PDBsum entry 5jrz

Hydrolase

PDB id: 5jrz

Contents

Protein chain

443 a.a.

Ligands

ACT ×6

POP

Waters ×552

PDB id:

5jrz

Name:

Hydrolase

Title:

Structure of the ns3 helicase from the french polynesia strain of the zika virus

Structure:

Helicase. Chain: a. Engineered: yes

Source:

Zika virus. Organism_taxid: 64320. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.62Å R-factor: 0.162 R-free: 0.193

Authors:

R.Jain,J.Coloma,A.K.Aggarwal

Key ref:

R.Jain et al. (2016). Structure of the NS3 helicase from Zika virus. Nat Struct Biol, 23, 752-754. PubMed id: 27399257 DOI: 10.1038/nsmb.3258

Date:

06-May-16 Release date: 06-Jul-16

Protein chain

Q32ZE1  (POLG_ZIKV) -  Genome polyprotein from Zika virus

Seq: 3419 a.a.

Struc: 443 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
• Enzyme class 2: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺
• Enzyme class 3: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) (Bound ligand (Het Group name = POP) corresponds exactly) + diphosphate

• Enzyme class 4: 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 5: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

ribonucleoside 5'-triphosphate + H2O = ribonucleoside 5'-diphosphate + phosphate + H(+) (Bound ligand (Het Group name = POP) matches with 55.56% similarity)

• Enzyme class 6: 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: 10.1038/nsmb.3258

Nat Struct Biol 23:752-754 (2016)

PubMed id: 27399257

Structure of the NS3 helicase from Zika virus.

R.Jain, J.Coloma, A.García-Sastre, A.K.Aggarwal.

ABSTRACT

Zika virus has emerged as a pathogen of major health concern. Here, we present a high-resolution (1.62-Å) crystal structure of the RNA helicase from the French Polynesia strain. The structure is similar to that of the RNA helicase from Dengue virus, with variability in the conformations of loops typically involved in binding ATP and RNA. We identify druggable 'hotspots' that are well suited for in silico and/or fragment-based high-throughput drug discovery.