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Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function

Source organism: Hepatitis C virus (isolate BK)
Biochemical function: serine-type peptidase activity
Biological process: symbiont-mediated transformation of host cell
Cellular component: not assigned

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EC 3.6.4.13: RNA helicase

Reaction catalysed:
ATP + H(2)O = ADP + phosphate
Systematic name:
ATP phosphohydrolase (RNA helix unwinding)
Alternative Name(s):
  • CSFV NS3 helicase
  • DBP2
  • DDX17
  • DDX25
  • DDX3
  • DDX3X
  • DDX3Y
  • DDX4
  • DDX5
  • DEAD-box RNA helicase
  • DEAD-box protein DED1
  • DEAH-box RNA helicase
  • DEAH-box protein 2
  • DED1
  • DbpA
  • Dex(H/D) RNA helicase
  • EIF4A helicase
  • EhDEAD1
  • EhDEAD1 RNA helicase
  • GRTH/DDX25
  • KOKV helicase
  • Mtr4p
  • NPH-II
  • Nonstructural protein 3 helicase
  • RHA
  • RNA helicase A
  • RNA helicase DDX3
  • RNA helicase Hera
  • RNA-dependent ATPase
  • TGBp1 NTPase/helicase domain
  • VRH1

EC 3.6.1.15: Nucleoside-triphosphate phosphatase

Reaction catalysed:
NTP + H(2)O = NDP + phosphate
Systematic name:
Unspecific diphosphate phosphohydrolase
Alternative Name(s):
  • NTPase
  • Nucleoside 5-triphosphatase
  • Nucleoside triphosphate hydrolase
  • Nucleoside triphosphate phosphohydrolase
  • Nucleoside-5-triphosphate phosphohydrolase
  • Nucleoside-triphosphatase

EC 3.4.21.98: Hepacivirin

Reaction catalysed:
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'.
Alternative Name(s):
  • Cpro-2
  • Hepatitis C virus NS3 serine proteinase
  • NS3-4A serine proteinase complex

EC 2.7.7.48: RNA-directed RNA polymerase

Reaction catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Systematic name:
Nucleoside-triphosphate:RNA nucleotidyltransferase (RNA-directed)
Alternative Name(s):
  • 3D polymerase
  • PB1 proteins
  • PB2 proteins
  • Phage f2 replicase
  • Polymerase L
  • Q-beta replicase
  • RDRP
  • RNA nucleotidyltransferase (RNA-directed)
  • RNA replicase
  • RNA synthetase
  • RNA transcriptase
  • RNA-dependent RNA polymerase
  • RNA-dependent RNA replicase
  • RNA-dependent ribonucleate nucleotidyltransferase
  • Ribonucleic acid replicase
  • Ribonucleic acid-dependent ribonucleate nucleotidyltransferase
  • Ribonucleic acid-dependent ribonucleic acid polymerase
  • Ribonucleic replicase
  • Ribonucleic synthetase
  • Transcriptase

GO terms

Biochemical function:
Biological process:
Cellular component:
  • not assigned

Sequence families

Pfam Protein families (Pfam)
PF22027
Domain description: NS3 RNA helicase, C-terminal helical domain
Occurring in:
  1. Serine protease/helicase NS3

PF07652
Domain description: Flavivirus DEAD domain
Occurring in:
  1. Serine protease/helicase NS3
The deposited structure of PDB entry 4b76 contains 2 copies of Pfam domain PF07652 (Flavivirus DEAD domain ) in Serine protease/helicase NS3. Showing 1 copy in chain A.

PF02907
Domain description: Hepatitis C virus NS3 protease
Occurring in:
  1. Serine protease/helicase NS3
The deposited structure of PDB entry 4b76 contains 2 copies of Pfam domain PF02907 (Hepatitis C virus NS3 protease) in Serine protease/helicase NS3. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR027417
Domain description: P-loop containing nucleoside triphosphate hydrolase
Occurring in:
  1. Serine protease/helicase NS3
IPR014001
Domain description: Helicase superfamily 1/2, ATP-binding domain
Occurring in:
  1. Serine protease/helicase NS3
IPR004109
Domain description: Hepatitis C virus, NS3 protease
Occurring in:
  1. Serine protease/helicase NS3
IPR001650
Domain description: Helicase, C-terminal domain-like
Occurring in:
  1. Serine protease/helicase NS3
IPR011492
Domain description: Non-structural protein NS3-like, DEAD box helicase, flavivirus
Occurring in:
  1. Serine protease/helicase NS3
IPR043504
Domain description: Peptidase S1, PA clan, chymotrypsin-like fold
Occurring in:
  1. Serine protease/helicase NS3
IPR009003
Domain description: Peptidase S1, PA clan
Occurring in:
  1. Serine protease/helicase NS3
IPR029048
Domain description: Heat shock protein 70kD, C-terminal domain superfamily
Occurring in:
  1. Serine protease/helicase NS3

Structure domains

CATH CATH domains
3.40.50.300
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: P-loop containing nucleotide triphosphate hydrolases
Occurring in:
  1. Serine protease/helicase NS3
The deposited structure of PDB entry 4b76 contains 4 copies of CATH domain 3.40.50.300 (Rossmann fold) in Serine protease/helicase NS3. Showing 2 copies in chain A.
2.40.10.10
Class: Mainly Beta
Architecture: Beta Barrel
Topology: Thrombin, subunit H
Homology: Trypsin-like serine proteases
Occurring in:
  1. Serine protease/helicase NS3
The deposited structure of PDB entry 4b76 contains 2 copies of CATH domain 2.40.10.10 (Thrombin, subunit H) in Serine protease/helicase NS3. Showing 1 copy in chain A.
2.40.10.120
Class: Mainly Beta
Architecture: Beta Barrel
Topology: Thrombin, subunit H
Homology: Thrombin, subunit H
Occurring in:
  1. Serine protease/helicase NS3
The deposited structure of PDB entry 4b76 contains 2 copies of CATH domain 2.40.10.120 (Thrombin, subunit H) in Serine protease/helicase NS3. Showing 1 copy in chain A.
1.10.820.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: RNA Helicase; Chain A, domain 3
Homology: RNA Helicase Chain A , domain 3
Occurring in:
  1. Serine protease/helicase NS3
The deposited structure of PDB entry 4b76 contains 2 copies of CATH domain 1.10.820.10 (RNA Helicase; Chain A, domain 3) in Serine protease/helicase NS3. Showing 1 copy in chain A.

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