PDBsum entry 1ri2

Transferase

PDB id: 1ri2

Contents

Protein chain

252 a.a. *

Ligands

GTG

Waters ×25

* Residue conservation analysis

PDB id:

1ri2

Name:

Transferase

Title:

Structure and mechanism of mRNA cap (guanine n-7) methyltransferase

Structure:

mRNA capping enzyme. Chain: a. Synonym: mRNA cap (guanine n-7) methyltransferase ecm1. Engineered: yes

Source:

Encephalitozoon cuniculi. Organism_taxid: 6035. Gene: ecu10_0380. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.70Å R-factor: 0.224 R-free: 0.295

Authors:

C.Fabrega,S.Hausmann,V.Shen,S.Shuman,C.D.Lima

Key ref:

C.Fabrega et al. (2004). Structure and mechanism of mRNA cap (guanine-N7) methyltransferase. Mol Cell, 13, 77-89. PubMed id: 14731396 DOI: 10.1016/S1097-2765(03)00522-7

Date:

16-Nov-03 Release date: 03-Feb-04

Protein chain

Q8SR66  (MCES_ENCCU) -  mRNA cap guanine-N7 methyltransferase from Encephalitozoon cuniculi (strain GB-M1)

Seq: 283 a.a.

Struc: 252 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine

5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine (Bound ligand (Het Group name = GTG) matches with 41.46% similarity)

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

Added reference

DOI no: 10.1016/S1097-2765(03)00522-7

Mol Cell 13:77-89 (2004)

PubMed id: 14731396

Structure and mechanism of mRNA cap (guanine-N7) methyltransferase.

C.Fabrega, S.Hausmann, V.Shen, S.Shuman, C.D.Lima.

ABSTRACT

A suite of crystal structures is reported for a cellular mRNA cap (guanine-N7) methyltransferase in complex with AdoMet, AdoHcy, and the cap guanylate. Superposition of ligand complexes suggests an in-line mechanism of methyl transfer, albeit without direct contacts between the enzyme and either the N7 atom of guanine (the attacking nucleophile), the methyl carbon of AdoMet, or the sulfur of AdoMet/AdoHcy (the leaving group). The structures indicate that catalysis of cap N7 methylation is accomplished by optimizing proximity and orientation of the substrates, assisted by a favorable electrostatic environment. The enzyme-ligand structures, together with new mutational data, fully account for the biochemical specificity of the cap guanine-N7 methylation reaction, an essential and defining step of eukaryotic mRNA synthesis.

Selected figure(s)

Figure 3.
Figure 3. Structures of the Active Site in Complex with Ligands(A), (B), (C), and (E) are shown in stereo. Potential hydrogen bonding interactions are shown by dashed lines, waters as red spheres.(A) The Ecm1-AdoMet complex.(B) The Ecm1-AdoHcy complex.(C) The Ecm1-cap complex.(D) 2.5 Å simulated annealing map contoured at 1.0σ covering the cap guanylate ligand.(E) The Ecm1-AdoHcy-cap complex.(F) 2.4 Å F[o] − F[c] map contoured at 1.5σ covering the cap guanylate and AdoHcy ligands.

Figure 5.
Figure 5. Electrostatic Surface DiagramsSurface representations for the Ecm1-AdoHcy-cap complex in 180° orientations. Electrostatic potential is shown on the Ecm1 surface and in contours at 2.0 k[b]T (blue) and −2.0 k[b]T (red) to highlight the complementary electrostatics observed for AdoMet (negative to counter the AdoMet positive charge) and cap-binding sites (positive to counter the negative phosphate charge). Electrostatic potential map and figure were prepared using GRASP (Nicholls et al., 1991).

The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 13, 77-89) copyright 2004.

Figures were selected by the author.