PDBsum entry 2vbc

Hydrolase

PDB id: 2vbc

Contents

Protein chains

600 a.a. *

15 a.a. *

Waters ×34

* Residue conservation analysis

PDB id:

2vbc

Name:

Hydrolase

Title:

Crystal structure of the ns3 protease-helicase from dengue virus

Structure:

Dengue 4 ns3 full-length protein. Chain: a. Fragment: residues 1475-2092. Engineered: yes. Partial polyprotein for ns2a and ns2b, type 4 prototype dv4 h241. Chain: b. Fragment: residues 101-118. Engineered: yes

Source:

Dengue virus type 4. Organism_taxid: 11070. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: codon plus.

Resolution:

3.15Å R-factor: 0.206 R-free: 0.277

Authors:

D.H.Luo,T.Xu,C.Hunke,G.Gruber,S.G.Vasudevan,J.Lescar

Key ref:

D.Luo et al. (2008). Crystal structure of the NS3 protease-helicase from dengue virus. J Virol, 82, 173-183. PubMed id: 17942558

Date:

10-Sep-07 Release date: 30-Oct-07

Protein chain

Q2TN89  (Q2TN89_9FLAV) -  Genome polyprotein from dengue virus type 4

Seq: 3387 a.a.

Struc: 600 a.a.*

Protein chain

Q91EQ2  (Q91EQ2_9FLAV) -  Partial polyprotein for NS2a and NS2b, type 4 prototype DV4 H241 (Fragment) from dengue virus type 4

Seq: 132 a.a.

Struc: 15 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.3.4.21.91 - flavivirin.
• Reaction: Selective hydrolysis of Xaa-Xaa-|-Xbb bonds in which each of the Xaa can be either Arg or Lys and Xbb can be either Ser or Ala.
• Enzyme class 3: Chain A: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 4: Chain A: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

J Virol 82:173-183 (2008)

PubMed id: 17942558

Crystal structure of the NS3 protease-helicase from dengue virus.

D.Luo, T.Xu, C.Hunke, G.Grüber, S.G.Vasudevan, J.Lescar.

ABSTRACT

Several flaviviruses are important human pathogens, including dengue virus, a disease against which neither a vaccine nor specific antiviral therapies currently exist. During infection, the flavivirus RNA genome is translated into a polyprotein, which is cleaved into several components. Nonstructural protein 3 (NS3) carries out enzymatic reactions essential for viral replication, including proteolysis of the polyprotein through its serine protease N-terminal domain, with a segment of 40 residues from the NS2B protein acting as a cofactor. The ATPase/helicase domain is located at the C terminus of NS3. Atomic structures are available for these domains separately, but a molecular view of the full-length flavivirus NS3 polypeptide is still lacking. We report a crystallographic structure of a complete NS3 molecule fused to 18 residues of the NS2B cofactor at a resolution of 3.15 A. The relative orientation between the protease and helicase domains is drastically different than the single-chain NS3-NS4A molecule from hepatitis C virus, which was caught in the act of cis cleavage at the NS3-NS4A junction. Here, the protease domain sits beneath the ATP binding site, giving the molecule an elongated shape. The domain arrangement found in the crystal structure fits nicely into an envelope determined ab initio using small-angle X-ray scattering experiments in solution, suggesting a stable molecular conformation. We propose that a basic patch located at the surface of the protease domain increases the affinity for nucleotides and could also participate in RNA binding, explaining the higher unwinding activity of the full-length enzyme compared to that of the isolated helicase domain.