PDBsum entry: 1qyr

Transferase, translation

PDB id: 1qyr

Contents

Protein chains

252 a.a. *

Waters ×236

* Residue conservation analysis

PDB id:

1qyr

Name:

Transferase, translation

Title:

2.1 angstrom crystal structure of ksga: a universally conser adenosine dimethyltransferase

Structure:

High level kasugamycin resistance protein. Chain: a, b. Synonym: ksga. Dimethyladenosine transferase. S-adenosylmet n',n'-adenosyl(rrna) dimethyltransferase. 16s rrna dimethy kasugamycin dimethyltransferase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: ksga. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.194 R-free: 0.238

Authors:

H.C.O'Farrell,J.N.Scarsdale,H.T.Wright,J.P.Rife

Key ref:

H.C.O'Farrell et al. (2004). Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. J Mol Biol, 339, 337-353. PubMed id: 15136037 DOI: 10.1016/j.jmb.2004.02.068

Date:

11-Sep-03 Release date: 29-Jun-04

Protein chains

P06992  (RSMA_ECOLI) -  Ribosomal RNA small subunit methyltransferase A

Seq: 273 a.a.

Struc: 252 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

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: response to antibiotic (7 terms)
• Biochemical function: transferase activity (9 terms)

Added reference

DOI no: 10.1016/j.jmb.2004.02.068

J Mol Biol 339:337-353 (2004)

PubMed id: 15136037

Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli.

H.C.O'Farrell, J.N.Scarsdale, J.P.Rife.

ABSTRACT

The bacterial enzyme KsgA catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaebacteria, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In yeast, and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. Another ortholog has been discovered recently, h-mtTFB in human mitochondria, which has a second function; this enzyme is a nuclear-encoded mitochondrial transcription factor. The KsgA enzymes are homologous to another family of RNA methyltransferases, the Erm enzymes, which methylate a single adenosine base in 23S rRNA and confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. We have crystallized KsgA from Escherichia coli and solved its structure to a resolution of 2.1A. The structure bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to sc-mtTFB, the Saccharomyces cerevisiae version of h-mtTFB. Comparison of the three crystal structures and further study of the KsgA protein will provide insight into this interesting group of enzymes.

Selected figure(s)

Figure 5.
Figure 5. Delphi surface maps of (a) KsgA, (b) ErmC', and (c) sc-mtTFB. Red indicates areas of negative charge; areas of positive charge are shown in blue.

Figure 8.
Figure 8. Cartoon model of helix 45/KsgA binding interaction. The A monomer of KsgA is shown in white, with colored residues as in Figure 2. Helix 45 is shown in blue, with the target adenosine residues extending outward from the loop. Placement of the SAM molecule, also in blue, is based on the ErmC'/SAM co-crystal structure. Roman numerals indicate structural motifs, while numbers indicate the six residues that are conserved in the N-terminal domain (see the text for details).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 339, 337-353) copyright 2004.

Figures were selected by an automated process.