PDBsum entry 3dmh

Transferase

PDB id: 3dmh

Contents

Protein chain

371 a.a. *

Ligands

SO4 ×2

SAM

GMP

Waters ×502

* Residue conservation analysis

PDB id:

3dmh

Name:

Transferase

Title:

T. Thermophilus 16s rrna n2 g1207 methyltransferase (rsmc) in complex with adomet and guanosine

Structure:

Probable ribosomal RNA small subunit methyltransferase. Chain: a. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: ttha0533. Expressed in: escherichia coli.

Resolution:

1.55Å R-factor: 0.195 R-free: 0.226

Authors:

H.Demirci,S.T.Gregory,A.E.Dahlberg,G.Jogl

Key ref:

H.Demirci et al. (2008). Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine. J Biol Chem, 283, 26548-26556. PubMed id: 18667428 DOI: 10.1074/jbc.M804005200

Date:

01-Jul-08 Release date: 29-Jul-08

Protein chain

Q5SKW0  (Q5SKW0_THET8) -  Probable ribosomal RNA small subunit methyltransferase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 375 a.a.

Struc: 371 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.- - ?????

DOI no: 10.1074/jbc.M804005200

J Biol Chem 283:26548-26556 (2008)

PubMed id: 18667428

Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine.

H.Demirci, S.T.Gregory, A.E.Dahlberg, G.Jogl.

ABSTRACT

Post-transcriptional modification is a ubiquitous feature of ribosomal RNA in all kingdoms of life. Modified nucleotides are generally clustered in functionally important regions of the ribosome, but the functional contribution to protein synthesis is not well understood. Here we describe high resolution crystal structures for the N(2)-guanine methyltransferase RsmC that modifies residue G1207 in 16 S rRNA near the decoding site of the 30 S ribosomal subunit. RsmC is a class I S-adenosyl-L-methionine-dependent methyltransferase composed of two methyltransferase domains. However, only one S-adenosyl-L-methionine molecule and one substrate molecule, guanosine, bind in the ternary complex. The N-terminal domain does not bind any cofactor. Two structures with bound S-adenosyl-L-methionine and S-adenosyl-L-homocysteine confirm that the cofactor binding mode is highly similar to other class I methyltransferases. Secondary structure elements of the N-terminal domain contribute to cofactor-binding interactions and restrict access to the cofactor-binding site. The orientation of guanosine in the active site reveals that G1207 has to disengage from its Watson-Crick base pairing interaction with C1051 in the 16 S rRNA and flip out into the active site prior to its modification. Inspection of the 30 S crystal structure indicates that access to G1207 by RsmC is incompatible with the native subunit structure, consistent with previous suggestions that this enzyme recognizes a subunit assembly intermediate.

Selected figure(s)

Figure 2.
FIGURE 2. Overall structure of RsmC. A, stereo diagram showing a schematic representation of the overall structure. Secondary structure elements are colored in orange, yellow, and red in the N-terminal domain and in blue, cyan, and purple in the C-terminal domain. AdoMet is shown as yellow sticks with atoms colored by elements; guanosine is shown as salmon sticks, and a sulfate molecule bound in the noncatalytic domain is shown in yellow. B, topology diagram with secondary structure elements colored as in A. C, least squares superposition of the two subdomains. The catalytic domain is shown in magenta, and the N-terminal domain is shown in yellow. AdoMet and guanosine bound to the catalytic subdomain are shown as sticks.

Figure 3.
FIGURE 3. The RsmC active site. A, AdoMet binding in the active site. AdoMet and guanosine are shown as yellow and salmon sticks, respectively. Solvent water molecules are shown as red spheres. B, final SigmaA-weighted 2F[o] - F[c] electron density map of the active site region contoured at 1 . C, guanosine binding in the active site. D, comparison of side chain orientation in the noncatalytic N-terminal domain with the active site region of the catalytic domain. Residues in the N-terminal domain are colored red and yellow. The C-terminal domain and AdoMet bound in the catalytic domain are shown in gray for reference.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 26548-26556) copyright 2008.

Figures were selected by the author.