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P04936

- POLG_HRV2

UniProt

P04936 - POLG_HRV2

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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

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
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

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.

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini2 – 14631462CytoplasmicSequence AnalysisAdd
BLAST
Intramembranei1464 – 147916Sequence AnalysisAdd
BLAST
Topological domaini1480 – 2150671CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

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

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.

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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        10         20         30         40         50
MGAQVSRQNV GTHSTQNSVS NGSSLNYFNI NYFKDAASNG ASKLEFTQDP
60 70 80 90 100
SKFTDPVKDV LEKGIPTLQS PTVEACGYSD RIIQITRGDS TITSQDVANA
110 120 130 140 150
IVAYGVWPHY LSSKDASAID KPSQPDTSSN RFYTLRSVTW SSSSKGWWWK
160 170 180 190 200
LPDALKDMGI FGENMFYHYL GRSGYTIHVQ CNASKFHQGT LIVALIPEHQ
210 220 230 240 250
IASALHGNVN VGYNYTHPGE TGREVKAETR LNPDLQPTEE YWLNFDGTLL
260 270 280 290 300
GNITIFPHQF INLRSNNSAT IIAPYVNAVP MDSMRSHNNW SLVIIPICPL
310 320 330 340 350
ETSSAINTIP ITISISPMCA EFSGARAKRQ GLPVFITPGS GQFLTTDDFQ
360 370 380 390 400
SPCALPWYHP TKEISIPGEV KNLVEICQVD SLVPINNTDT YINSENMYSV
410 420 430 440 450
VLQSSINAPD KIFSIRTDVA SQPLATTLIG EISSYFTHWT GSLRFSFMFC
460 470 480 490 500
GTANTTVKLL LAYTPPGIAE PTTRKDAMLG THVIWDVGLQ STISMVVPWI
510 520 530 540 550
SASHYRNTSP GRSTSGYITC WYQTRLVIPP QTPPTARLLC FVSGCKDFCL
560 570 580 590 600
RMARDTNLHL QSGAIAQNPV ENYIDEVLNE VLVVPNINSS NPTTSNSAPA
610 620 630 640 650
LDAAETGHTS SVQPEDVIET RYVQTSQTRD EMSLESFLGR SGCIHESKLE
660 670 680 690 700
VTLANYNKEN FTVWAINLQE MAQIRRKFEL FTYTRFDSEI TLVPCISALS
710 720 730 740 750
QDIGHITMQY MYVPPGAPVP NSRDDYAWQS GTNASVFWQH GQAYPRFSLP
760 770 780 790 800
FLSVASAYYM FYDGYDEQDQ NYGTANTNNM GSLCSRIVTE KHIHKVHIMT
810 820 830 840 850
RIYHKAKHVK AWCPRPPRAL EYTRAHRTNF KIEDRSIQTA IVTRPIITTA
860 870 880 890 900
GPSDMYVHVG NLIYRNLHLF NSEMHESILV SYSSDLIIYR TNTVGDDYIP
910 920 930 940 950
SCDCTQATYY CKHKNRYFPI TVTSHDWYEI QESEYYPKHI QYNLLIGEGP
960 970 980 990 1000
CEPGDCGGKL LCKHGVIGIV TAGGDNHVAF IDLRHFHCAE EQGVTDYIHM
1010 1020 1030 1040 1050
LGEAFGNGFV DSVKEHIHAI NPVGNISKKI IKWMLRIISA MVIIIRNSSD
1060 1070 1080 1090 1100
PQTILATLTL IGCSGSPWRF LKEKFCKWTQ LNYIHKESDS WLKKFTEACN
1110 1120 1130 1140 1150
AARGLEWIGN KISKFIEWMK SMLPQAQLKV KYLNELKKLN LYEKQVESLR
1160 1170 1180 1190 1200
VADMKTQEKI KMEIDTLHDL SRKFLPLYAS EAKRIKTLYI KCDNIIKQKK
1210 1220 1230 1240 1250
RCEPVAIVIH GPPGAGKSIT TNFLAKMITN DSDIYSLPPD PKYFDGYDQQ
1260 1270 1280 1290 1300
SVVIMDDIMQ NPAGDDMTLF CQMVSSVTFI PPMADLPDKG KAFDSRFVLC
1310 1320 1330 1340 1350
STNHSLLTPP TITSLPAMNR RFFLDLDIIV HDNFKDPQGK LNVAAAFRPC
1360 1370 1380 1390 1400
DVDNRIGNAR CCPFVCGKAV SFKDRNSCNK YSLAQVYNIM IEEDRRRRQV
1410 1420 1430 1440 1450
VDVMTAIFQG PIDMKNPPPP AITDLLQSVR TPEVIKYCEG NRWIIPAECK
1460 1470 1480 1490 1500
IEKELNLANT IITIIANVIG MARIIYVIYK LFCTLQGPYS GEPKPKTKIP
1510 1520 1530 1540 1550
ERRVVTQGPE EEFGMSLIKH NSCVITTENG KFTGLGVYDR FVVVPTHADP
1560 1570 1580 1590 1600
GKEIQVDGIT TKVIDSYDLY NKNGIKLEIT VLKLDRNEKF RDIRRYIPNN
1610 1620 1630 1640 1650
EDDYPNCNLA LLANQPEPTI INVGDVVSYG NILLSGNQTA RMLKYSYPTK
1660 1670 1680 1690 1700
SGYCGGVLYK IGQVLGIHVG GNGRDGFSAM LLRSYFTDVQ GQITLSKKTS
1710 1720 1730 1740 1750
ECNLPSIHTP CKTKLQPSVF YDVFPGSKEP AVLSEKDARL QVDFNEALFS
1760 1770 1780 1790 1800
KYKGNTDCSI NDHIRIASSH YAAQLITLDI DPKPITLEDS VFGTDGLEAL
1810 1820 1830 1840 1850
DLNTSAGFPY IAMGVKKRDL INNKTKDISK LKEAIDKYGV DLPMVTFLKD
1860 1870 1880 1890 1900
ELRKHEKVIK GKTRVIEASS VNDTLLFRTT FGNLFSKFHL NPGIVTGSAV
1910 1920 1930 1940 1950
GCDPEVFWSK IPAMLDDKCI MAFDYTNYDG SIHPIWFEAL KQVLVDLSFN
1960 1970 1980 1990 2000
PTLIDRLCKS KHIFKNTYYE VEGGVPSGCS GTSIFNTMIN NIIIRTLVLD
2010 2020 2030 2040 2050
AYKNIDLDKL KIIAYGDDVI FSYIHELDME AIAIEGVKYG LTITPADKSN
2060 2070 2080 2090 2100
TFVKLDYSNV TFLKRGFKQD EKYNFLIHPT FPEDEIFESI RWTKKPSQMH
2110 2120 2130 2140 2150
EHVLSLCHLM WHNGRDAYKK FVEKIRSVSA GRALYIPPYD LLLHEWYEKF
Length:2,150
Mass (Da):241,978
Last modified:January 23, 2007 - v3
Checksum:i6E0DF9F4945D9D0C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
X02316 Genomic RNA. Translation: CAA26181.1 .
PIRi A03902. GNNYH2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 160 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