PDBsum entry: 3fux

Transferase

PDB id: 3fux

Contents

Protein chains

264 a.a. *

Ligands

MTA ×3

Waters ×733

* Residue conservation analysis

PDB id:

3fux

Name:

Transferase

Title:

T. Thermophilus 16s rrna a1518 and a1519 methyltransferase ( complex with 5'-methylthioadenosine in space group p212121

Structure:

Dimethyladenosine transferase. Chain: a, b, c. Synonym: s-adenosylmethionine-6-n', n'-adenosyl(rrna) dimethyltransferase, 16s rrna dimethylase, high level kasug resistance protein ksga, kasugamycin dimethyltransferase. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: ksga, ttha0083. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.68Å R-factor: 0.202 R-free: 0.239

Authors:

H.Demirci,R.Belardinelli,E.Seri,S.T.Gregory,C.Gualerzi,A.E.D G.Jogl

Key ref:

H.Demirci et al. (2009). Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. J Mol Biol, 388, 271-282. PubMed id: 19285505 DOI: 10.1016/j.jmb.2009.02.066

Date:

14-Jan-09 Release date: 31-Mar-09

Protein chains

Q5SM60  (RSMA_THET8) -  Ribosomal RNA small subunit methyltransferase A

Seq: 271 a.a.

Struc: 264 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.182 - 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase.
• Reaction: 4 S-adenosyl-L-methionine + adenine₁₅₁₈/adenine₁₅₁₉ in 16S rRNA = 4 S-adenosyl-L-homocysteine + N₆-dimethyladenine₁₅₁₈/N₆- dimethyladenine₁₅₁₉ in 16S rRNA

4 × S-adenosyl-L-methionine + adenine(1518)/adenine(1519) in 16S rRNA = 4 × S-adenosyl-L-homocysteine (Bound ligand (Het Group name = MTA) matches with 76.92% similarity) + N(6)-dimethyladenine(1518)/N(6)- dimethyladenine(1519) in 16S rRNA

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: methylation (4 terms)
• Biochemical function: transferase activity (6 terms)

Added reference

DOI no: 10.1016/j.jmb.2009.02.066

J Mol Biol 388:271-282 (2009)

PubMed id: 19285505

Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.

H.Demirci, R.Belardinelli, E.Seri, S.T.Gregory, C.Gualerzi, A.E.Dahlberg, G.Jogl.

ABSTRACT

Posttranscriptional modification of ribosomal RNA (rRNA) occurs in all kingdoms of life. The S-adenosyl-L-methionine-dependent methyltransferase KsgA introduces the most highly conserved rRNA modification, the dimethylation of A1518 and A1519 of 16S rRNA. Loss of this dimethylation confers resistance to the antibiotic kasugamycin. Here, we report biochemical studies and high-resolution crystal structures of KsgA from Thermus thermophilus. Methylation of 30S ribosomal subunits by T. thermophilus KsgA is more efficient at low concentrations of magnesium ions, suggesting that partially unfolded RNA is the preferred substrate. The overall structure is similar to that of other methyltransferases but contains an additional alpha-helix in a novel N-terminal extension. Comparison of the apoenzyme with complex structures with 5'-methylthioadenosine or adenosine bound in the cofactor-binding site reveals novel features when compared with related enzymes. Several mobile loop regions that restrict access to the cofactor-binding site are observed. In addition, the orientation of residues in the substrate-binding site indicates that conformational changes are required for binding two adjacent residues of the substrate rRNA.

Selected figure(s)

Figure 3.
Fig. 3. Overall structure of KsgA. (a) Schematic representation of helix 45 in 16S rRNA. The substrate bases A1518 and A1519 are in dark blue. Coordinated magnesium ions are shown as orange spheres. (b) Schematic representation of the overall structure of KsgA. Secondary-structure elements are in orange and yellow in the catalytic domain and in salmon in the substrate recognition domain. The bound 5′-methylthioadenosine molecule is shown as blue sticks. (c) Cofactor-binding site in KsgA. 5′-Methylthioadenosine is shown as purple sticks. Hydrogen bonds formed with the bound 5′-methylthioadenosine molecule are indicated. (d) Final σ[A]-weighted 2F[o] − F[c] electron density map of the cofactor-binding site contoured at the 1 σ level.

Figure 5.
Fig. 5. Comparison with other methyltransferases. (a) Differences between the overall structures of KsgA from T. thermophilus (yellow) and E. coli (cyan). Adenosine is shown as blue sticks. (b) Structural differences between KsgA (yellow) and ErmC′ (blue). (c) Comparison of the overall structure of KsgA with the DNA-bound complex structure of M.TaqI (PDB code 1G38). M.TaqI is in light green, and DNA is in salmon. (d) Comparison of the active site of KsgA with that of M.TaqI. KsgA is colored as before, the AdoMet analog bound in M.TaqI is shown as light green sticks, and the substrate adenosine is shown as salmon sticks.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 388, 271-282) copyright 2009.

Figures were selected by the author.