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Transferase, translation PDB-id
1qyr
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252 a.a. *
Waters ×236

* Residue conservation analysis
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PDB id: 1qyr
Name: Transferase, translation
Title: 2.1 angstrom crystal structure of ksga: a universally conserved adenosine dimethyltransferase

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

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

UniProt:
Chains A, B: P06992 (KSGA_ECOLI)
Pfam   ArchSchema ?
Seq:
Struc:
Seq: 273 a.a.
Struc: 252 a.a.
Key:    PfamA domain
 Secondary structure  CATH domain

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
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    Key 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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19001112 K.Ochi, J.Y.Kim, Y.Tanaka, G.Wang, K.Masuda, H.Nanamiya, S.Okamoto, S.Tokuyama, Y.Adachi, and F.Kawamura (2009).
Inactivation of KsgA, a 16S rRNA methyltransferase, causes vigorous emergence of mutants with high-level kasugamycin resistance.
  Antimicrob Agents Chemother, 53, 193-201.  
19730693 M.A.Bergman, W.P.Loomis, J.Mecsas, M.N.Starnbach, and R.R.Isberg (2009).
CD8(+) T cells restrict Yersinia pseudotuberculosis infection: bypass of anti-phagocytosis by targeting antigen-presenting cells.
  PLoS Pathog, 5, e1000573.  
20043826 R.Binet, and A.T.Maurelli (2009).
The chlamydial functional homolog of KsgA confers kasugamycin sensitivity to Chlamydia trachomatis and impacts bacterial fitness.
  BMC Microbiol, 9, 279.  
19386620 T.Monecke, A.Dickmanns, and R.Ficner (2009).
Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1.
  Nucleic Acids Res, 37, 3865-3877.
PDB code: 3gdh
18959795 H.C.O'Farrell, Z.Xu, G.M.Culver, and J.P.Rife (2008).
Sequence and structural evolution of the KsgA/Dim1 methyltransferase family.
  BMC Res Notes, 1, 108.  
18990185 K.Connolly, J.P.Rife, and G.Culver (2008).
Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA.
  Mol Microbiol, 70, 1062-1075.  
18223068 T.L.Campbell, and E.D.Brown (2008).
Genetic interaction screens with ordered overexpression and deletion clone sets implicate the Escherichia coli GTPase YjeQ in late ribosome biogenesis.
  J Bacteriol, 190, 2537-2545.  
18391965 Z.Xu, H.C.O'Farrell, J.P.Rife, and G.M.Culver (2008).
A conserved rRNA methyltransferase regulates ribosome biogenesis.
  Nat Struct Mol Biol, 15, 534-536.  
17890303 K.Inoue, S.Basu, and M.Inouye (2007).
Dissection of 16S rRNA methyltransferase (KsgA) function in Escherichia coli.
  J Bacteriol, 189, 8510-8518.  
16998486 B.S.Schuwirth, J.M.Day, C.W.Hau, G.R.Janssen, A.E.Dahlberg, J.H.Cate, and A.Vila-Sanjurjo (2006).
Structural analysis of kasugamycin inhibition of translation.
  Nat Struct Mol Biol, 13, 879-886.
PDB codes: 1vs5 1vs6 1vs7 1vs8
16540698 H.C.O'Farrell, N.Pulicherla, P.M.Desai, and J.P.Rife (2006).
Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution.
  RNA, 12, 725-733.  
17031457 J.Cotney, and G.S.Shadel (2006).
Evidence for an early gene duplication event in the evolution of the mitochondrial transcription factor B family and maintenance of rRNA methyltransferase activity in human mtTFB1 and mtTFB2.
  J Mol Evol, 63, 707-717.  
15749697 Y.Matsushima, C.Adán, R.Garesse, and L.S.Kaguni (2005).
Drosophila mitochondrial transcription factor B1 modulates mitochondrial translation but not transcription or DNA copy number in Schneider cells.
  J Biol Chem, 280, 16815-16820.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.