5GP1 image
Entry Detail
PDB ID:
5GP1
Keywords:
TRANSFERASE
Title:
Crystal structure of ZIKV NS5 Methyltransferase in complex with GTP and SAH
Biological Source:
Source Organism:
Zika virus
Host Organism:
Escherichia coli
PDB Version:
Deposition Date:
2016-07-30
Release Date:
2016-12-07
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.44 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 61
5GP1 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:RNA-directed RNA polymerase NS5
Chain IDs:A, B, C
Chain Length:269
Number of Molecules:3
Biological Source:Zika virus
UniProt ID:A0A024B7W1 Pfam ID:PF01728 EC:2.7.7.48
Ligand Molecules
GTA
NI
SAH
SO4
Primary Citation
Structure of the NS5 methyltransferase from Zika virus and implications in inhibitor design
Biochem. Biophys. Res. Commun. 492 624 630 (2017)
PMID: 27866982 DOI: 10.1016/j.bbrc.2016.11.098

Abstact

Recent outbreak of flavivirus Zika virus (ZIKV) in America has urged the basic as well as translational studies of this important human pathogen. The nonstructural protein 5 (NS5) of the flavivirus has an N-terminal methyltransferase (MTase) domain that plays critical roles in viral RNA genome capping. The null mutant of NS5 MTase is lethal for virus. Therefore, NS5 is a potential drug target for the treatment of Zika virus infection. In this study, we determined crystal structures of the ZIKV MTase in complex with GTP and RNA cap analogue 7meGpppA. Structural analyses revealed highly conserved GTP/cap-binding pocket and S-adenosylmethionine (SAM)-binding pocket. Two conformations of the second base of the cap were identified, which suggests the flexibility of RNA conformation. In addition, the ligand-binding pockets identified a continuous region of hotspots suitable for drug design. Docking calculation shows that the Dengue virus inhibitor compound 10 may bind to the ZIKV MTase.

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Primary Citation of related structures
5GOZ