2P41: Dengue Methyltransferase

Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppG2'OMe and S-Adenosyl-L-homocysteine. Determined by X-ray diffraction at 1.8 Å resolution. Released 28 Aug 2007.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Dengue virus 2
Chains: 1
Atoms: 2,562
Mol. weight: 36.74 kDa
Ligands: CIT, SAH, G1G
Released: 28 Aug 2007

Explore 2P41 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2P41 contains 12 α-helices and 9 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	22-30	9
β-strand	34-37	4	1
α-helix	39-46	8
α-helix	58-67	10
β-strand	75-80	6	2
α-helix	86-92	7
β-strand	97-103	7	2
α-helix	111-113	3
α-helix	121-123	3
β-strand	124-127	4	2
α-helix	136-137	2
β-strand	142-145	4	2
α-helix	154-171	18
β-strand	177-182	6	2
α-helix	188-201	14
β-strand	204-206	3	2
β-strand	218-221	4	2
α-helix	228-243	16
β-strand	251-254	4	1
α-helix	255-256	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
type II methyltransferase	A	protein	305	Dengue virus 2	P12823

Sequence of entity 1 (A), FASTA

>2P41_1 type II methyltransferase (chains A)
MRGSHHHHHHGSNIGETLGEKWKSRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETD
HHAVSRGSAKLRWFVERNLVTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTKGGPGHE
EPIPMSTYGWNLVRLQSGVDVFFIPPERCDTLLCDIGESSPNPTVEAGRTLRVLNLVENW
LSNNTQFCVKVLNPYMSSVIEKMEALQRKHGGALVRNPLSRNSTHEMYWVSNASGNIVSS
VNMISRMLINRFTMRHKKATYEPDVDLGSGTRNIGIESETPNLDIIGKRIEKIKQEHETS
WHYDQ

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
G1G	7-methyl-guanosine-5'-triphosphate-5'-(2'-O-methyl)-guanosine	C22 H32 N10 O18 P3	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5. Egloff, M.P., Decroly, E., Malet, H. et al. J Mol Biol (2007) 372:723-736. DOI 10.1016/j.jmb.2007.07.005 · PubMed

Other PDB entries of the same protein (UniProt P12823), best resolution first:

4M9K 1.46 Å, NS2B-NS3 protease from dengue virus at pH 5.5
4M9M 1.53 Å, NS2B-NS3 protease from dengue virus at pH 8.5
4M9T 1.74 Å, NS2B-NS3 protease from dengue virus in the presence of DTNB, a covalent allosteric…
1OK8 2.0 Å, Crystal structure of the dengue 2 virus envelope glycoprotein in the postfusion…
2P3L 2.2 Å, Crystal Structure of Dengue Methyltransferase in Complex with GpppA and…
5HHG 2.2 Å, Mouse importin alpha: Dengue 2 NS5 C-terminal NLS peptide complex
1L9K 2.4 Å, dengue methyltransferase
1OKE 2.4 Å, Crystal structure of the dengue 2 virus envelope protein in complex with…
4M9I 2.4 Å, A125C NS2B-NS3 protease from dengue virus at pH 5.5
1R6A 2.6 Å, Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl…
4M9F 2.7 Å, Dengue virus NS2B-NS3 protease A125C variant at pH 8.5
2P40 2.7 Å, Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppG

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