Function and Biology

Crystal Structure of the NS3 protease-helicase from Murray Valley encephalitis virus

Source organism: Murray valley encephalitis virus (strain MVE-1-51)
Biochemical function: ATP binding
Biological process: not assigned
Cellular component: virion component

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 3.4.21.91: Flavivirin

Reaction catalysed:
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Alternative Name(s):
  • NS2B-3 proteinase
  • Yellow fever virus (flavivirus) protease
  • Yellow fever virus protease

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

EC 2.1.1.57: Methyltransferase cap1

Reaction catalysed:
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Systematic name:
S-adenosyl-L-methionine:5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] 2-O-methyltransferase
Alternative Name(s):
  • Cap1-MTase
  • MTR1
  • Messenger RNA (nucleoside-2'-)-methyltransferase
  • Messenger ribonucleate nucleoside 2'-methyltransferase
  • S-adenosyl-L-methionine:mRNA (nucleoside-2'-O)-methyltransferase
  • mRNA (nucleoside-2'-O)-methyltransferase

EC 2.1.1.56: mRNA (guanine-N(7))-methyltransferase

Reaction catalysed:
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
Systematic name:
S-adenosyl-L-methionine:mRNA (guanine-N(7))-methyltransferase
Alternative Name(s):
  • Guanine-7-methyltransferase
  • Messenger RNA guanine 7-methyltransferase
  • Messenger ribonucleate guanine 7-methyltransferase
  • S-adenosyl-L-methionine:mRNA (guanine-7-N)-methyltransferase

GO terms

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

Sequence families

Pfam Protein families (Pfam)
PF20907
Domain description: Flavivirus NS3 helicase, C-terminal helical domain
Occurring in:
  1. Serine protease NS3
The deposited structure of PDB entry 2wv9 contains 1 copy of Pfam domain PF20907 (Flavivirus NS3 helicase, C-terminal helical domain) in Serine protease NS3. Showing 1 copy in chain A.

PF07652
Domain description: Flavivirus DEAD domain
Occurring in:
  1. Serine protease NS3
The deposited structure of PDB entry 2wv9 contains 1 copy of Pfam domain PF07652 (Flavivirus DEAD domain ) in Serine protease NS3. Showing 1 copy in chain A.

PF00949
Domain description: Peptidase S7, Flavivirus NS3 serine protease
Occurring in:
  1. Serine protease NS3
The deposited structure of PDB entry 2wv9 contains 1 copy of Pfam domain PF00949 (Peptidase S7, Flavivirus NS3 serine protease ) in Serine protease NS3. Showing 1 copy in chain A.

PF01002
Domain description: Flavivirus non-structural protein NS2B
Occurring in:
  1. Serine protease NS3
The deposited structure of PDB entry 2wv9 contains 1 copy of Pfam domain PF01002 (Flavivirus non-structural protein NS2B) in Serine protease NS3. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR027417
Domain description: P-loop containing nucleoside triphosphate hydrolase
Occurring in:
  1. Serine protease NS3
IPR001650
Domain description: Helicase, C-terminal domain-like
Occurring in:
  1. Serine protease NS3
IPR014001
Domain description: Helicase superfamily 1/2, ATP-binding domain
Occurring in:
  1. Serine protease NS3
IPR001850
Domain description: Non-structural protein NS3, peptidase S7, flavivirus
Occurring in:
  1. Serine protease NS3
IPR000487
Domain description: Non-structural protein NS2B, flavivirus
Occurring in:
  1. Serine protease NS3
IPR011492
Domain description: Non-structural protein NS3-like, DEAD box helicase, flavivirus
Occurring in:
  1. Serine protease NS3
IPR009003
Domain description: Peptidase S1, PA clan
Occurring in:
  1. Serine protease 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 NS3
The deposited structure of PDB entry 2wv9 contains 2 copies of CATH domain 3.40.50.300 (Rossmann fold) in Serine protease NS3. Showing 2 copies 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 NS3
The deposited structure of PDB entry 2wv9 contains 1 copy of CATH domain 2.40.10.120 (Thrombin, subunit H) in Serine protease NS3. Showing 1 copy in chain A.