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Q5I2N3 (POLG_HCV6A) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 90. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Genome polyprotein

Cleaved into the following 11 chains:

  1. Core protein p21
    Alternative name(s):
    Capsid protein C
    p21
  2. Core protein p19
  3. Envelope glycoprotein E1
    Alternative name(s):
    gp32
    gp35
  4. Envelope glycoprotein E2
    Alternative name(s):
    NS1
    gp68
    gp70
  5. p7
  6. Protease NS2-3
    Short name=p23
    EC=3.4.22.-
  7. Serine protease NS3
    EC=3.4.21.98
    EC=3.6.1.15
    EC=3.6.4.13
    Alternative name(s):
    Hepacivirin
    NS3P
    p70
  8. Non-structural protein 4A
    Short name=NS4A
    Alternative name(s):
    p8
  9. Non-structural protein 4B
    Short name=NS4B
    Alternative name(s):
    p27
  10. Non-structural protein 5A
    Short name=NS5A
    Alternative name(s):
    p56
  11. RNA-directed RNA polymerase
    EC=2.7.7.48
    Alternative name(s):
    NS5B
    p68
OrganismHepatitis C virus genotype 6a (isolate 6a33) (HCV) [Complete proteome]
Taxonomic identifier356391 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageFlaviviridaeHepacivirus
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length3019 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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/Sp110bin 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.

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.

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.

Protease NS2-3 is a cysteine protease responsible for the autocatalytic cleavage of NS2-NS3. Seems to undergo self-inactivation following maturation 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.

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.

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.

NS5B is an RNA-dependent RNA polymerase that plays an essential role in the virus replication By similarity.

Catalytic activity

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).

NTP + H2O = NDP + phosphate.

ATP + H2O = ADP + phosphate.

Cofactor

Binds 1 zinc ion per NS3 protease domain By similarity.

Binds 1 zinc ion per NS5A N-terminal domain By similarity.

Enzyme regulation

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.

Subunit structure

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. Ref.4

Subcellular location

Core protein p21: Host endoplasmic reticulum membrane; Single-pass membrane protein By similarity. Host mitochondrion membrane; 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. Ref.3

Core protein p19: Virion By similarity. Host cytoplasm By similarity. Host nucleus By similarity. Secreted By similarity Ref.3.

Envelope glycoprotein E1: Virion membrane; Single-pass type I membrane protein Potential. Host endoplasmic reticulum membrane; 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. Ref.3

Envelope glycoprotein E2: Virion membrane; Single-pass type I membrane protein Potential. Host endoplasmic reticulum membrane; 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. Ref.3

p7: Host endoplasmic reticulum membrane; Multi-pass membrane protein By similarity Ref.3. 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. Ref.3

Protease NS2-3: Host endoplasmic reticulum membrane; Multi-pass membrane protein Potential Ref.3.

Serine protease NS3: Host endoplasmic reticulum membrane; Peripheral membrane protein By similarity. Note: NS3 is associated to the ER membrane through its binding to NS4A. Ref.3

Non-structural protein 4A: Host endoplasmic reticulum membrane; Single-pass type I membrane protein Potential. Note: Host membrane insertion occurs after processing by the NS3 protease. Ref.3

Non-structural protein 4B: Host endoplasmic reticulum membrane; Multi-pass membrane protein By similarity Ref.3.

Non-structural protein 5A: Host endoplasmic reticulum membrane; 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. Ref.3

RNA-directed RNA polymerase: Host endoplasmic reticulum membrane; Single-pass type I membrane protein Potential. Note: Host membrane insertion occurs after processing by the NS3 protease. Ref.3

Domain

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.

The N-terminus of NS5A acts as membrane anchor. The central part of NS5A seems to be intrinsically disordered and interacts with NS5B and host PKR 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.

Post-translational modification

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.

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.

NS4B is palmitoylated. This modification may play a role in its polymerization or in protein-protein interactions 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.

Core protein is ubiquitinated; mediated by UBE3A and leading to core protein subsequent proteasomal degradation By similarity.

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.

Sequence similarities

Belongs to the hepacivirus polyprotein family.

Contains 1 helicase ATP-binding domain.

Contains 1 peptidase C18 domain.

Contains 1 peptidase S29 domain.

Contains 1 RdRp catalytic domain.

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.

Ontologies

Keywords
   Biological processActivation 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
   Cellular componentCapsid protein
Host cell membrane
Host cytoplasm
Host endoplasmic reticulum
Host lipid droplet
Host membrane
Host mitochondrion
Host nucleus
Membrane
Secreted
Viral envelope protein
Virion
   DiseaseOncogene
   DomainSH3-binding
Transmembrane
Transmembrane helix
   LigandATP-binding
Metal-binding
Nucleotide-binding
RNA-binding
Viral nucleoprotein
Zinc
   Molecular functionHelicase
Hydrolase
Ion channel
Nucleotidyltransferase
Protease
Ribonucleoprotein
RNA-directed RNA polymerase
Serine protease
Thiol protease
Transferase
Viral ion channel
   PTMAcetylation
Disulfide bond
Glycoprotein
Lipoprotein
Palmitate
Phosphoprotein
Ubl conjugation
   Technical termComplete proteome
Multifunctional enzyme
Gene Ontology (GO)
   Biological_processapoptotic process

Inferred from electronic annotation. Source: UniProtKB-KW

clathrin-mediated endocytosis of virus by host cell

Inferred from electronic annotation. Source: UniProtKB-KW

fusion of virus membrane with host endosome membrane

Inferred from electronic annotation. Source: UniProtKB-KW

induction by virus of host autophagy

Inferred from electronic annotation. Source: UniProtKB-KW

modulation by virus of host G1/S transition checkpoint

Inferred from electronic annotation. Source: UniProtKB-KW

pore formation by virus in membrane of host cell

Inferred from electronic annotation. Source: UniProtKB-KW

protein oligomerization

Inferred from electronic annotation. Source: UniProtKB-KW

proteolysis

Inferred from electronic annotation. Source: UniProtKB-KW

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host MAVS activity

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host STAT1 activity

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host TRAF activity

Inferred from electronic annotation. Source: UniProtKB-KW

suppression by virus of host type I interferon-mediated signaling pathway

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

transformation of host cell by virus

Inferred from electronic annotation. Source: InterPro

viral RNA genome replication

Inferred from electronic annotation. Source: InterPro

virion attachment to host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componenthost cell endoplasmic reticulum membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell lipid particle

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell mitochondrial membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell perinuclear region of cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

host cell plasma membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

integral component of membrane

Inferred from electronic annotation. Source: UniProtKB-KW

integral to membrane of host cell

Inferred from electronic annotation. Source: UniProtKB-KW

ribonucleoprotein complex

Inferred from electronic annotation. Source: UniProtKB-KW

viral envelope

Inferred from electronic annotation. Source: UniProtKB-KW

viral nucleocapsid

Inferred from electronic annotation. Source: UniProtKB-KW

virion membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

ATP-dependent helicase activity

Inferred from electronic annotation. Source: InterPro

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA-directed RNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

cysteine-type endopeptidase activity

Inferred from electronic annotation. Source: InterPro

ion channel activity

Inferred from electronic annotation. Source: UniProtKB-KW

serine-type endopeptidase activity

Inferred from electronic annotation. Source: InterPro

serine-type exopeptidase activity

Inferred from electronic annotation. Source: InterPro

structural molecule activity

Inferred from electronic annotation. Source: InterPro

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host By similarity
Chain2 – 191190Core protein p21 Potential
PRO_0000045508
Chain2 – 177176Core protein p19 By similarity
PRO_0000045509
Propeptide178 – 19114ER anchor for the core protein, removed in mature form by host signal peptidase By similarity
PRO_0000045510
Chain192 – 383192Envelope glycoprotein E1 Potential
PRO_0000045511
Chain384 – 751368Envelope glycoprotein E2 Potential
PRO_0000045512
Chain752 – 81463p7 By similarity
PRO_0000045513
Chain815 – 1031217Protease NS2-3 Potential
PRO_0000045514
Chain1032 – 1662631Serine protease NS3 Potential
PRO_0000045515
Chain1663 – 171654Non-structural protein 4A Potential
PRO_0000045516
Chain1717 – 1977261Non-structural protein 4B Potential
PRO_0000045517
Chain1978 – 2428451Non-structural protein 5A Potential
PRO_0000045518
Chain2429 – 3019591RNA-directed RNA polymerase Potential
PRO_0000045519

Regions

Topological domain2 – 168167Cytoplasmic Potential
Transmembrane169 – 18921Helical; Potential
Topological domain190 – 358169Lumenal Potential
Transmembrane359 – 37921Helical; Potential
Topological domain380 – 730351Lumenal Potential
Transmembrane731 – 75121Helical; Potential
Topological domain752 – 76211Lumenal Potential
Transmembrane763 – 78321Helical; Potential
Topological domain784 – 7874Cytoplasmic Potential
Transmembrane788 – 80821Helical; Potential
Topological domain809 – 81810Lumenal Potential
Transmembrane819 – 83921Helical; Potential
Topological domain840 – 88647Cytoplasmic Potential
Transmembrane887 – 90721Helical; Potential
Topological domain908 – 93326Lumenal Potential
Transmembrane934 – 95421Helical; Potential
Topological domain955 – 1662708Cytoplasmic Potential
Transmembrane1663 – 168321Helical; Potential
Topological domain1684 – 1810127Cytoplasmic Potential
Transmembrane1811 – 183121Helical; Potential
Topological domain1832 – 18332Lumenal Potential
Transmembrane1834 – 185421Helical; Potential
Topological domain18551Cytoplasmic Potential
Transmembrane1856 – 187621Helical; Potential
Topological domain1877 – 188610Lumenal Potential
Transmembrane1887 – 190721Helical; Potential
Topological domain1908 – 197770Cytoplasmic Potential
Intramembrane1978 – 200730 By similarity
Topological domain2008 – 2998991Cytoplasmic Potential
Transmembrane2999 – 301921Helical; By similarity
Domain908 – 1031124Peptidase C18
Domain1222 – 1374153Helicase ATP-binding
Domain2642 – 2760119RdRp catalytic
Nucleotide binding1235 – 12428ATP Potential
Region2 – 5958Interaction with DDX3X By similarity
Region2 – 2322Interaction with STAT1 By similarity
Region122 – 17352Interaction with APOA2 By similarity
Region150 – 15910Mitochondrial targeting signal By similarity
Region164 – 1674Important for lipid droplets localization By similarity
Region265 – 29632Fusion peptide Potential
Region384 – 41027HVR1 By similarity
Region483 – 49513CD81-binding 1 Potential
Region523 – 55432CD81-binding 2 Potential
Region665 – 67612PKR/eIF2-alpha phosphorylation homology domain (PePHD) By similarity
Region1684 – 169512NS3-binding (by NS4A) Potential
Region2125 – 2338214Transcriptional activation Potential
Region2125 – 221389FKBP8-binding Potential
Region2205 – 225551Basal phosphorylation By similarity
Region2215 – 228066PKR-binding Potential
Region2254 – 231259NS4B-binding Potential
Region2357 – 242872Basal phosphorylation By similarity
Motif5 – 139Nuclear localization signal Potential
Motif38 – 436Nuclear localization signal Potential
Motif58 – 647Nuclear localization signal Potential
Motif66 – 716Nuclear localization signal Potential
Motif1321 – 13244DECH box By similarity
Motif2328 – 23314SH3-binding Potential
Motif2333 – 23419Nuclear localization signal Potential
Compositional bias2282 – 233352Pro-rich
Compositional bias2999 – 30079Poly-Leu

Sites

Active site9571For protease NS2-3 activity; shared with dimeric partner By similarity
Active site9771For protease NS2-3 activity; shared with dimeric partner By similarity
Active site9981For protease NS2-3 activity; shared with dimeric partner By similarity
Active site10881Charge relay system; for serine protease NS3 activity By similarity
Active site11121Charge relay system; for serine protease NS3 activity By similarity
Active site11701Charge relay system; for serine protease NS3 activity By similarity
Metal binding11281Zinc By similarity
Metal binding11301Zinc By similarity
Metal binding11761Zinc By similarity
Metal binding11801Zinc By similarity
Metal binding20161Zinc By similarity
Metal binding20341Zinc By similarity
Metal binding20361Zinc By similarity
Metal binding20571Zinc By similarity
Site177 – 1782Cleavage; by host signal peptidase By similarity
Site191 – 1922Cleavage; by host signal peptidase Potential
Site383 – 3842Cleavage; by host signal peptidase Potential
Site751 – 7522Cleavage; by host signal peptidase By similarity
Site814 – 8152Cleavage; by host signal peptidase By similarity
Site1031 – 10322Cleavage; by protease NS2-3 Potential
Site1662 – 16632Cleavage; by serine protease NS3 Potential
Site1716 – 17172Cleavage; by serine protease NS3 Potential
Site1977 – 19782Cleavage; by serine protease NS3 Potential
Site2428 – 24292Cleavage; by serine protease NS3 Potential

Amino acid modifications

Modified residue21N-acetylserine; by host By similarity
Modified residue531Phosphoserine; by host By similarity
Modified residue991Phosphoserine; by host By similarity
Modified residue1161Phosphoserine; by host PKA By similarity
Modified residue21991Phosphoserine; by host; in p56 By similarity
Modified residue22021Phosphoserine; by host; in p58 By similarity
Modified residue22061Phosphoserine; by host; in p58 By similarity
Modified residue22091Phosphoserine; by host; in p58 By similarity
Lipidation19771S-palmitoyl cysteine; by host By similarity
Glycosylation1961N-linked (GlcNAc...); by host Potential
Glycosylation2091N-linked (GlcNAc...); by host Potential
Glycosylation2341N-linked (GlcNAc...); by host Potential
Glycosylation2501N-linked (GlcNAc...); by host Potential
Glycosylation3051N-linked (GlcNAc...); by host Potential
Glycosylation4151N-linked (GlcNAc...); by host Potential
Glycosylation4221N-linked (GlcNAc...); by host Potential
Glycosylation4291N-linked (GlcNAc...); by host Potential
Glycosylation4471N-linked (GlcNAc...); by host Potential
Glycosylation4761N-linked (GlcNAc...); by host Potential
Glycosylation5331N-linked (GlcNAc...); by host Potential
Glycosylation5571N-linked (GlcNAc...); by host Potential
Glycosylation5781N-linked (GlcNAc...); by host Potential
Glycosylation6281N-linked (GlcNAc...); by host Potential
Glycosylation6501N-linked (GlcNAc...); by host Potential
Disulfide bond2119 ↔ 2167 By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5I2N3 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: FF1161164B164DF3

FASTA3,019328,857
        10         20         30         40         50         60 
MSTLPKPQRK TKRNTNRRPM DVKFPGGGQI VGGVYLLPRR GPRLGVRATR KTSERSQPRG 

        70         80         90        100        110        120 
RRQPIPKARQ PQGRHWAQPG YPWPLYGNEG CGWAGWLLSP RGSRPHWGPN DPRRRSRNLG 

       130        140        150        160        170        180 
KVIDTLTCGF ADLMGYIPVV GAPLGGVAAA LAHGVRAIED GINYATGNLP GCSFSIFLLA 

       190        200        210        220        230        240 
LLSCLTTPAS ALTYGNSSGL YHLTNDCPNS SIVLEADAMI LHLPGCLPCV KVGNQSTCWH 

       250        260        270        280        290        300 
AVSPTLAIPN ASTPATGFRR HVDLLAGAAV VCSSLYIGDL CGSLFLAGQL FTFQPRRHWT 

       310        320        330        340        350        360 
VQECNCSIYT GHVTGHRMAW DMMMSWSPTT TLVLSSILRV PEICASVIFG GHWGILLAVA 

       370        380        390        400        410        420 
YFGMAGNWLK VLAVLFLFAG VEATTTVGHG VARTTAGITG LFSPGASQNL QLIKNGSSWH 

       430        440        450        460        470        480 
INRTALNCND SLQTGFLASL FYVRKFNSSG CPERMAVCKS LADFRQGWGQ ITYKVNISGP 

       490        500        510        520        530        540 
SDDRPYCWHY APRPCDVVPA STVCGPVYCF TPSPVVIGTT DRRGNPTYTW GENETDVFML 

       550        560        570        580        590        600 
ESLRPPTGGW FGCTWMNSTG FTKTCGAPPC QIIPGDYNSS ANELLCPTDC FRKHPEATYQ 

       610        620        630        640        650        660 
RCGSGPWVTP RCLVDYPYRL WHYPCTVNFT VHKVRMFVGG IEHRFDAACN WTRGERCELH 

       670        680        690        700        710        720 
DRDRIEMSPL LFSTTQLAIL PCSFSTMPAL STGLIHLHQN IVDVQYLYGV SSSVTSWVVK 

       730        740        750        760        770        780 
WEYIVLMFLV LADARICTCL WLMLLISNVE AAVERLVVLN AASAAGTAGW WWAVLFLCCV 

       790        800        810        820        830        840 
WYVKGRLVPA CTYMALGMWP LLLTILALPH RAYAMDNEQA ASLGAVGLLA ITIFTITPTY 

       850        860        870        880        890        900 
KKLLTCFIWW NQYFLARAEA MVHEWVPDLR VRGGRDSIIL LTCLLHPQLG FEVTKILLAI 

       910        920        930        940        950        960 
LAPLYILQYS LLKVPYFVRA HILLRACLLV RRLAGGRYVQ ACLLRLGAWT GTFIYDHLAP 

       970        980        990       1000       1010       1020 
LSDWASDGLR DLAVAVEPVI FSPMEKKIIT WGADTAACGD ILSGLPVSAR LGNLVLLGPA 

      1030       1040       1050       1060       1070       1080 
DDMQRGGWKL LAPITAYAQQ TRGLVGTIVT SLTGRDKNEV EGEVQVVSTA TQSFLATSIN 

      1090       1100       1110       1120       1130       1140 
GVMWTVYHGA GSKTLAGPKG PVCQMYTNVD KDLVGWPSPP GARSLTPCTC GSSDLYLVTR 

      1150       1160       1170       1180       1190       1200 
EADVIPARRR GDNRAALLSP RPISTLKGSS GGPVMCPSGH VVGLFRAAVC TRGVAKSLDF 

      1210       1220       1230       1240       1250       1260 
IPVENMETTM RSPSFTDNST PPAVPQTYQV GYLHAPTGSG KSTRVPAAYA SQGYKVLVLN 

      1270       1280       1290       1300       1310       1320 
PSVAATLSFG SYMRQAYGVE PNVRTGVRTV TTGGAITYST YGKFLADGGC SGGAYDIIIC 

      1330       1340       1350       1360       1370       1380 
DECHSTDPTT VLGIGTVLDQ AETAGARLTV LATATPPGSI TVPHPNITET ALPTTGEIPF 

      1390       1400       1410       1420       1430       1440 
YGKAIPLEYI KGGRHLIFCH SKKKCDELAG KLKSLGLNAV AFYRGVDVSV IPTSGDVVIC 

      1450       1460       1470       1480       1490       1500 
ATDALMTGYT GDFDSVIDCN VAVTQVVDFS LDPTFSIETT TVPQDAVSRS QRRGRTGRGK 

      1510       1520       1530       1540       1550       1560 
PGVYRFVSQG ERPSGMFDTV VLCEAYDTGC AWYELTPSET TVRLRAYMNT PGLPVCQDHL 

      1570       1580       1590       1600       1610       1620 
EFWEGVFTGL THIDAHFLSQ TKQGGENFAY LVAYQATVCA RAKAPPPSWD TMWKCLIRLK 

      1630       1640       1650       1660       1670       1680 
PTLTGPTPLL YRLGAVQNEI ITTHPITKYI MTCMSADLEV ITSTWVLVGG VLAALAAYCL 

      1690       1700       1710       1720       1730       1740 
SVGCVVICGR ITLTGKPAVV PDREILYQQF DEMEECSRHI PYLAEGQQIA EQFRQKVLGL 

      1750       1760       1770       1780       1790       1800 
LQASAKQAEE LKPAVHSAWP RMEEFWRKHM WNFVSGIQYL AGLSTLPGNP AVASLMSFTA 

      1810       1820       1830       1840       1850       1860 
SLTSPLRTSQ TLLLNILGGW IAAQVAPPPA STAFVVSGLA GAAVGSIRLG RVLVDVLAGY 

      1870       1880       1890       1900       1910       1920 
GAGVSGALVA FKIMSGDCPT TEDMVNLLPA LLSPGALVVG VVCAAILRRH VGPAEGANQW 

      1930       1940       1950       1960       1970       1980 
MNRLIAFASR GNHVSPTHYV PETDASKNVT QILTSLTITS LLRRLHQWVN EDTATPCATS 

      1990       2000       2010       2020       2030       2040 
WLRDVWDWVC TVLSDFKVWL QAKLFPRLPG IPFLSCQTGY RGVWAGDGVC HTTCTCGAVI 

      2050       2060       2070       2080       2090       2100 
AGHVKNGTMK ITGPKTCSNT WHGTFPINAT TTGPSTPRPA PNYQRALWRV SAEDYVEVRR 

      2110       2120       2130       2140       2150       2160 
LGDCHYVVGV TAEGLKCPCQ VPAPEFFTEV DGVRIHRYAP PCKPLLRDEV TFSVGLSNYA 

      2170       2180       2190       2200       2210       2220 
IGSQLPCEPE PDVTVVTSML TDPTHITAET ASRRLKRGSP PSLASSSASQ LSAPSLKATC 

      2230       2240       2250       2260       2270       2280 
TTSKDHPDME LIEANLLWRQ EMGGNITRVE SENKVVVLDS FEPLTAEYDE REISVSAECH 

      2290       2300       2310       2320       2330       2340 
RPPRHKFPPA LPIWARPDYN PPLLQAWQMP GYEPPVVSGC AVAPPKPAPI PPPRRKRLVH 

      2350       2360       2370       2380       2390       2400 
LDESTVSRAL AQLADKVFVE GSSDPGPSSD SGLSITSPDP PAPTTPDDAC SEAESYSSMP 

      2410       2420       2430       2440       2450       2460 
PLEGEPGDPD LSSGSWSTVS DQDDVVCCSM SYSWTGALIT PCAAEEEKLP INPLSNSLIR 

      2470       2480       2490       2500       2510       2520 
HHNMVYSTTS RSASLRQKKV TFDRLQVFDQ HYQDVLKEIK LRASTVQARL LSIEEACDLT 

      2530       2540       2550       2560       2570       2580 
PSHSARSKYG YGAQDVRSHA SKAINHIRSV WEDLLEDSDT PIPTTIMAKN EVFCVDPSKG 

      2590       2600       2610       2620       2630       2640 
GRKPARLIVY PDLGVRVCEK MALYDVTRKL PQAVMGSAYG FQYSPNQRVE YLLKMWRSKK 

      2650       2660       2670       2680       2690       2700 
VPMGFSYDTR CFDSTVTERD IRTENDIYQS CQLDPVARRA VSSLTERLYV GGPMVNSKGQ 

      2710       2720       2730       2740       2750       2760 
SCGYRRCRAS GVLPTSMGNT LTCYLKAQAA CRAANIKDCD MLVCGDDLVV ICESAGVQED 

      2770       2780       2790       2800       2810       2820 
TASLRAFTDA MTRYSAPPGD VPQPTYDLEL ITSCSSNVSV AHDGNGKRYY YLTRDCTTPL 

      2830       2840       2850       2860       2870       2880 
ARAAWETARH TPVNSWLGNI IMFAPTIWVR MVLMTHFFSI LQSQEQLEKA LDFDIYGVTY 

      2890       2900       2910       2920       2930       2940 
SVSPLDLPAI IQRLHGMAAF SLHGYSPTEL NRVGACLRKL GVPPLRAWRH RARAVRAKLI 

      2950       2960       2970       2980       2990       3000 
AQGGKAAICG KYLFNWAVKT KLKLTPLVSA SKLDLSGWFV AGYDGGDIYH SVSQARPRLL 

      3010 
LLGLLLLTVG VGIFLVPAR 

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References

[1]"Full genome sequence of HCV 6a virus strains isolated in Hong Kong."
Zhou X.M., Chan P.K.S., Tam J.S.L.
Submitted (DEC-2004) to the EMBL/GenBank/DDBJ databases
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]"Structural biology of hepatitis C virus."
Penin F., Dubuisson J., Rey F.A., Moradpour D., Pawlotsky J.-M.
Hepatology 39:5-19(2004) [PubMed] [Europe PMC] [Abstract]
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.

Web resources

euHCVdb

The European HCV database

Virus Pathogen Resource

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY859526 Genomic RNA. Translation: AAW56714.1.

3D structure databases

ProteinModelPortalQ5I2N3.
SMRQ5I2N3. Positions 2-45, 907-1031, 1034-1662, 1980-2008, 2013-2175, 2429-2991.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Organism-specific databases

euHCVdbAY859526.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR011492. DEAD_Flavivir.
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]
PfamPF07652. Flavi_DEAD. 1 hit.
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]
ProDomPD001388. HCV_env. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00487. DEXDc. 1 hit.
[Graphical view]
SUPFAMSSF50494. SSF50494. 1 hit.
SSF52540. SSF52540. 2 hits.
PROSITEPS51693. HCV_NS2_PRO. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50507. RDRP_SSRNA_POS. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOLG_HCV6A
AccessionPrimary (citable) accession number: Q5I2N3
Entry history
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 90 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries