3LKZ | pdb_00003lkz

Structural and functional analyses of a conserved hydrophobic pocket of flavivirus methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb3LKZ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): West Nile virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-28 Released: 2010-08-04 
• Deposition Author(s): Liu, L.H., Li, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Structural and functional analyses of a conserved hydrophobic pocket of flavivirus methyltransferase.

Dong, H., Liu, L., Zou, G., Zhao, Y., Li, Z., Lim, S.P., Shi, P.Y., Li, H.

(2010) J Biological Chem 285: 32586-32595

• PubMed: 20685660 
• DOI: https://doi.org/10.1074/jbc.M110.129197
• Primary Citation Related Structures: 
  3LKZ


• PubMed Abstract: 
  

  The flavivirus methyltransferase (MTase) sequentially methylates the N7 and 2'-O positions of the viral RNA cap (GpppA-RNA → m(7)GpppA-RNA → m(7)GpppAm-RNA), using S-adenosyl-l-methionine (AdoMet) as a methyl donor. We report here that sinefungin (SIN), an AdoMet analog, inhibits several flaviviruses through suppression of viral MTase. The crystal structure of West Nile virus MTase in complex with SIN inhibitor at 2.0-Å resolution revealed a flavivirus-conserved hydrophobic pocket located next to the AdoMet-binding site. The pocket is functionally critical in the viral replication and cap methylations. In addition, the N7 methylation efficiency was found to correlate with the viral replication ability. Thus, SIN analogs with modifications that interact with the hydrophobic pocket are potential specific inhibitors of flavivirus MTase.

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Organizational Affiliation: 
• Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.43 kDa 
• Atom Count: 4,771 
• Modeled Residue Count: 524 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 5	A, B	321	West Nile virus	Mutation(s): 0  Gene Names: Non-structural protein 5
UniProt
Find proteins for Q9Q6P4 (West Nile virus (strain NY-99)) Explore Q9Q6P4  Go to UniProtKB:  Q9Q6P4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFG	C [auth A], E [auth B]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.363	α = 112.01
b = 65.74	β = 102.65
c = 77.119	γ = 90.19

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): Liu, L.H., Li, H.M.

Revision History  

• Version 1.0: 2010-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description