 |
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
|
|
|
|
|
|
|
|
|
Transferase, translation
|
PDB id
|
|
|
|
1qyr
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
 |
|
|
 |
 |
 |
 |
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
|
+
|
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
|
response to antibiotic
|
7 terms
|
 |
|
Biochemical function
|
transferase activity
|
9 terms
|
 |
|
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
|
|
| |
|
|
| |
|
DOI no:
|
J Mol Biol
339:337-353
(2004)
|
|
PubMed id:
|
|
|
|
|
| |
|
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
|
 |
|
|
|
 |
H.Demirci,
L.H.Larsen,
T.Hansen,
A.Rasmussen,
A.Cadambi,
S.T.Gregory,
F.Kirpekar,
and
G.Jogl
(2010).
Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.
|
| |
RNA, 16,
1584-1596.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
K.L.Tkaczuk
(2010).
Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site.
|
| |
J Mol Model, 16,
599-606.
|
 |
|
|
|
|
 |
M.Savkina,
D.Temiakov,
W.T.McAllister,
and
M.Anikin
(2010).
Multiple functions of yeast mitochondrial transcription factor Mtf1p during initiation.
|
| |
J Biol Chem, 285,
3957-3964.
|
 |
|
|
|
|
 |
A.C.Kaberdina,
W.Szaflarski,
K.H.Nierhaus,
and
I.Moll
(2009).
An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis?
|
| |
Mol Cell, 33,
227-236.
|
 |
|
|
|
|
 |
C.Tu,
J.E.Tropea,
B.P.Austin,
D.L.Court,
D.S.Waugh,
and
X.Ji
(2009).
Structural basis for binding of RNA and cofactor by a KsgA methyltransferase.
|
| |
Structure, 17,
374-385.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
H.Demirci,
R.Belardinelli,
E.Seri,
S.T.Gregory,
C.Gualerzi,
A.E.Dahlberg,
and
G.Jogl
(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.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
N.Pulicherla,
L.A.Pogorzala,
Z.Xu,
H.C.O Farrell,
F.N.Musayev,
J.N.Scarsdale,
E.A.Sia,
G.M.Culver,
and
J.P.Rife
(2009).
Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.
|
| |
J Mol Biol, 391,
884-893.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
P.M.Duffin,
and
H.S.Seifert
(2009).
ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.
|
| |
Int J Antimicrob Agents, 33,
321-327.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
K.Inoue,
S.Basu,
and
M.Inouye
(2007).
Dissection of 16S rRNA methyltransferase (KsgA) function in Escherichia coli.
|
| |
J Bacteriol, 189,
8510-8518.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
N.D.Bonawitz,
D.A.Clayton,
and
G.S.Shadel
(2006).
Initiation and beyond: multiple functions of the human mitochondrial transcription machinery.
|
| |
Mol Cell, 24,
813-825.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
G.S.Shadel
(2004).
Coupling the mitochondrial transcription machinery to human disease.
|
| |
Trends Genet, 20,
513-519.
|
 |
|
 |
 |
|
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
codes are
shown on the right.
|
|