PDBsum entry 1vpt

Methyltransferase

PDB id: 1vpt

Contents

Protein chain

291 a.a. *

Ligands

SAM

Waters ×203

* Residue conservation analysis

PDB id:

1vpt

Name:

Methyltransferase

Title:

As11 variant of vaccinia virus protein vp39 in complex with s- adenosyl-l-methionine

Structure:

Vp39. Chain: a. Synonym: poly(a) polymerase regulatory subunit. Engineered: yes. Mutation: yes

Source:

Vaccinia virus. Organism_taxid: 10254. Strain: wr. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.215 R-free: 0.250

Authors:

A.E.Hodel,P.D.Gershon,X.Shi,F.A.Quiocho

Key ref:

A.E.Hodel et al. (1996). The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends. Cell, 85, 247-256. PubMed id: 8612277 DOI: 10.1016/S0092-8674(00)81101-0

Date:

20-Mar-96 Release date: 17-Aug-96

Protein chain

P07617  (MCE_VACCW) -  Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase from Vaccinia virus (strain Western Reserve)

Seq: 333 a.a.

Struc: 291 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: 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⁺

5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) = 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/S0092-8674(00)81101-0

Cell 85:247-256 (1996)

PubMed id: 8612277

The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends.

A.E.Hodel, P.D.Gershon, X.Shi, F.A.Quiocho.

ABSTRACT

VP39 is a bifunctional vaccinia virus protein that acts as both an mRNA cap-specific RNA 2'-O-methyltransferase and a poly(A) polymerase processivity factor. Here, we report the 1.85 A crystal structure of a VP39 variant complexed with its AdoMet cofactor. VP39 comprises a single core domain with structural similarity to the catalytic domains of other methyltransferases. Surface features and mutagenesis data suggest two possible RNA-binding sites with novel underlying architecture, one of which forms a cleft spanning the region adjacent to the methyltransferase active site. This report provides a prototypic structure for an RNA methyltransferase, a protein that interacts with the mRNA 5' cap, and an intact poxvirus protein.

Selected figure(s)

Figure 4.
Figure 4. Stereo Diagram Showing Electron Density at the AdoMet-Binding Site and the Interactions between AdoMet and Nearby Residues of AS11The F[o]-F[c] electron density map, contoured at 2.5 σ, was calculated at 1.85 Å from a model that did not contain the AdoMet molecule. As shown, the AdoMet molecule is clearly defined including its donor methyl group. Residues appropriately positioned to make either hydrogen bonding or van der Waals contact with AdoMet are shown. Carbon atoms/bonds are colored gray/white; sulfur, yellow; nitrogen, blue; and oxygen, red. The 13 potential hydrogen bonds whose lengths were in the range 2.5–3.3 Å are represented by dashed green lines. For clarity, G68 (whose backbone carbonyl oxygen forms the near vertical hydrogen bond with the α-ammonium group of the AdoMet methionine moiety) is not labeled. One of the three potential hydrogen bonds to the 3′ OH of the AdoMet ribose is almost completely hidden in the view shown.

Figure 5.
Figure 5. Schematic Showing a Model for the Binding of a 5′-Capped RNA Strand to the Cleft and Methyltransferase Active SiteThe cleft is viewed from an angle similar to that in Figure 3A, Figure 3D, and 3G. Important regions of the surface are labeled, including the putative binding site for the terminal (m^7G) nucleotide of cap 0 (cap binding); the position at which the donor methyl of AdoMet protrudes into the cleft (donor methyl); the active site and associated basic region (basic region/active site); the missing 142–147 loop (which contains basic side chains in wild-type VP39) and the hydrophobic pocket at the distal end of the cleft. RNA nucleotides are represented by dark ovals. An internucleotide spacing of vert, similar 5 Å per base was used, based upon the spacing determined for single-stranded DNA bound to gp32 (in which DNA bases were unstacked; [44]).

The above figures are reprinted by permission from Cell Press: Cell (1996, 85, 247-256) copyright 1996.

Figures were selected by an automated process.