PDBsum entry 5gjb

Hydrolase/RNA

PDB id: 5gjb

Contents

Protein chain

440 a.a.

DNA/RNA

Waters ×549

PDB id:

5gjb

Name:

Hydrolase/RNA

Title:

Zika virus ns3 helicase in complex with ssrna

Structure:

Ns3 helicase. Chain: a. Fragment: unp residues 1674-2119. Engineered: yes. RNA (5'-r( Ap Gp Ap Up Cp Ap A)-3'). Chain: b. Engineered: yes

Source:

Zika virus (strain mr 766). Zikv. Organism_taxid: 64320. Strain: mr 766. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. 32.

Resolution:

1.70Å R-factor: 0.156 R-free: 0.196

Authors:

H.L.Tian,X.Y.Ji,X.Y.Yang,Z.X.Zhang,Z.K.Lu,K.L.Yang,C.Chen,Q.Zhao, H.Chi,Z.Y.Mu,W.Xie,Z.F.Wang,H.Q.Lou,H.T.Yang,Z.H.Rao

Key ref:

H.Tian et al. (2016). Structural basis of Zika virus helicase in recognizing its substrates. Protein Cell, 7, 562-570. PubMed id: 27430951 DOI: 10.1007/s13238-016-0293-2

Date:

28-Jun-16 Release date: 20-Jul-16

Protein chain

A0A0U4DG08  (A0A0U4DG08_ZIKV) -  Genome polyprotein from Zika virus

Seq: 3423 a.a.

Struc: 440 a.a.

DNA/RNA chain

A-G-A-U-C 5 bases

Enzyme reactions

• Enzyme class 1: 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 2: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 3: 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

DOI no: 10.1007/s13238-016-0293-2

Protein Cell 7:562-570 (2016)

PubMed id: 27430951

Structural basis of Zika virus helicase in recognizing its substrates.

H.Tian, X.Ji, X.Yang, Z.Zhang, Z.Lu, K.Yang, C.Chen, Q.Zhao, H.Chi, Z.Mu, W.Xie, Z.Wang, H.Lou, H.Yang, Z.Rao.

ABSTRACT

The recent explosive outbreak of Zika virus (ZIKV) infection has been reported in South and Central America and the Caribbean. Neonatal microcephaly associated with ZIKV infection has already caused a public health emergency of international concern. No specific vaccines or drugs are currently available to treat ZIKV infection. The ZIKV helicase, which plays a pivotal role in viral RNA replication, is an attractive target for therapy. We determined the crystal structures of ZIKV helicase-ATP-Mn(2+) and ZIKV helicase-RNA. This is the first structure of any flavivirus helicase bound to ATP. Comparisons with related flavivirus helicases have shown that although the critical P-loop in the active site has variable conformations among different species, it adopts an identical mode to recognize ATP/Mn(2+). The structure of ZIKV helicase-RNA has revealed that upon RNA binding, rotations of the motor domains can cause significant conformational changes. Strikingly, although ZIKV and dengue virus (DENV) apo-helicases share conserved residues for RNA binding, their different manners of motor domain rotations result in distinct individual modes for RNA recognition. It suggests that flavivirus helicases could have evolved a conserved engine to convert chemical energy from nucleoside triphosphate to mechanical energy for RNA unwinding, but different motor domain rotations result in variable RNA recognition modes to adapt to individual viral replication.