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O39929

- POLG_HCVED

UniProt

O39929 - POLG_HCVED

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Protein

Genome polyprotein

Gene
N/A
Organism
Hepatitis C virus genotype 4a (isolate ED43) (HCV)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Core protein packages viral RNA to form a viral nucleocapsid, and promotes virion budding. Modulates viral translation initiation by interacting with HCV IRES and 40S ribosomal subunit. Also regulates many host cellular functions such as signaling pathways and apoptosis. Prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) and IFN-gamma signaling pathways and by inducing human STAT1 degradation. Thought to play a role in virus-mediated cell transformation leading to hepatocellular carcinomas. Interacts with, and activates STAT3 leading to cellular transformation. May repress the promoter of p53, and sequester CREB3 and SP110 isoform 3/Sp110b in the cytoplasm. Also represses cell cycle negative regulating factor CDKN1A, thereby interrupting an important check point of normal cell cycle regulation. Targets transcription factors involved in the regulation of inflammatory responses and in the immune response: suppresses NK-kappaB activation, and activates AP-1. Could mediate apoptotic pathways through association with TNF-type receptors TNFRSF1A and LTBR, although its effect on death receptor-induced apoptosis remains controversial. Enhances TRAIL mediated apoptosis, suggesting that it might play a role in immune-mediated liver cell injury. Seric core protein is able to bind C1QR1 at the T-cell surface, resulting in down-regulation of T-lymphocytes proliferation. May transactivate human MYC, Rous sarcoma virus LTR, and SV40 promoters. May suppress the human FOS and HIV-1 LTR activity. Alters lipid metabolism by interacting with hepatocellular proteins involved in lipid accumulation and storage. Core protein induces up-regulation of FAS promoter activity, and thereby probably contributes to the increased triglyceride accumulation in hepatocytes (steatosis) (By similarity).By similarity
E1 and E2 glycoproteins form a heterodimer that is involved in virus attachment to the host cell, virion internalization through clathrin-dependent endocytosis and fusion with host membrane. E1/E2 heterodimer binds to human LDLR, CD81 and SCARB1/SR-BI receptors, but this binding is not sufficient for infection, some additional liver specific cofactors may be needed. The fusion function may possibly be carried by E1. E2 inhibits human EIF2AK2/PKR activation, preventing the establishment of an antiviral state. E2 is a viral ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on liver sinusoidal endothelial cells and macrophage-like cells of lymph node sinuses. These interactions allow capture of circulating HCV particles by these cells and subsequent transmission to permissive cells. DCs act as sentinels in various tissues where they entrap pathogens and convey them to local lymphoid tissue or lymph node for establishment of immunity. Capture of circulating HCV particles by these SIGN+ cells may facilitate virus infection of proximal hepatocytes and lymphocyte subpopulations and may be essential for the establishment of persistent infection (By similarity).By similarity
P7 seems to be a heptameric ion channel protein (viroporin) and is inhibited by the antiviral drug amantadine. Also inhibited by long-alkyl-chain iminosugar derivatives. Essential for infectivity (By similarity).By similarity
Protease NS2-3 is a cysteine protease responsible for the autocatalytic cleavage of NS2-NS3. Seems to undergo self-inactivation following maturation (By similarity).By similarity
NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS4A, is responsible for the cleavages of NS3-NS4A, NS4A-NS4B, NS4B-NS5A and NS5A-NS5B. NS3/NS4A complex also prevents phosphorylation of human IRF3, thus preventing the establishment of dsRNA induced antiviral state. NS3 RNA helicase binds to RNA and unwinds dsRNA in the 3' to 5' direction, and likely RNA stable secondary structure in the template strand. Cleaves and inhibits the host antiviral protein MAVS (By similarity).By similarity
NS4B induces a specific membrane alteration that serves as a scaffold for the virus replication complex. This membrane alteration gives rise to the so-called ER-derived membranous web that contains the replication complex (By similarity).By similarity
NS5A is a component of the replication complex involved in RNA-binding. Its interaction with Human VAPB may target the viral replication complex to vesicles. Down-regulates viral IRES translation initiation. Mediates interferon resistance, presumably by interacting with and inhibiting human EIF2AK2/PKR. Seems to inhibit apoptosis by interacting with BIN1 and FKBP8. The hyperphosphorylated form of NS5A is an inhibitor of viral replication (By similarity).By similarity
NS5B is an RNA-dependent RNA polymerase that plays an essential role in the virus replication.By similarity

Catalytic activityi

Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).PROSITE-ProRule annotation
NTP + H2O = NDP + phosphate.
ATP + H2O = ADP + phosphate.

Cofactori

Protein has several cofactor binding sites:
  • Zn2+By similarityNote: Binds 1 zinc ion per NS3 protease domain.By similarity
  • Zn2+By similarityNote: Binds 1 zinc ion per NS5A N-terminal domain.By similarity

Enzyme regulationi

Activity of auto-protease NS2-3 is dependent on zinc ions and completely inhibited by EDTA. Serine protease NS3 is also activated by zinc ions (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei177 – 1782Cleavage; by host signal peptidaseBy similarity
Sitei191 – 1922Cleavage; by host signal peptidaseSequence Analysis
Sitei383 – 3842Cleavage; by host signal peptidaseSequence Analysis
Sitei746 – 7472Cleavage; by host signal peptidaseBy similarity
Sitei809 – 8102Cleavage; by host signal peptidaseBy similarity
Active sitei952 – 9521For protease NS2-3 activity; shared with dimeric partnerPROSITE-ProRule annotation
Active sitei972 – 9721For protease NS2-3 activity; shared with dimeric partnerPROSITE-ProRule annotation
Active sitei993 – 9931For protease NS2-3 activity; shared with dimeric partnerPROSITE-ProRule annotation
Sitei1026 – 10272Cleavage; by protease NS2-3PROSITE-ProRule annotation
Active sitei1083 – 10831Charge relay system; for serine protease NS3 activityBy similarity
Active sitei1107 – 11071Charge relay system; for serine protease NS3 activityBy similarity
Metal bindingi1123 – 11231ZincBy similarity
Metal bindingi1125 – 11251ZincBy similarity
Active sitei1165 – 11651Charge relay system; for serine protease NS3 activityBy similarity
Metal bindingi1171 – 11711ZincBy similarity
Metal bindingi1175 – 11751ZincBy similarity
Sitei1657 – 16582Cleavage; by serine protease NS3Sequence Analysis
Sitei1711 – 17122Cleavage; by serine protease NS3Sequence Analysis
Sitei1972 – 19732Cleavage; by serine protease NS3Sequence Analysis
Metal bindingi2029 – 20291ZincBy similarity
Metal bindingi2031 – 20311ZincBy similarity
Metal bindingi2052 – 20521ZincBy similarity
Sitei2417 – 24182Cleavage; by serine protease NS3Sequence Analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1230 – 12378ATPPROSITE-ProRule annotation

GO - Molecular functioni

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

GO - Biological processi

  1. apoptotic process Source: UniProtKB-KW
  2. clathrin-mediated endocytosis of virus by host cell Source: UniProtKB-KW
  3. fusion of virus membrane with host endosome membrane Source: UniProtKB-KW
  4. induction by virus of host autophagy Source: UniProtKB-KW
  5. modulation by virus of host G1/S transition checkpoint Source: UniProtKB-KW
  6. pore formation by virus in membrane of host cell Source: UniProtKB-KW
  7. protein oligomerization Source: UniProtKB-KW
  8. regulation of transcription, DNA-templated Source: UniProtKB-KW
  9. suppression by virus of host MAVS activity Source: UniProtKB-KW
  10. suppression by virus of host STAT1 activity Source: UniProtKB-KW
  11. suppression by virus of host TRAF activity Source: UniProtKB-KW
  12. suppression by virus of host type I interferon-mediated signaling pathway Source: UniProtKB-KW
  13. transcription, DNA-templated Source: UniProtKB-KW
  14. transformation of host cell by virus Source: InterPro
  15. viral RNA genome replication Source: InterPro
  16. virion attachment to host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

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

Keywords - Biological processi

Activation of host autophagy by virus, Apoptosis, Clathrin-mediated endocytosis of virus by host, Fusion of virus membrane with host endosomal membrane, Fusion of virus membrane with host membrane, G1/S host cell cycle checkpoint dysregulation by virus, Host-virus interaction, Inhibition of host innate immune response by virus, Inhibition of host interferon signaling pathway by virus, Inhibition of host MAVS by virus, Inhibition of host RLR pathway by virus, Inhibition of host STAT1 by virus, Inhibition of host TRAFs by virus, Interferon antiviral system evasion, Ion transport, Modulation of host cell cycle by virus, Transcription, Transcription regulation, 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, Metal-binding, Nucleotide-binding, RNA-binding, Viral nucleoprotein, Zinc

Protein family/group databases

MEROPSiS29.001.

Names & Taxonomyi

Protein namesi
Recommended name:
Genome polyprotein
Cleaved into the following 11 chains:
Alternative name(s):
Capsid protein C
p21
Alternative name(s):
gp32
gp35
Alternative name(s):
NS1
gp68
gp70
Protease NS2-3 (EC:3.4.22.-)
Short name:
p23
Alternative name(s):
Hepacivirin
NS3P
p70
Alternative name(s):
p8
Alternative name(s):
p27
Alternative name(s):
p56
Alternative name(s):
NS5B
p68
OrganismiHepatitis C virus genotype 4a (isolate ED43) (HCV)
Taxonomic identifieri356418 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageFlaviviridaeHepacivirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
ProteomesiUP000007415: Genome

Subcellular locationi

Chain Core protein p21 : Host endoplasmic reticulum membrane By similarity; Single-pass membrane protein By similarity. Host mitochondrion membrane By similarity; Single-pass type I membrane protein By similarity. Host lipid droplet By similarity
Note: The C-terminal transmembrane domain of core protein p21 contains an ER signal leading the nascent polyprotein to the ER membrane. Only a minor proportion of core protein is present in the nucleus and an unknown proportion is secreted.
Chain Core protein p19 : Virion By similarity. Host cytoplasm By similarity. Host nucleus By similarity. Secreted By similarity
Chain Envelope glycoprotein E1 : Virion membrane Curated; Single-pass type I membrane protein Curated. Host endoplasmic reticulum membrane By similarity; Single-pass type I membrane protein By similarity
Note: The C-terminal transmembrane domain acts as a signal sequence and forms a hairpin structure before cleavage by host signal peptidase. After cleavage, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor. A reorientation of the second hydrophobic stretch occurs after cleavage producing a single reoriented transmembrane domain. These events explain the final topology of the protein. ER retention of E1 is leaky and, in overexpression conditions, only a small fraction reaches the plasma membrane.
Chain Envelope glycoprotein E2 : Virion membrane Curated; Single-pass type I membrane protein Curated. Host endoplasmic reticulum membrane By similarity; Single-pass type I membrane protein By similarity
Note: The C-terminal transmembrane domain acts as a signal sequence and forms a hairpin structure before cleavage by host signal peptidase. After cleavage, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor. A reorientation of the second hydrophobic stretch occurs after cleavage producing a single reoriented transmembrane domain. These events explain the final topology of the protein. ER retention of E2 is leaky and, in overexpression conditions, only a small fraction reaches the plasma membrane.
Chain p7 : Host endoplasmic reticulum membrane By similarity; Multi-pass membrane protein By similarity. Host cell membrane By similarity
Note: The C-terminus of p7 membrane domain acts as a signal sequence. After cleavage by host signal peptidase, the membrane sequence is retained at the C-terminus of the protein, serving as ER membrane anchor. Only a fraction localizes to the plasma membrane.
Chain Serine protease NS3 : Host endoplasmic reticulum membrane By similarity; Peripheral membrane protein By similarity
Note: NS3 is associated to the ER membrane through its binding to NS4A.
Chain Non-structural protein 4A : Host endoplasmic reticulum membrane Curated; Single-pass type I membrane protein Curated
Note: Host membrane insertion occurs after processing by the NS3 protease.
Chain Non-structural protein 5A : Host endoplasmic reticulum membrane By similarity; Peripheral membrane protein By similarity. Host cytoplasmhost perinuclear region By similarity. Host mitochondrion By similarity
Note: Host membrane insertion occurs after processing by the NS3 protease.
Chain RNA-directed RNA polymerase : Host endoplasmic reticulum membrane Curated; Single-pass type I membrane protein Curated
Note: Host membrane insertion occurs after processing by the NS3 protease.

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini2 – 168167CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei169 – 18921HelicalSequence AnalysisAdd
BLAST
Topological domaini190 – 358169LumenalSequence AnalysisAdd
BLAST
Transmembranei359 – 37921HelicalSequence AnalysisAdd
BLAST
Topological domaini380 – 725346LumenalSequence AnalysisAdd
BLAST
Transmembranei726 – 74621HelicalSequence AnalysisAdd
BLAST
Topological domaini747 – 75711LumenalSequence AnalysisAdd
BLAST
Transmembranei758 – 77821HelicalSequence AnalysisAdd
BLAST
Topological domaini779 – 7824CytoplasmicSequence Analysis
Transmembranei783 – 80321HelicalSequence AnalysisAdd
BLAST
Topological domaini804 – 81310LumenalSequence Analysis
Transmembranei814 – 83421HelicalSequence AnalysisAdd
BLAST
Topological domaini835 – 88147CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei882 – 90221HelicalSequence AnalysisAdd
BLAST
Topological domaini903 – 92826LumenalSequence AnalysisAdd
BLAST
Transmembranei929 – 94921HelicalSequence AnalysisAdd
BLAST
Topological domaini950 – 1657708CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei1658 – 167821HelicalSequence AnalysisAdd
BLAST
Topological domaini1679 – 1805127CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei1806 – 182621HelicalSequence AnalysisAdd
BLAST
Topological domaini1827 – 18282LumenalSequence Analysis
Transmembranei1829 – 184921HelicalSequence AnalysisAdd
BLAST
Topological domaini1850 – 18501CytoplasmicSequence Analysis
Transmembranei1851 – 187121HelicalSequence AnalysisAdd
BLAST
Topological domaini1872 – 188110LumenalSequence Analysis
Transmembranei1882 – 190221HelicalSequence AnalysisAdd
BLAST
Topological domaini1903 – 197270CytoplasmicSequence AnalysisAdd
BLAST
Intramembranei1973 – 200230By similarityAdd
BLAST
Topological domaini2003 – 2987985CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei2988 – 300821HelicalBy similarityAdd
BLAST

GO - Cellular componenti

  1. host cell endoplasmic reticulum Source: UniProtKB-KW
  2. host cell lipid particle Source: UniProtKB-KW
  3. host cell mitochondrion Source: UniProtKB-KW
  4. host cell nucleus Source: UniProtKB-KW
  5. host cell plasma membrane Source: UniProtKB-KW
  6. integral component of membrane Source: UniProtKB-KW
  7. integral to membrane of host cell Source: UniProtKB-KW
  8. ribonucleoprotein complex Source: UniProtKB-KW
  9. viral envelope Source: UniProtKB-KW
  10. viral nucleocapsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host endoplasmic reticulum, Host lipid droplet, Host membrane, Host mitochondrion, Host nucleus, Membrane, Secreted, Viral envelope protein, Virion

Pathology & Biotechi

Keywords - Diseasei

Oncogene

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed; by hostBy similarity
Chaini2 – 191190Core protein p21Sequence AnalysisPRO_0000045532Add
BLAST
Chaini2 – 177176Core protein p19By similarityPRO_0000045533Add
BLAST
Propeptidei178 – 19114ER anchor for the core protein, removed in mature form by host signal peptidaseBy similarityPRO_0000045534Add
BLAST
Chaini192 – 383192Envelope glycoprotein E1Sequence AnalysisPRO_0000045535Add
BLAST
Chaini384 – 746363Envelope glycoprotein E2Sequence AnalysisPRO_0000045536Add
BLAST
Chaini747 – 80963p7By similarityPRO_0000045537Add
BLAST
Chaini810 – 1026217Protease NS2-3PROSITE-ProRule annotationPRO_0000045538Add
BLAST
Chaini1027 – 1657631Serine protease NS3Sequence AnalysisPRO_0000045539Add
BLAST
Chaini1658 – 171154Non-structural protein 4ASequence AnalysisPRO_0000045540Add
BLAST
Chaini1712 – 1972261Non-structural protein 4BSequence AnalysisPRO_0000045541Add
BLAST
Chaini1973 – 2417445Non-structural protein 5ASequence AnalysisPRO_0000045542Add
BLAST
Chaini2418 – 3008591RNA-directed RNA polymeraseSequence AnalysisPRO_0000045543Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine; by hostBy similarity
Modified residuei53 – 531Phosphoserine; by hostBy similarity
Modified residuei99 – 991Phosphoserine; by hostBy similarity
Modified residuei116 – 1161Phosphoserine; by host PKABy similarity
Glycosylationi196 – 1961N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi209 – 2091N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi234 – 2341N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi305 – 3051N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi417 – 4171N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi423 – 4231N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi430 – 4301N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi448 – 4481N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi476 – 4761N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi533 – 5331N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi541 – 5411N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi557 – 5571N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi576 – 5761N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi623 – 6231N-linked (GlcNAc...); by hostSequence Analysis
Glycosylationi645 – 6451N-linked (GlcNAc...); by hostSequence Analysis
Lipidationi1968 – 19681S-palmitoyl cysteine; by hostBy similarity
Lipidationi1972 – 19721S-palmitoyl cysteine; by hostBy similarity
Disulfide bondi2114 ↔ 2162By similarity
Modified residuei2194 – 21941Phosphoserine; by host; in p56By similarity
Modified residuei2197 – 21971Phosphoserine; by host; in p58By similarity
Modified residuei2201 – 22011Phosphoserine; by host; in p58By similarity
Modified residuei2204 – 22041Phosphoserine; by host; in p58By similarity

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. The structural proteins, core, E1, E2 and p7 are produced by proteolytic processing by host signal peptidases. The core protein is synthesized as a 21 kDa precursor which is retained in the ER membrane through the hydrophobic signal peptide. Cleavage by the signal peptidase releases the 19 kDa mature core protein. The other proteins (p7, NS2-3, NS3, NS4A, NS4B, NS5A and NS5B) are cleaved by the viral proteases (By similarity).By similarity
Envelope E1 and E2 glycoproteins are highly N-glycosylated.By similarity
Core protein is phosphorylated by host PKC and PKA.By similarity
NS5A is phosphorylated in a basal form termed p56. p58 is a hyperphosphorylated form of p56. p56 and p58 coexist in the cell in roughly equivalent amounts. Hyperphosphorylation is dependent on the presence of NS4A. Human AKT1, RPS6KB1/p70S6K, MAP2K1/MEK1, MAP2K6/MKK6 and CSNK1A1/CKI-alpha kinases may be responsible for NS5A phosphorylation (By similarity).By similarity
NS4B is palmitoylated. This modification may play a role in its polymerization or in protein-protein interactions (By similarity).By similarity
The N-terminus of a fraction of NS4B molecules seems to be relocated post-translationally from the cytoplasm to the ER lumen, with a 5th transmembrane segment. The C-terminus of NS2 may be lumenal with a fourth transmembrane segment (By similarity).By similarity
Core protein is ubiquitinated; mediated by UBE3A and leading to core protein subsequent proteasomal degradation.By similarity

Keywords - PTMi

Acetylation, Disulfide bond, Glycoprotein, Lipoprotein, Palmitate, Phosphoprotein, Ubl conjugation

Interactioni

Subunit structurei

Core protein is a homomultimer that binds the C-terminal part of E1 and interacts with numerous cellular proteins. Interaction with human STAT1 SH2 domain seems to result in decreased STAT1 phosphorylation, leading to decreased IFN-stimulated gene transcription. In addition to blocking the formation of phosphorylated STAT1, the core protein also promotes ubiquitin-mediated proteasome-dependent degradation of STAT1. Interacts with, and constitutively activates human STAT3. Associates with human LTBR and TNFRSF1A receptors and possibly induces apoptosis. Binds to human SP110 isoform 3/Sp110b, HNRPK, C1QR1, YWHAE, UBE3A/E6AP, DDX3X, APOA2 and RXRA proteins. Interacts with human CREB3 nuclear transcription protein, triggering cell transformation. May interact with human p53. Also binds human cytokeratins KRT8, KRT18, KRT19 and VIM (vimentin). E1 and E2 glycoproteins form a heterodimer that binds to human LDLR, CLDN1, CD81 and SCARB1 receptors. E2 binds and inhibits human EIF2AK2/PKR. Also binds human CD209/DC-SIGN and CLEC4M/DC-SIGNR. p7 forms a homoheptamer in vitro. NS2 forms a homodimer containing a pair of composite active sites at the dimerization interface. NS2 seems to interact with all other non-structural (NS) proteins. NS4A interacts with NS3 serine protease and stabilizes its folding. NS3-NS4A complex is essential for the activation of the latter and allows membrane anchorage of NS3. NS3 interacts with human TANK-binding kinase TBK1 and MAVS. NS4B and NS5A form homodimers and seem to interact with all other non-structural (NS) proteins. NS5A also interacts with human EIF2AK2/PKR, FKBP8, GRB2, BIN1, PIK3R1, SRCAP, VAPB and with most Src-family kinases. NS5B is a homooligomer and interacts with human VAPB, HNRNPA1 and SEPT6 (By similarity).By similarity

Structurei

3D structure databases

ProteinModelPortaliO39929.
SMRiO39929. Positions 2-45, 902-1026, 1029-1657, 1973-2003, 2008-2170, 2418-2982.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini903 – 1026124Peptidase C18PROSITE-ProRule annotationAdd
BLAST
Domaini1217 – 1369153Helicase ATP-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini2631 – 2749119RdRp catalyticPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni2 – 5958Interaction with DDX3XBy similarityAdd
BLAST
Regioni2 – 2322Interaction with STAT1By similarityAdd
BLAST
Regioni122 – 17352Interaction with APOA2By similarityAdd
BLAST
Regioni150 – 15910Mitochondrial targeting signalBy similarity
Regioni164 – 1674Important for lipid droplets localizationBy similarity
Regioni265 – 29632Fusion peptideSequence AnalysisAdd
BLAST
Regioni385 – 41127HVR1By similarityAdd
BLAST
Regioni483 – 49513CD81-binding 1Sequence AnalysisAdd
BLAST
Regioni523 – 55432CD81-binding 2Sequence AnalysisAdd
BLAST
Regioni660 – 67112PKR/eIF2-alpha phosphorylation homology domain (PePHD)By similarityAdd
BLAST
Regioni1679 – 169012NS3-binding (by NS4A)Sequence AnalysisAdd
BLAST
Regioni2120 – 2329210Transcriptional activationSequence AnalysisAdd
BLAST
Regioni2120 – 220889FKBP8-bindingSequence AnalysisAdd
BLAST
Regioni2200 – 224647Basal phosphorylationBy similarityAdd
BLAST
Regioni2210 – 227263PKR-bindingSequence AnalysisAdd
BLAST
Regioni2245 – 230359NS4B-bindingSequence AnalysisAdd
BLAST
Regioni2348 – 241770Basal phosphorylationBy similarityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi5 – 139Nuclear localization signalSequence Analysis
Motifi38 – 436Nuclear localization signalSequence Analysis
Motifi58 – 647Nuclear localization signalSequence Analysis
Motifi66 – 716Nuclear localization signalSequence Analysis
Motifi1316 – 13194DECH box; atypicalBy similarity
Motifi2319 – 23224SH3-bindingSequence Analysis
Motifi2325 – 23339Nuclear localization signalSequence Analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi784 – 7907Poly-Ala
Compositional biasi798 – 8036Poly-Leu
Compositional biasi2274 – 232451Pro-richAdd
BLAST

Domaini

The transmembrane regions of envelope E1 and E2 glycoproteins are involved in heterodimer formation, ER localization, and assembly of these proteins. Envelope E2 glycoprotein contain a highly variable region called hypervariable region 1 (HVR1). E2 also contains two segments involved in CD81-binding. HVR1 is implicated in the SCARB1-mediated cell entry. CD81-binding regions may be involved in sensitivity and/or resistance to IFN-alpha therapy (By similarity).By similarity
The N-terminus of NS5A act as membrane anchor. The central part of NS5A seems to be intrinsically disordered and interacts with NS5B and host PKR (By similarity).By similarity
The SH3-binding domain of NS5A is involved in the interaction with human Bin1, GRB2 and Src-family kinases.By similarity
The N-terminal one-third of serine protease NS3 contains the protease activity. This region contains a zinc atom that does not belong to the active site, but may play a structural rather than a catalytic role. This region is essential for the activity of protease NS2-3, maybe by contributing to the folding of the latter. The helicase activity is located in the C-terminus of NS3 (By similarity).By similarity

Sequence similaritiesi

Belongs to the hepacivirus polyprotein family.Curated
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 peptidase C18 domain.PROSITE-ProRule annotation
Contains 1 peptidase S29 domain.Curated
Contains 1 RdRp catalytic domain.PROSITE-ProRule annotation

Keywords - Domaini

SH3-binding, Transmembrane, Transmembrane helix

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR002521. HCV_core_C.
IPR002522. HCV_core_N.
IPR002519. HCV_env.
IPR002531. HCV_NS1.
IPR002518. HCV_NS2.
IPR000745. HCV_NS4a.
IPR001490. HCV_NS4b.
IPR002868. HCV_NS5a.
IPR013193. HCV_NS5a_1B_dom.
IPR024350. HCV_NS5a_C.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR013192. NS5A_1a.
IPR027417. P-loop_NTPase.
IPR004109. Peptidase_S29.
IPR007094. RNA-dir_pol_PSvirus.
IPR002166. RNA_pol_HCV.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]
PfamiPF01543. HCV_capsid. 1 hit.
PF01542. HCV_core. 1 hit.
PF01539. HCV_env. 1 hit.
PF01560. HCV_NS1. 1 hit.
PF01538. HCV_NS2. 1 hit.
PF01006. HCV_NS4a. 1 hit.
PF01001. HCV_NS4b. 1 hit.
PF01506. HCV_NS5a. 1 hit.
PF08300. HCV_NS5a_1a. 1 hit.
PF08301. HCV_NS5a_1b. 1 hit.
PF12941. HCV_NS5a_C. 1 hit.
PF02907. Peptidase_S29. 1 hit.
PF00998. RdRP_3. 1 hit.
[Graphical view]
ProDomiPD001388. HCV_env. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00487. DEXDc. 1 hit.
[Graphical view]
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEiPS51693. HCV_NS2_PRO. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O39929-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSTNPKPQRK TKRNTNRRPM DVKFPGGGQI VGGVYLLPRR GPRLGVRATR
60 70 80 90 100
KTSERSQPRG RRQPIPKARR PEGRSWAQPG YPWPLYGNEG CGWAGWLLSP
110 120 130 140 150
RGSRPSWGPN DPRGRSRNLG KVIDTLTCGF ADLMGYIPLV GAPVGSVARA
160 170 180 190 200
LAHGVRALED GINYATGNLP GCSFSIFLLA LLSCLTVPAS AVNYRNVSGI
210 220 230 240 250
YHVTNDCPNS SIVYEADHHI MHLPGCVPCV REGNQSRCWV ALTPTVAAPY
260 270 280 290 300
IGAPLESLRS HVDLMVGAAT VCSGLYIGDL CGGLFLVGQM FSFRPRRHWT
310 320 330 340 350
TQDCNCSIYT GHITGHRMAW DMMMNWSPTT TLVLAQVMRI PTTLVDLLSG
360 370 380 390 400
GHWGVLVGVA YFSMQANWAK VILVLFLFAG VDAETHVSGA AVGRSTAGLA
410 420 430 440 450
NLFSSGSKQN LQLINSNGSW HINRTALNCN DSLNTGFLAS LFYTHKFNSS
460 470 480 490 500
GCSERLACCK SLDSYGQGWG PLGVANISGS SDDRPYCWHY APRPCGIVPA
510 520 530 540 550
SSVCGPVYCF TPSPVVVGTT DHVGVPTYTW GENETDVFLL NSTRPPHGAW
560 570 580 590 600
FGCVWMNSTG FTKTCGAPPC EVNTNNGTWH CPTDCFRKHP ETTYAKCGSG
610 620 630 640 650
PWITPRCLID YPYRLWHFPC TANFSVFNIR TFVGGIEHRM QAACNWTRGE
660 670 680 690 700
VCGLEHRDRV ELSPLLLTTT AWQILPCSFT TLPALSTGLI HLHQNIVDVQ
710 720 730 740 750
YLYGVGSAVV SWALKWEYVV LAFLLLADAR VSAYLWMMFM VSQVEAALSN
760 770 780 790 800
LININAASAA GAQGFWYAIL FICIVWHVKG RFPAAAAYAA CGLWPCFLLL
810 820 830 840 850
LMLPERAYAY DQEVAGSLGG AIVVMLTILT LSPHYKLWLA RGLWWIQYFI
860 870 880 890 900
ARTEAVLHVY IPSFNVRGPR DSVIVLAVLV CPDLVFDITK YLLAILGPLH
910 920 930 940 950
ILQASLLRIP YFVRAQALVK ICSLLRGVVY GKYFQMVVLK SRGLTGTYIY
960 970 980 990 1000
DHLTPMSDWP PYGLRDLAVA LEPVVFTPME KKVIVWGADT AACGDIIRGL
1010 1020 1030 1040 1050
PVSARLGNEI LLGPADTETS KGWRLLAPIT AYAQQTRGLF STIVTSLTGR
1060 1070 1080 1090 1100
DTNENCGEVQ VLSTATQSFL GTAVNGVMWT VYHGAGAKTI SGPKGPVNQM
1110 1120 1130 1140 1150
YTNVDQDLVG WPAPPGVRSL APCTCGSADL YLVTRHADVI PVRRRGDTRG
1160 1170 1180 1190 1200
ALLSPRPISI LKGSSGGPLL CPMGHRAGIF RAAVCTRGVA KAVDFVPVES
1210 1220 1230 1240 1250
LETTMRSPVF TDNSTPPAVP QTYQVAHLHA PTGSGKSTKV PAAHAAQGYK
1260 1270 1280 1290 1300
VLVLNPSVAA TLGFGVYMSK AYGIDPNIRS GVRTITTGAP ITYSTYGKFL
1310 1320 1330 1340 1350
ADGGCSGGAY DIIICDECYS TDSTTILGIG TVLDQAETAG VRLTVLATAT
1360 1370 1380 1390 1400
PPGSVTTPHS NIEEVALPTT GEIPFYGKAI PLELIKGGRH LIFCHSKKKC
1410 1420 1430 1440 1450
DELARQLTSL GLNAVAYYRG LDVSVIPTSG DVVVCATDAL MTGFTGDFDS
1460 1470 1480 1490 1500
VIDCNTSVIQ TVDFSLDPTF SIEITTVPQD AVSRSQRRGR TGRGRLGTYR
1510 1520 1530 1540 1550
YVTPGERPSG MFDTAELCEC YDAGCAWYEL TPAETTTRLK AYFDTPGLPV
1560 1570 1580 1590 1600
CQDHLEFWES VFTGLTHIDG HFLSQTKQSG ENFPYLVAYQ ATVSAKVWLA
1610 1620 1630 1640 1650
PPSWDTMWKC LIRLKPTLHG PTPLLYRLGS VQNEVVLTHP ITKYIMACMS
1660 1670 1680 1690 1700
ADLEVVTSTW VLVGGVLAAL AAYCLSVGSV VIVGRVVLSG QPAVIPDREV
1710 1720 1730 1740 1750
LYQQFDEMEE CSKHLPLVEH GLQLAEQFKQ KALGLLNFAG KQAQEATPVI
1760 1770 1780 1790 1800
QSNFAKLEQF WANDMWNFIS GIQYLAGLST LPGNPAIASL MSFTAAVTSP
1810 1820 1830 1840 1850
LTTQQTLLFN ILGGWVASQI RDSDASTAFV VSGLAGAAVG SVGLGKILVD
1860 1870 1880 1890 1900
ILPGYGAGVR GAVVTFKIMS GEMPSTEDLV NLLPAILSPG ALVVEVVCPA
1910 1920 1930 1940 1950
ILRRHVGPGE GAVQWMNRLI AFASRGNHVS PTHYVPESDA ARRVTTILSS
1960 1970 1980 1990 2000
LTVTSLLRRL HKWINEDCST PCAESWLWEV WDWVLHVLSD FKTCLKAKFV
2010 2020 2030 2040 2050
PLMPGIPLLS WPRGYKGEWR GDGVMHTTCP CGADLAGHIK NGSMRITGPK
2060 2070 2080 2090 2100
TCSNTWHGTF PINAYTTGPG VPIPAPNYKF ALWRVSAEDY VEVRRVGDFH
2110 2120 2130 2140 2150
YVTGVTQDNI KFPCQVPAPE LFTEVDGIRI HRHAPKCKPL LRDEVSFSVG
2160 2170 2180 2190 2200
LNSFVVGSQL PCEPEPDVAV LTSMLTDPSH ITAESARRRL ARGSRPSLAS
2210 2220 2230 2240 2250
SSASQLSPRL LQATCTAPHD SPGTDLLEAN LLWGSTATRV ETDEKVIILD
2260 2270 2280 2290 2300
SFESCVAEQN DDREVSVAAE ILRPTKKFPP ALPIWARPDY NPPLTETWKQ
2310 2320 2330 2340 2350
QDYQAPTVHG CALPPAKQPP VPSPRRKRTV QLTESVVSTA LAELAAKTFG
2360 2370 2380 2390 2400
QSEPSSDRDT DLTTPTETTD SGPIVVDDAS DDGSYSSMPP LEGEPGDPDL
2410 2420 2430 2440 2450
TSDSWSTVSG SEDVVCCSMS YSWTGALVTP CAAEESKLPI SPLSNSLLRH
2460 2470 2480 2490 2500
HNMVYATTTR SAVTRQKKVT FDRLQVVDST YNEVLKEIKA RASRVKPRLL
2510 2520 2530 2540 2550
TTEEACDLTP PHSARSKFGY GKKDVRSHSR KAINHISSVW KDLLDDNNTP
2560 2570 2580 2590 2600
IPTTIMAKNE VFAVNPAKGG RKPARLIVYP DLGSRVCEKR ALHDVIKKTA
2610 2620 2630 2640 2650
LAVMGAAYGF QYSPAQRVEF LLTAWKSKND PMGFSYDTRC FDSTVTEKDI
2660 2670 2680 2690 2700
RVEEEVYQCC DLEPEARKVI TALTDRLYVG GPMHNSKGDL CGYRRCRATG
2710 2720 2730 2740 2750
VYTTSFGNTL TCYLKATAAI RAAALRDCTM LVCGDDLVVI AESDGVEEDN
2760 2770 2780 2790 2800
RALRAFTEAM TRYSAPPGDA PQPAYDLELI TSCSSNVSVA HDVTGKKVYY
2810 2820 2830 2840 2850
LTRDPETPLA RAVWETVRHT PVNSWLGNII VYAPTIWVRM ILMTHFFSIL
2860 2870 2880 2890 2900
QSQEALEKAL DFDMYGVTYS ITPLDLPAII QRLHGLSAFT LHGYSPHELN
2910 2920 2930 2940 2950
RVAGALRKLG VPPLRAWRHR ARAVRAKLIA QGGRAKICGI YLFNWAVKTK
2960 2970 2980 2990 3000
LKLTPLPAAA KLDLSGWFTV GAGGGDIYHS MSHARPRYLL LCLLILTVGV

GIFLLPAR
Length:3,008
Mass (Da):327,599
Last modified:January 23, 2007 - v3
Checksum:i8E7FC932E27C406F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y11604 Genomic RNA. Translation: CAA72338.1.
PIRiPQ0804.
RefSeqiYP_001469632.1. NC_009825.1.

Genome annotation databases

GeneIDi11027168.

Cross-referencesi

Web resourcesi

euHCVdb

The European HCV database

Virus Pathogen Resource

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y11604 Genomic RNA. Translation: CAA72338.1 .
PIRi PQ0804.
RefSeqi YP_001469632.1. NC_009825.1.

3D structure databases

ProteinModelPortali O39929.
SMRi O39929. Positions 2-45, 902-1026, 1029-1657, 1973-2003, 2008-2170, 2418-2982.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi S29.001.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 11027168.

Organism-specific databases

euHCVdbi Y11604.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR002521. HCV_core_C.
IPR002522. HCV_core_N.
IPR002519. HCV_env.
IPR002531. HCV_NS1.
IPR002518. HCV_NS2.
IPR000745. HCV_NS4a.
IPR001490. HCV_NS4b.
IPR002868. HCV_NS5a.
IPR013193. HCV_NS5a_1B_dom.
IPR024350. HCV_NS5a_C.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR013192. NS5A_1a.
IPR027417. P-loop_NTPase.
IPR004109. Peptidase_S29.
IPR007094. RNA-dir_pol_PSvirus.
IPR002166. RNA_pol_HCV.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view ]
Pfami PF01543. HCV_capsid. 1 hit.
PF01542. HCV_core. 1 hit.
PF01539. HCV_env. 1 hit.
PF01560. HCV_NS1. 1 hit.
PF01538. HCV_NS2. 1 hit.
PF01006. HCV_NS4a. 1 hit.
PF01001. HCV_NS4b. 1 hit.
PF01506. HCV_NS5a. 1 hit.
PF08300. HCV_NS5a_1a. 1 hit.
PF08301. HCV_NS5a_1b. 1 hit.
PF12941. HCV_NS5a_C. 1 hit.
PF02907. Peptidase_S29. 1 hit.
PF00998. RdRP_3. 1 hit.
[Graphical view ]
ProDomi PD001388. HCV_env. 1 hit.
[Graphical view ] [Entries sharing at least one domain ]
SMARTi SM00487. DEXDc. 1 hit.
[Graphical view ]
SUPFAMi SSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEi PS51693. HCV_NS2_PRO. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East."
    Chamberlain R.W., Adams N., Saeed A.A., Simmonds P., Elliott R.M.
    J. Gen. Virol. 78:1341-1347(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Properties of the hepatitis C virus core protein: a structural protein that modulates cellular processes."
    McLauchlan J.
    J. Viral Hepat. 7:2-14(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  3. Cited for: REVIEW, SUBCELLULAR LOCATION.
  4. "An RNA-binding protein, hnRNP A1, and a scaffold protein, septin 6, facilitate hepatitis C virus replication."
    Kim C.S., Seol S.K., Song O.-K., Park J.H., Jang S.K.
    J. Virol. 81:3852-3865(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HNRNPA1 AND SEPT6.

Entry informationi

Entry nameiPOLG_HCVED
AccessioniPrimary (citable) accession number: O39929
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

Cell culture adaptation of the virus leads to mutations in NS5A, reducing its inhibitory effect on replication.By similarity
Core protein exerts viral interference on hepatitis B virus when HCV and HBV coinfect the same cell, by suppressing HBV gene expression, RNA encapsidation and budding.By similarity

Caution

The core gene probably also codes for alternative reading frame proteins (ARFPs). Many functions depicted for the core protein might belong to the ARFPs.Curated

Keywords - Technical termi

Complete proteome, Multifunctional enzyme

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3