
    IASALHGNVN VGYNYTHPGE TGREVKAETR LNPDLQPTEE YWLNFDGTLL 250
    GNITIFPHQF INLRSNNSAT IIAPYVNAVP MDSMRSHNNW SLVIIPICPL 300
    ETSSAINTIP ITISISPMCA EFSGARAKRQ GLPVFITPGS GQFLTTDDFQ 350
    SPCALPWYHP TKEISIPGEV KNLVEICQVD SLVPINNTDT YINSENMYSV 400
    VLQSSINAPD KIFSIRTDVA SQPLATTLIG EISSYFTHWT GSLRFSFMFC 450
    GTANTTVKLL LAYTPPGIAE PTTRKDAMLG THVIWDVGLQ STISMVVPWI 500
    SASHYRNTSP GRSTSGYITC WYQTRLVIPP QTPPTARLLC FVSGCKDFCL 550
    RMARDTNLHL QSGAIAQNPV ENYIDEVLNE VLVVPNINSS NPTTSNSAPA 600
    LDAAETGHTS SVQPEDVIET RYVQTSQTRD EMSLESFLGR SGCIHESKLE 650
    VTLANYNKEN FTVWAINLQE MAQIRRKFEL FTYTRFDSEI TLVPCISALS 700
    QDIGHITMQY MYVPPGAPVP NSRDDYAWQS GTNASVFWQH GQAYPRFSLP 750
    FLSVASAYYM FYDGYDEQDQ NYGTANTNNM GSLCSRIVTE KHIHKVHIMT 800
    RIYHKAKHVK AWCPRPPRAL EYTRAHRTNF KIEDRSIQTA IVTRPIITTA 850
    GPSDMYVHVG NLIYRNLHLF NSEMHESILV SYSSDLIIYR TNTVGDDYIP 900
    SCDCTQATYY CKHKNRYFPI TVTSHDWYEI QESEYYPKHI QYNLLIGEGP 950
    CEPGDCGGKL LCKHGVIGIV TAGGDNHVAF IDLRHFHCAE EQGVTDYIHM 1000
    LGEAFGNGFV DSVKEHIHAI NPVGNISKKI IKWMLRIISA MVIIIRNSSD 1050
    PQTILATLTL IGCSGSPWRF LKEKFCKWTQ LNYIHKESDS WLKKFTEACN 1100
    AARGLEWIGN KISKFIEWMK SMLPQAQLKV KYLNELKKLN LYEKQVESLR 1150
    VADMKTQEKI KMEIDTLHDL SRKFLPLYAS EAKRIKTLYI KCDNIIKQKK 1200
    RCEPVAIVIH GPPGAGKSIT TNFLAKMITN DSDIYSLPPD PKYFDGYDQQ 1250
    SVVIMDDIMQ NPAGDDMTLF CQMVSSVTFI PPMADLPDKG KAFDSRFVLC 1300
    STNHSLLTPP TITSLPAMNR RFFLDLDIIV HDNFKDPQGK LNVAAAFRPC 1350
    DVDNRIGNAR CCPFVCGKAV SFKDRNSCNK YSLAQVYNIM IEEDRRRRQV 1400
    VDVMTAIFQG PIDMKNPPPP AITDLLQSVR TPEVIKYCEG NRWIIPAECK 1450
    IEKELNLANT IITIIANVIG MARIIYVIYK LFCTLQGPYS GEPKPKTKIP 1500
    ERRVVTQGPE EEFGMSLIKH NSCVITTENG KFTGLGVYDR FVVVPTHADP 1550
    GKEIQVDGIT TKVIDSYDLY NKNGIKLEIT VLKLDRNEKF RDIRRYIPNN 1600
    EDDYPNCNLA LLANQPEPTI INVGDVVSYG NILLSGNQTA RMLKYSYPTK 1650
    SGYCGGVLYK IGQVLGIHVG GNGRDGFSAM LLRSYFTDVQ GQITLSKKTS 1700
    ECNLPSIHTP CKTKLQPSVF YDVFPGSKEP AVLSEKDARL QVDFNEALFS 1750
    KYKGNTDCSI NDHIRIASSH YAAQLITLDI DPKPITLEDS VFGTDGLEAL 1800
    DLNTSAGFPY IAMGVKKRDL INNKTKDISK LKEAIDKYGV DLPMVTFLKD 1850
    ELRKHEKVIK GKTRVIEASS VNDTLLFRTT FGNLFSKFHL NPGIVTGSAV 1900
    GCDPEVFWSK IPAMLDDKCI MAFDYTNYDG SIHPIWFEAL KQVLVDLSFN 1950
    PTLIDRLCKS KHIFKNTYYE VEGGVPSGCS GTSIFNTMIN NIIIRTLVLD 2000
    AYKNIDLDKL KIIAYGDDVI FSYIHELDME AIAIEGVKYG LTITPADKSN 2050
    TFVKLDYSNV TFLKRGFKQD EKYNFLIHPT FPEDEIFESI RWTKKPSQMH 2100
    EHVLSLCHLM WHNGRDAYKK FVEKIRSVSA GRALYIPPYD LLLHEWYEKF 2150
    Length:2,150
    Mass (Da):241,978
    Last modified:January 23, 2007 - v3
    Checksum:i6E0DF9F4945D9D0C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X02316 Genomic RNA. Translation: CAA26181.1.
    PIRiA03902. GNNYH2.

    Cross-referencesi

    Web resourcesi

    Virus Particle ExploreR db

    Icosahedral capsid structure associated with cellular receptor

    Virus Particle ExploreR db

    Icosahedral capsid structure complexed with cellular receptor fragment

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X02316 Genomic RNA. Translation: CAA26181.1 .
    PIRi A03902. GNNYH2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1A3R X-ray 2.10 P 225-239 [» ]
    1CQQ X-ray 1.85 A 1508-1687 [» ]
    1FPN X-ray 2.60 1 568-856 [» ]
    2 70-330 [» ]
    3 331-567 [» ]
    4 2-69 [» ]
    1V9U X-ray 3.60 1 568-856 [» ]
    2 70-330 [» ]
    3 331-567 [» ]
    4 2-69 [» ]
    2HRV X-ray 1.95 A/B 851-992 [» ]
    2XYA X-ray 2.40 A 1508-1687 [» ]
    3DPR X-ray 3.50 A 568-856 [» ]
    B 70-330 [» ]
    C 331-567 [» ]
    D 2-69 [» ]
    3TN9 X-ray 3.00 1 568-856 [» ]
    2 70-330 [» ]
    3 331-567 [» ]
    3VDD X-ray 3.20 A 568-850 [» ]
    B 70-330 [» ]
    C 331-567 [» ]
    D 1-69 [» ]
    4L3B X-ray 6.50 A 568-856 [» ]
    B 70-330 [» ]
    C 331-567 [» ]
    ProteinModelPortali P04936.
    SMRi P04936. Positions 2-68, 81-567, 582-989, 1508-1687, 1691-2150.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi C03.007.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    SABIO-RK P04936.

    Miscellaneous databases

    EvolutionaryTracei P04936.

    Family and domain databases

    Gene3Di 2.60.120.20. 3 hits.
    3.40.50.300. 1 hit.
    4.10.80.10. 2 hits.
    InterProi IPR003593. AAA+_ATPase.
    IPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR014759. Helicase_SF3_ssRNA_vir.
    IPR027417. P-loop_NTPase.
    IPR014838. P3A.
    IPR000081. Peptidase_C3.
    IPR000199. Peptidase_C3A/C3B_picornavir.
    IPR003138. Pico_P1A.
    IPR002527. Pico_P2B.
    IPR001676. Picornavirus_capsid.
    IPR001205. RNA-dir_pol_C.
    IPR007094. RNA-dir_pol_PSvirus.
    IPR009003. Trypsin-like_Pept_dom.
    IPR029053. Viral_coat.
    [Graphical view ]
    Pfami PF08727. P3A. 1 hit.
    PF00548. Peptidase_C3. 1 hit.
    PF02226. Pico_P1A. 1 hit.
    PF00947. Pico_P2A. 1 hit.
    PF01552. Pico_P2B. 1 hit.
    PF00680. RdRP_1. 1 hit.
    PF00073. Rhv. 3 hits.
    PF00910. RNA_helicase. 1 hit.
    [Graphical view ]
    ProDomi PD001306. Peptidase_C3. 1 hit.
    PD649346. Pico_P2B. 1 hit.
    [Graphical view ] [Entries sharing at least one domain ]
    SMARTi SM00382. AAA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50494. SSF50494. 2 hits.
    SSF52540. SSF52540. 1 hit.
    SSF89043. SSF89043. 1 hit.
    PROSITEi PS50507. RDRP_SSRNA_POS. 1 hit.
    PS51218. SF3_HELICASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Human rhinovirus 2: complete nucleotide sequence and proteolytic processing signals in the capsid protein region."
      Skern T., Sommergruber W., Blaas D., Gruendler P., Fraundorfer F., Pieler C., Fogy I., Kuechler E.
      Nucleic Acids Res. 13:2111-2126(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    2. Kuechler E.
      Submitted (FEB-1986) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION.
    3. "Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro."
      Glaser W., Skern T.
      FEBS Lett. 480:151-155(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE LEADER PROTEASE.
    4. "The concerted conformational changes during human rhinovirus 2 uncoating."
      Hewat E.A., Neumann E., Blaas D.
      Mol. Cell 10:317-326(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF VP1 AND VP4.
    5. "Specific cleavage of the nuclear pore complex protein Nup62 by a viral protease."
      Park N., Skern T., Gustin K.E.
      J. Biol. Chem. 285:28796-28805(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF PROTEASE 2A.
    6. Cited for: REVIEW.
    7. "Productive entry pathways of human rhinoviruses."
      Fuchs R., Blaas D.
      Adv. Virol. 2012:826301-826301(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    8. "Three-dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2."
      Tormo J., Stadler E., Skern T., Auer H., Kanzler O., Betzel C., Blaas D., Fita I.
      Protein Sci. 1:1154-1161(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 225-239.
    9. "The structure of the 2A proteinase from a common cold virus: a proteinase responsible for the shut-off of host-cell protein synthesis."
      Petersen J.F., Cherney M.M., Liebig H.D., Skern T., Kuechler E., James M.N.
      EMBO J. 18:5463-5475(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 851-992.
    10. "Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes."
      Matthews D.A., Dragovich P.S., Webber S.E., Fuhrman S.A., Patick A.K., Zalman L.S., Hendrickson T.F., Love R.A., Prins T.J., Marakovits J.T., Zhou R., Tikhe J., Ford C.E., Meador J.W., Ferre R.A., Brown E.L., Binford S.L., Brothers M.A., DeLisle D.M., Worland S.T.
      Proc. Natl. Acad. Sci. U.S.A. 96:11000-11007(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 1508-1687.
    11. "Structure of human rhinovirus serotype 2 (HRV2)."
      Verdaguer N., Blaas D., Fita I.
      J. Mol. Biol. 300:1179-1194(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 71-856.

    Entry informationi

    Entry nameiPOLG_HRV2
    AccessioniPrimary (citable) accession number: P04936
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 158 of the entry and version 3 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