PDBsum entry 1av6

Transferase/RNA

PDB id: 1av6

Contents

Protein chain

289 a.a. *

DNA/RNA

Ligands

MGT

SAH

* Residue conservation analysis

PDB id:

1av6

Name:

Transferase/RNA

Title:

Vaccinia methyltransferase vp39 complexed with m7g capped RNA hexamer and s-adenosylhomocysteine

Structure:

RNA (5'-r( Gp Ap Ap Ap Ap A)-3'). Chain: b. Synonym: 5' capped RNA hexamer. Engineered: yes. Cap-specific mRNA (nucleoside-2'-o-)-methyltransferase. Chain: a. Synonym: poly(a) polymerase regulatory subunit, poly(a) polymerase small subunit, pap-s, vp39. Engineered: yes.

Source:

Vaccinia virus wr. Vacv. Organism_taxid: 10254. Strain: western reserve. Gene: paps, vacwr095, f9. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Monomer (from PDB file)

Resolution:

2.80Å R-factor: 0.215 R-free: 0.285

Authors:

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

Key ref:

A.E.Hodel et al. (1998). Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme. Mol Cell, 1, 443-447. PubMed id: 9660928 DOI: 10.1016/S1097-2765(00)80044-1

Date:

26-Sep-97 Release date: 25-Feb-98

Protein chain

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

Seq: 333 a.a.

Struc: 289 a.a.

DNA/RNA chain

G-A-A-A-A-A 6 bases

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

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

Added reference

DOI no: 10.1016/S1097-2765(00)80044-1

Mol Cell 1:443-447 (1998)

PubMed id: 9660928

Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme.

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

ABSTRACT

Sequence-nonspecific binding of RNA, recognition of a 7-methylguanosine 5' mRNA cap, and methylation of a nucleic acid backbone are three crucial and ubiquitous events in eukaryotic nucleic acid processing and function. These three events occur concurrently in the modification of vaccinia transcripts by the methyltransferase VP39. We report the crystal structure of a ternary complex comprising VP39, coenzyme product S-adenosylhomocysteine, and a 5' m7 G-capped, single-stranded RNA hexamer. This structure reveals a novel and general mechanism for sequence-non-specific recognition of the mRNA transcript in which the protein interacts solely with the sugar-phosphate backbone of a short, single-stranded RNA helix. This report represents the first direct and detailed view of a protein complexed with single-stranded RNA or 5'-capped mRNA.

Selected figure(s)

Figure 1.
Figure 1. Electron Density for the First Trimer of RNA Bound in the Methyltransferase Active SiteThe 2.7 Å density is calculated as a 2F[o] − F[c] map using only the protein model to calculate the phases. Contoured at 1σ, only the density near the RNA is displayed for clarity. The surrounding atoms of the protein are shown without density for context. This figure was rendered using RIBBONS ([5]).

Figure 2.
Figure 2. mRNA–VP39 Complex(A) Stick model showing RNA bound to the active site cleft of VP39. The protein is rendered as a solvent-accessible surface. The sulfur atom of AdoHcy (colored green and labeled with an arrow) defines the methyltransferase active site.(B) The two RNA contacts mapped on a single VP39 molecule resulting from the interaction of the RNA with two symmetry-related protein molecules. The protein is rendered as a transparent solvent-accessible surface. Shown in front of the protein is the second trimer (A4-A5-A6) binding site based on the interactions with a symmetry-related molecule. Behind the protein are the 5′ cap and the first trimer (G1-A2-A3) of the transcript bound in the methyltransferase active site.(C) The proximity of the second RNA contact site to the VP55 dimerization interface. The major red patch denotes surface residues defined in [20] as the VP55 dimerization 'hot spot.' The smaller red patch (R107 to the right) is another part of the dimerization interface (see [20]). This figure was produced using GRASP ( [17]).

The above figures are reprinted by permission from Cell Press: Mol Cell (1998, 1, 443-447) copyright 1998.