2PX8 | pdb_00002px8

Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH and 7M-GTP

• PDB DOI: https://doi.org/10.2210/pdb2PX8/pdb

• Classification: TRANSFERASE
• Organism(s): Murray valley encephalitis virus (strain MVE-1-51)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-14 Released: 2007-05-29 
• Deposition Author(s): Assenberg, R., Ren, J., Verma, A., Walter, T.S., Alderton, D., Hurrelbrink, R.J., Fuller, S.D., Owens, R.J., Stuart, D.I., Grimes, J.M., Oxford Protein Production Facility (OPPF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.217 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues.

Assenberg, R., Ren, J., Verma, A., Walter, T.S., Alderton, D., Hurrelbrink, R.J., Fuller, S.D., Bressanelli, S., Owens, R.J., Stuart, D.I., Grimes, J.M.

(2007) J Gen Virol 88: 2228-2236

• PubMed: 17622627 
• DOI: https://doi.org/10.1099/vir.0.82757-0
• Primary Citation Related Structures: 
  2PX2, 2PX4, 2PX5, 2PX8, 2PXA, 2PXC


• PubMed Abstract: 
  

  We have determined the high resolution crystal structure of the methyltransferase domain of the NS5 polypeptide from the Murray Valley encephalitis virus. This domain is unusual in having both the N7 and 2'-O methyltransferase activity required for Cap 1 synthesis. We have also determined structures for complexes of this domain with nucleotides and cap analogues providing information on cap binding, based on which we suggest a model of how the sequential methylation of the N7 and 2'-O groups of the cap may be coordinated.

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Organizational Affiliation: 
• Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK.
Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK.
Department of Virology, Telethon Institute for Child Health Research, University of Western Australia, Perth, WA 6008, Australia.
INRA, UMR1157, Virologie Moléculaire et Structurale, 91198 Gif sur Yvette, France.
CNRS, UMR2472, IFR 115, Virologie Moléculaire et Structurale, 91198 Gif sur Yvette, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.95 kDa 
• Atom Count: 4,823 
• Modeled Residue Count: 529 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]	A, B	269	Murray valley encephalitis virus (strain MVE-1-51)	Mutation(s): 4  Gene Names: NS5 EC: 2.7.7.48
UniProt
Find proteins for P05769 (Murray valley encephalitis virus (strain MVE-1-51)) Explore P05769  Go to UniProtKB:  P05769

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGT	C [auth A], H [auth B], I [auth B]	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C11 H20 N5 O14 P3 BUJQMJUTTBGELS-KQYNXXCUSA-N
SAH	E [auth A], K [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
3PO	D [auth A], J [auth B]	TRIPHOSPHATE H5 O10 P3 UNXRWKVEANCORM-UHFFFAOYSA-N
GOL	F [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.217 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.579	α = 90
b = 87.445	β = 90
c = 100.914	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Assenberg, R., Ren, J., Verma, A., Walter, T.S., Alderton, D., Hurrelbrink, R.J., Fuller, S.D., Owens, R.J., Stuart, D.I., Grimes, J.M., Oxford Protein Production Facility (OPPF)

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description