|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
197 a.a.*
|
|
|
|
|
|
|
|
|
|
|
130 a.a.*
|
|
|
|
|
|
|
|
|
|
|
58 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
* C-alpha coords only
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Ribosome
|
|
|
Title:
|
|
Structural basis for the interaction of antibiotics with the peptidyl transferase center in eubacteria
|
|
Structure:
|
|
23s rrna. Chain: a. Ribosomal protein l4. Chain: k. Ribosomal protein l22. Chain: l. Ribosomal protein l32. Chain: m. Synonym: 50s ribosomal protein l32
|
|
Source:
|
|
Deinococcus radiodurans. Organism_taxid: 1299. Organism_taxid: 1299
|
|
Biol. unit:
|
|
Tetramer (from
)
|
|
Resolution:
|
|
|
3.80Å
|
R-factor:
|
0.209
|
R-free:
|
0.274
|
|
|
Authors:
|
|
F.Schluenzen,R.Zarivach,J.Harms,A.Bashan,A.Tocilj,R.Albrecht, A.Yonath,F.Franceschi
|
Key ref:
|
|
F.Schlünzen
et al.
(2001).
Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria.
Nature,
413,
814-821.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
17-Sep-01
|
Release date:
|
26-Oct-01
|
|
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
Q9RXK1
(RL4_DEIRA) -
Large ribosomal subunit protein uL4 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)
|
|
|
|
Seq:
Struc:
|
|
|
|
205 a.a.
197 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chains K, L, M:
E.C.?
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Nature
413:814-821
(2001)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria.
|
|
F.Schlünzen,
R.Zarivach,
J.Harms,
A.Bashan,
A.Tocilj,
R.Albrecht,
A.Yonath,
F.Franceschi.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Ribosomes, the site of protein synthesis, are a major target for natural and
synthetic antibiotics. Detailed knowledge of antibiotic binding sites is central
to understanding the mechanisms of drug action. Conversely, drugs are excellent
tools for studying the ribosome function. To elucidate the structural basis of
ribosome-antibiotic interactions, we determined the high-resolution X-ray
structures of the 50S ribosomal subunit of the eubacterium Deinococcus
radiodurans, complexed with the clinically relevant antibiotics chloramphenicol,
clindamycin and the three macrolides erythromycin, clarithromycin and
roxithromycin. We found that antibiotic binding sites are composed exclusively
of segments of 23S ribosomal RNA at the peptidyl transferase cavity and do not
involve any interaction of the drugs with ribosomal proteins. Here we report the
details of antibiotic interactions with the components of their binding sites.
Our results also show the importance of putative Mg+2 ions for the binding of
some drugs. This structural analysis should facilitate rational drug design.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 1.
Figure 1: Interaction of chloramphenicol with the peptidyl
transferase cavity. a, Chemical structure diagram of
chloramphenicol showing the interactions (arrows) of its
reactive groups with the nucleotides of the peptidyl transferase
cavity. Arrows between two chemical moieties indicate that the
two groups are less than 4.4 Å apart. b, Secondary structure of
the peptidyl transferase ring of D. radiodurans showing the
nucleotides involved in the interaction with chloramphenicol
(coloured nucleotides). The colours in the secondary structure
diagram match those of the chemical diagram. c, Stereo view
showing the nucleotides interacting with chloramphenicol at the
peptidyl transferase cavity of D. radiodurans. The difference
electron density map (2F[o] - F[c]) is contoured at 1.2  .
The antibiotic is shown in green. Nucleotide numbering is
according to the E. coli sequence. Putative Mg ions (Mg-C1,
Mg-C2) are indicated.
|
|
Figure 4.
Figure 4: Relative position of chloramphenicol, clindamycin and
macrolides with respect to CC-puromycin and the
3'-cytosine-adenine (CA) end of P-site and A-site tRNAs. The
location of CC-puromycin was obtained by docking the position
reported by ref. 2 into the peptidyl transferase centre of D.
radiodurans. The location of the 3'-CA end of P- and A-site
tRNAs was obtained by docking the position reported by ref. 42
into the peptidyl transferase centre of D. radiodurans. Light
blue, 3'-CA end of A-site tRNA; light yellow, 3'-CA end of
P-site tRNA; grey, puromycin; gold, chloramphenicol; green,
clindamycin; cyan, macrolides (erythromycin). Oxygen atoms are
shown in red and nitrogen atoms in dark blue. CHCl[2] indicates
the location of the dichloromethyl moiety of chloramphenicol.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2001,
413,
814-821)
copyright 2001.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
C.Fan,
and
J.He
(2011).
Proliferation of antibiotic resistance genes in microbial consortia of sequencing batch reactors (SBRs) upon exposure to trace erythromycin or erythromycin-H(2)O.
|
| |
Water Res,
45,
3098-3106.
|
|
|
|
|
|
|
F.Yan,
and
D.G.Fujimori
(2011).
RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift.
|
| |
Proc Natl Acad Sci U S A,
108,
3930-3934.
|
|
|
|
|
|
|
H.Ramu,
N.Vázquez-Laslop,
D.Klepacki,
Q.Dai,
J.Piccirilli,
R.Micura,
and
A.S.Mankin
(2011).
Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center.
|
| |
Mol Cell,
41,
321-330.
|
|
|
|
|
|
|
M.J.Belousoff,
T.Shapira,
A.Bashan,
E.Zimmerman,
H.Rozenberg,
K.Arakawa,
H.Kinashi,
and
A.Yonath
(2011).
Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
|
| |
Proc Natl Acad Sci U S A,
108,
2717-2722.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Y.Liao,
Y.S.Choi,
J.D.Dinman,
and
K.H.Lee
(2011).
The many paths to frameshifting: kinetic modelling and analysis of the effects of different elongation steps on programmed -1 ribosomal frameshifting.
|
| |
Nucleic Acids Res,
39,
300-312.
|
|
|
|
|
|
|
T.Siibak,
L.Peil,
A.Dönhöfer,
A.Tats,
M.Remm,
D.N.Wilson,
T.Tenson,
and
J.Remme
(2011).
Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins.
|
| |
Mol Microbiol,
80,
54-67.
|
|
|
|
|
|
|
A.Aakra,
H.Vebø,
U.Indahl,
L.Snipen,
O.Gjerstad,
M.Lunde,
and
I.F.Nes
(2010).
The Response of Enterococcus faecalis V583 to Chloramphenicol Treatment.
|
| |
Int J Microbiol,
2010,
483048.
|
|
|
|
|
|
|
A.L.Starosta,
V.V.Karpenko,
A.V.Shishkina,
A.Mikolajka,
N.V.Sumbatyan,
F.Schluenzen,
G.A.Korshunova,
A.A.Bogdanov,
and
D.N.Wilson
(2010).
Interplay between the ribosomal tunnel, nascent chain, and macrolides influences drug inhibition.
|
| |
Chem Biol,
17,
504-514.
|
|
|
|
|
|
|
C.E.Aitken,
and
J.D.Puglisi
(2010).
Following the intersubunit conformation of the ribosome during translation in real time.
|
| |
Nat Struct Mol Biol,
17,
793-800.
|
|
|
|
|
|
|
C.M.Logue,
G.T.Danzeisen,
J.S.Sherwood,
J.L.Thorsness,
B.M.Mercier,
and
J.E.Axtman
(2010).
Repeated therapeutic dosing selects macrolide-resistant Campylobacter spp. in a turkey facility.
|
| |
J Appl Microbiol,
109,
1379-1388.
|
|
|
|
|
|
|
C.Ma,
Z.Liu,
H.Song,
R.Jiang,
F.He,
and
S.Ma
(2010).
Synthesis and antibacterial activity of novel 11,12-cyclic carbonate azithromycin 4''-O-carbamate derivatives.
|
| |
J Antibiot (Tokyo),
63,
3-8.
|
|
|
|
|
|
|
D.Bulkley,
C.A.Innis,
G.Blaha,
and
T.A.Steitz
(2010).
Revisiting the structures of several antibiotics bound to the bacterial ribosome.
|
| |
Proc Natl Acad Sci U S A,
107,
17158-17163.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.Lucent,
C.D.Snow,
C.E.Aitken,
and
V.S.Pande
(2010).
Non-bulk-like solvent behavior in the ribosome exit tunnel.
|
| |
PLoS Comput Biol,
6,
e1000963.
|
|
|
|
|
|
|
D.Pacheu-Grau,
A.Gómez-Durán,
J.Montoya,
and
E.Ruiz-Pesini
(2010).
Influence of mtDNA genetic variation on antibiotic therapy.
|
| |
Pharmacogenomics,
11,
1185-1187.
|
|
|
|
|
|
|
E.Cundliffe,
and
A.L.Demain
(2010).
Avoidance of suicide in antibiotic-producing microbes.
|
| |
J Ind Microbiol Biotechnol,
37,
643-672.
|
|
|
|
|
|
|
H.C.Nguyen,
F.Karray,
S.Lautru,
J.Gagnat,
A.Lebrihi,
T.D.Huynh,
and
J.L.Pernodet
(2010).
Glycosylation steps during spiramycin biosynthesis in Streptomyces ambofaciens: involvement of three glycosyltransferases and their interplay with two auxiliary proteins.
|
| |
Antimicrob Agents Chemother,
54,
2830-2839.
|
|
|
|
|
|
|
H.David-Eden,
A.S.Mankin,
and
Y.Mandel-Gutfreund
(2010).
Structural signatures of antibiotic binding sites on the ribosome.
|
| |
Nucleic Acids Res,
38,
5982-5994.
|
|
|
|
|
|
|
J.A.Dunkle,
L.Xiong,
A.S.Mankin,
and
J.H.Cate
(2010).
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
|
| |
Proc Natl Acad Sci U S A,
107,
17152-17157.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.C.Kwan,
and
H.Luesch
(2010).
Weapons in disguise--activating mechanisms and protecting group chemistry in nature.
|
| |
Chemistry,
16,
13020-13029.
|
|
|
|
|
|
|
J.J.Holstein,
P.Luger,
R.Kalinowski,
S.Mebs,
C.Paulman,
and
B.Dittrich
(2010).
Validation of experimental charge densities: refinement of the macrolide antibiotic roxithromycin.
|
| |
Acta Crystallogr B,
66,
568-577.
|
|
|
|
|
|
|
K.J.Simmons,
I.Chopra,
and
C.W.Fishwick
(2010).
Structure-based discovery of antibacterial drugs.
|
| |
Nat Rev Microbiol,
8,
501-510.
|
|
|
|
|
|
|
M.H.Rhodin,
and
J.D.Dinman
(2010).
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding.
|
| |
Nucleic Acids Res,
38,
8377-8389.
|
|
|
|
|
|
|
M.Morar,
and
G.D.Wright
(2010).
The genomic enzymology of antibiotic resistance.
|
| |
Annu Rev Genet,
44,
25-51.
|
|
|
|
|
|
|
N.Vázquez-Laslop,
H.Ramu,
D.Klepacki,
K.Kannan,
and
A.S.Mankin
(2010).
The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide.
|
| |
EMBO J,
29,
3108-3117.
|
|
|
|
|
|
|
S.Douthwaite
(2010).
Designer drugs for discerning bugs.
|
| |
Proc Natl Acad Sci U S A,
107,
17065-17066.
|
|
|
|
|
|
|
S.Uemura,
C.E.Aitken,
J.Korlach,
B.A.Flusberg,
S.W.Turner,
and
J.D.Puglisi
(2010).
Real-time tRNA transit on single translating ribosomes at codon resolution.
|
| |
Nature,
464,
1012-1017.
|
|
|
|
|
|
|
T.Auerbach,
I.Mermershtain,
C.Davidovich,
A.Bashan,
M.Belousoff,
I.Wekselman,
E.Zimmerman,
L.Xiong,
D.Klepacki,
K.Arakawa,
H.Kinashi,
A.S.Mankin,
and
A.Yonath
(2010).
The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics.
|
| |
Proc Natl Acad Sci U S A,
107,
1983-1988.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.M.Bakheet,
and
A.J.Doig
(2010).
Properties and identification of antibiotic drug targets.
|
| |
BMC Bioinformatics,
11,
195.
|
|
|
|
|
|
|
U.Allas,
and
T.Tenson
(2010).
A method for selecting cis-acting regulatory sequences that respond to small molecule effectors.
|
| |
BMC Mol Biol,
11,
56.
|
|
|
|
|
|
|
Y.Qi,
B.Jiao,
X.Ma,
W.Cui,
and
S.Ma
(2010).
Synthesis and antibacterial activity of novel 4''-O-carbamoyl erythromycin-A derivatives.
|
| |
Arch Pharm (Weinheim),
343,
458-464.
|
|
|
|
|
|
|
Y.Xie,
A.V.Dix,
and
Y.Tor
(2010).
Antibiotic selectivity for prokaryotic vs. eukaryotic decoding sites.
|
| |
Chem Commun (Camb),
46,
5542-5544.
|
|
|
|
|
|
|
Z.Wu,
Y.Lu,
M.Luo,
X.He,
Y.Xiao,
J.Yang,
Y.Pan,
G.Qiu,
Y.Xu,
W.Huang,
P.Long,
R.Li,
and
X.Hu
(2010).
Synthesis and antibacterial activity of novel 4''-carbamates of 6,11-di-O-methylerythromycin A.
|
| |
J Antibiot (Tokyo),
63,
343-350.
|
|
|
|
|
|
|
A.M.Giessing,
S.S.Jensen,
A.Rasmussen,
L.H.Hansen,
A.Gondela,
K.Long,
B.Vester,
and
F.Kirpekar
(2009).
Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria.
|
| |
RNA,
15,
327-336.
|
|
|
|
|
|
|
A.Pei,
C.W.Nossa,
P.Chokshi,
M.J.Blaser,
L.Yang,
D.M.Rosmarin,
and
Z.Pei
(2009).
Diversity of 23S rRNA genes within individual prokaryotic genomes.
|
| |
PLoS ONE,
4,
e5437.
|
|
|
|
|
|
|
B.Marciniec,
M.Stawny,
P.Kachlicki,
E.Jaroszkiewicz,
and
M.Needham
(2009).
Radiostability of florfenicol in the solid state.
|
| |
Anal Sci,
25,
1255-1260.
|
|
|
|
|
|
|
C.W.Carter
(2009).
E pluribus tres: the 2009 nobel prize in chemistry.
|
| |
Structure,
17,
1558-1561.
|
|
|
|
|
|
|
D.M.Pettigrew,
P.Roversi,
S.G.Davies,
A.J.Russell,
and
S.M.Lea
(2009).
A structural study of the interaction between the Dr haemagglutinin DraE and derivatives of chloramphenicol.
|
| |
Acta Crystallogr D Biol Crystallogr,
65,
513-522.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.N.Wilson
(2009).
The A-Z of bacterial translation inhibitors.
|
| |
Crit Rev Biochem Mol Biol,
44,
393-433.
|
|
|
|
|
|
|
E.Breukink
(2009).
Cell biology. Lethal traffic jam.
|
| |
Science,
325,
684-685.
|
|
|
|
|
|
|
E.C.Kouvela,
D.L.Kalpaxis,
D.N.Wilson,
and
G.P.Dinos
(2009).
Distinct mode of interaction of a novel ketolide antibiotic that displays enhanced antimicrobial activity.
|
| |
Antimicrob Agents Chemother,
53,
1411-1419.
|
|
|
|
|
|
|
E.J.Diner,
and
C.S.Hayes
(2009).
Recombineering reveals a diverse collection of ribosomal proteins L4 and L22 that confer resistance to macrolide antibiotics.
|
| |
J Mol Biol,
386,
300-315.
|
|
|
|
|
|
|
E.Zimmerman,
and
A.Yonath
(2009).
Biological implications of the ribosome's stunning stereochemistry.
|
| |
Chembiochem,
10,
63-72.
|
|
|
|
|
|
|
G.Gürel,
G.Blaha,
P.B.Moore,
and
T.A.Steitz
(2009).
U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
|
| |
J Mol Biol,
389,
146-156.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.Gürel,
G.Blaha,
T.A.Steitz,
and
P.B.Moore
(2009).
Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui.
|
| |
Antimicrob Agents Chemother,
53,
5010-5014.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Ramu,
A.Mankin,
and
N.Vazquez-Laslop
(2009).
Programmed drug-dependent ribosome stalling.
|
| |
Mol Microbiol,
71,
811-824.
|
|
|
|
|
|
|
J.A.Sundlov,
and
A.M.Gulick
(2009).
Insights into resistance against lincosamide antibiotics.
|
| |
Structure,
17,
1549-1550.
|
|
|
|
|
|
|
J.B.Locke,
M.Hilgers,
and
K.J.Shaw
(2009).
Novel ribosomal mutations in Staphylococcus aureus strains identified through selection with the oxazolidinones linezolid and torezolid (TR-700).
|
| |
Antimicrob Agents Chemother,
53,
5265-5274.
|
|
|
|
|
|
|
J.B.Thoden,
C.Schäffer,
P.Messner,
and
H.M.Holden
(2009).
Structural analysis of QdtB, an aminotransferase required for the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-glucose.
|
| |
Biochemistry,
48,
1553-1561.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.D.Kittendorf,
and
D.H.Sherman
(2009).
The methymycin/pikromycin pathway: a model for metabolic diversity in natural product biosynthesis.
|
| |
Bioorg Med Chem,
17,
2137-2146.
|
|
|
|
|
|
|
J.E.McLaughlin,
M.A.Bin-Umer,
A.Tortora,
N.Mendez,
S.McCormick,
and
N.E.Tumer
(2009).
A genome-wide screen in Saccharomyces cerevisiae reveals a critical role for the mitochondria in the toxicity of a trichothecene mycotoxin.
|
| |
Proc Natl Acad Sci U S A,
106,
21883-21888.
|
|
|
|
|
|
|
J.Feng,
A.Lupien,
H.Gingras,
J.Wasserscheid,
K.Dewar,
D.Légaré,
and
M.Ouellette
(2009).
Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance.
|
| |
Genome Res,
19,
1214-1223.
|
|
|
|
|
|
|
K.S.Long,
J.Poehlsgaard,
L.H.Hansen,
S.N.Hobbie,
E.C.Böttger,
and
B.Vester
(2009).
Single 23S rRNA mutations at the ribosomal peptidyl transferase centre confer resistance to valnemulin and other antibiotics in Mycobacterium smegmatis by perturbation of the drug binding pocket.
|
| |
Mol Microbiol,
71,
1218-1227.
|
|
|
|
|
|
|
M.Lovmar,
K.Nilsson,
E.Lukk,
V.Vimberg,
T.Tenson,
and
M.Ehrenberg
(2009).
Erythromycin resistance by L4/L22 mutations and resistance masking by drug efflux pump deficiency.
|
| |
EMBO J,
28,
736-744.
|
|
|
|
|
|
|
M.Morar,
K.Bhullar,
D.W.Hughes,
M.Junop,
and
G.D.Wright
(2009).
Structure and mechanism of the lincosamide antibiotic adenylyltransferase LinB.
|
| |
Structure,
17,
1649-1659.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Simonović,
and
T.A.Steitz
(2009).
A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.
|
| |
Biochim Biophys Acta,
1789,
612-623.
|
|
|
|
|
|
|
M.Sprinzl,
and
V.A.Erdmann
(2009).
Protein biosynthesis on ribosomes in molecular resolution: nobel prize for chemistry 2009 goes to three chemical biologists.
|
| |
Chembiochem,
10,
2851-2853.
|
|
|
|
|
|
|
M.de la Peña,
D.Dufour,
and
J.Gallego
(2009).
Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold.
|
| |
RNA,
15,
1949-1964.
|
|
|
|
|
|
|
N.E.Scangarella-Oman,
R.M.Shawar,
S.Bouchillon,
and
D.Hoban
(2009).
Microbiological profile of a new topical antibacterial: retapamulin ointment 1%.
|
| |
Expert Rev Anti Infect Ther,
7,
269-279.
|
|
|
|
|
|
|
P.H.Szu,
M.W.Ruszczycky,
S.H.Choi,
F.Yan,
and
H.W.Liu
(2009).
Characterization and mechanistic studies of DesII: a radical S-adenosyl-L-methionine enzyme involved in the biosynthesis of TDP-D-desosamine.
|
| |
J Am Chem Soc,
131,
14030-14042.
|
|
|
|
|
|
|
S.Li,
M.R.Chaulagain,
A.R.Knauff,
L.M.Podust,
J.Montgomery,
and
D.H.Sherman
(2009).
Selective oxidation of carbolide C-H bonds by an engineered macrolide P450 mono-oxygenase.
|
| |
Proc Natl Acad Sci U S A,
106,
18463-18468.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.Siibak,
L.Peil,
L.Xiong,
A.Mankin,
J.Remme,
and
T.Tenson
(2009).
Erythromycin- and chloramphenicol-induced ribosomal assembly defects are secondary effects of protein synthesis inhibition.
|
| |
Antimicrob Agents Chemother,
53,
563-571.
|
|
|
|
|
|
|
Y.Xie,
A.V.Dix,
and
Y.Tor
(2009).
FRET enabled real time detection of RNA-small molecule binding.
|
| |
J Am Chem Soc,
131,
17605-17614.
|
|
|
|
|
|
|
A.D.Petropoulos,
E.C.Kouvela,
G.P.Dinos,
and
D.L.Kalpaxis
(2008).
Stepwise binding of tylosin and erythromycin to Escherichia coli ribosomes, characterized by kinetic and footprinting analysis.
|
| |
J Biol Chem,
283,
4756-4765.
|
|
|
|
|
|
|
A.S.Bommakanti,
L.Lindahl,
and
J.M.Zengel
(2008).
Mutation from guanine to adenine in 25S rRNA at the position equivalent to E. coli A2058 does not confer erythromycin sensitivity in Sacchromyces cerevisae.
|
| |
RNA,
14,
460-464.
|
|
|
|
|
|
|
A.S.Mankin
(2008).
Macrolide myths.
|
| |
Curr Opin Microbiol,
11,
414-421.
|
|
|
|
|
|
|
A.Sadeghi-Khomami,
M.D.Lumsden,
and
D.L.Jakeman
(2008).
Glycosidase inhibition by macrolide antibiotics elucidated by STD-NMR spectroscopy.
|
| |
Chem Biol,
15,
739-749.
|
|
|
|
|
|
|
A.Vourekas,
V.Stamatopoulou,
C.Toumpeki,
M.Tsitlaidou,
and
D.Drainas
(2008).
Insights into functional modulation of catalytic RNA activity.
|
| |
IUBMB Life,
60,
669-683.
|
|
|
|
|
|
|
B.J.Wolff,
W.L.Thacker,
S.B.Schwartz,
and
J.M.Winchell
(2008).
Detection of macrolide resistance in Mycoplasma pneumoniae by real-time PCR and high-resolution melt analysis.
|
| |
Antimicrob Agents Chemother,
52,
3542-3549.
|
|
|
|
|
|
|
C.Davidovich,
A.Bashan,
and
A.Yonath
(2008).
Structural basis for cross-resistance to ribosomal PTC antibiotics.
|
| |
Proc Natl Acad Sci U S A,
105,
20665-20670.
|
|
|
|
|
|
|
C.Foster,
and
W.S.Champney
(2008).
Characterization of a 30S ribosomal subunit assembly intermediate found in Escherichia coli cells growing with neomycin or paromomycin.
|
| |
Arch Microbiol,
189,
441-449.
|
|
|
|
|
|
|
D.N.Wilson,
F.Schluenzen,
J.M.Harms,
A.L.Starosta,
S.R.Connell,
and
P.Fucini
(2008).
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning.
|
| |
Proc Natl Acad Sci U S A,
105,
13339-13344.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.R.Gentry,
and
D.J.Holmes
(2008).
Selection for high-level telithromycin resistance in Staphylococcus aureus yields mutants resulting from an rplB-to-rplV gene conversion-like event.
|
| |
Antimicrob Agents Chemother,
52,
1156-1158.
|
|
|
|
|
|
|
D.Rodriguez-Correa,
and
A.E.Dahlberg
(2008).
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus.
|
| |
RNA,
14,
2314-2318.
|
|
|
|
|
|
|
E.M.Driggers,
S.P.Hale,
J.Lee,
and
N.K.Terrett
(2008).
The exploration of macrocycles for drug discovery--an underexploited structural class.
|
| |
Nat Rev Drug Discov,
7,
608-624.
|
|
|
|
|
|
|
E.Rimbara,
N.Noguchi,
T.Kawai,
and
M.Sasatsu
(2008).
Novel mutation in 23S rRNA that confers low-level resistance to clarithromycin in Helicobacter pylori.
|
| |
Antimicrob Agents Chemother,
52,
3465-3466.
|
|
|
|
|
|
|
E.Skripkin,
T.S.McConnell,
J.DeVito,
L.Lawrence,
J.A.Ippolito,
E.M.Duffy,
J.Sutcliffe,
and
F.Franceschi
(2008).
R chi-01, a new family of oxazolidinones that overcome ribosome-based linezolid resistance.
|
| |
Antimicrob Agents Chemother,
52,
3550-3557.
|
|
|
|
|
|
|
G.Blaha,
G.Gürel,
S.J.Schroeder,
P.B.Moore,
and
T.A.Steitz
(2008).
Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
|
| |
J Mol Biol,
379,
505-519.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.David-Eden,
and
Y.Mandel-Gutfreund
(2008).
Revealing unique properties of the ribosome using a network based analysis.
|
| |
Nucleic Acids Res,
36,
4641-4652.
|
|
|
|
|
|
|
H.Ishida,
and
S.Hayward
(2008).
Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.
|
| |
Biophys J,
95,
5962-5973.
|
|
|
|
|
|
|
I.Miroshnyk,
S.Mirza,
P.M.Zorky,
J.Heinämäki,
J.Yli-Kauhaluoma,
and
J.Yliruusi
(2008).
A new insight into solid-state conformation of macrolide antibiotics.
|
| |
Bioorg Med Chem,
16,
232-239.
|
|
|
|
|
|
|
J.M.Harms,
D.N.Wilson,
F.Schluenzen,
S.R.Connell,
T.Stachelhaus,
Z.Zaborowska,
C.M.Spahn,
and
P.Fucini
(2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
|
| |
Mol Cell,
30,
26-38.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.K.Smith,
and
A.S.Mankin
(2008).
Transcriptional and translational control of the mlr operon, which confers resistance to seven classes of protein synthesis inhibitors.
|
| |
Antimicrob Agents Chemother,
52,
1703-1712.
|
|
|
|
|
|
|
M.Bailey,
T.Chettiath,
and
A.S.Mankin
(2008).
Induction of erm(C) expression by noninducing antibiotics.
|
| |
Antimicrob Agents Chemother,
52,
866-874.
|
|
|
|
|
|
|
M.G.Lawrence,
L.Lindahl,
and
J.M.Zengel
(2008).
Effects on translation pausing of alterations in protein and RNA components of the ribosome exit tunnel.
|
| |
J Bacteriol,
190,
5862-5869.
|
|
|
|
|
|
|
M.I.Kotev,
and
P.M.Ivanov
(2008).
Molecular mechanics (MM3(pi)) conformational analysis of molecules containing conjugated pi-electron fragments: Leucomycin-V.
|
| |
Chirality,
20,
400-410.
|
|
|
|
|
|
|
M.S.Jurica
(2008).
Searching for a wrench to throw into the splicing machine.
|
| |
Nat Chem Biol,
4,
3-6.
|
|
|
|
|
|
|
N.Vazquez-Laslop,
C.Thum,
and
A.S.Mankin
(2008).
Molecular mechanism of drug-dependent ribosome stalling.
|
| |
Mol Cell,
30,
190-202.
|
|
|
|
|
|
|
P.Seibel,
C.Di Nunno,
C.Kukat,
I.Schäfer,
R.Del Bo,
A.Bordoni,
G.P.Comi,
A.Schön,
F.Capuano,
D.Latorre,
and
G.Villani
(2008).
Cosegregation of novel mitochondrial 16S rRNA gene mutations with the age-associated T414G variant in human cybrids.
|
| |
Nucleic Acids Res,
36,
5872-5881.
|
|
|
|
|
|
|
S.B.Luppens,
D.Kara,
L.Bandounas,
M.J.Jonker,
F.R.Wittink,
O.Bruning,
T.M.Breit,
J.M.Ten Cate,
and
W.Crielaard
(2008).
Effect of Veillonella parvula on the antimicrobial resistance and gene expression of Streptococcus mutans grown in a dual-species biofilm.
|
| |
Oral Microbiol Immunol,
23,
183-189.
|
|
|
|
|
|
|
S.D.Moore,
and
R.T.Sauer
(2008).
Revisiting the mechanism of macrolide-antibiotic resistance mediated by ribosomal protein L22.
|
| |
Proc Natl Acad Sci U S A,
105,
18261-18266.
|
|
|
|
|
|
|
S.M.Toh,
L.Xiong,
T.Bae,
and
A.S.Mankin
(2008).
The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA.
|
| |
RNA,
14,
98.
|
|
|
|
|
|
|
T.Morimura,
M.Hashiba,
H.Kameda,
M.Takami,
H.Takahama,
M.Ohshige,
and
F.Sugawara
(2008).
Identification of macrolide antibiotic-binding Human_p8 protein.
|
| |
J Antibiot (Tokyo),
61,
291-296.
|
|
|
|
|
|
|
U.Schell,
S.F.Haydock,
A.L.Kaja,
I.Carletti,
R.E.Lill,
E.Read,
L.S.Sheehan,
L.Low,
M.J.Fernandez,
F.Grolle,
H.A.McArthur,
R.M.Sheridan,
P.F.Leadlay,
B.Wilkinson,
and
S.Gaisser
(2008).
Engineered biosynthesis of hybrid macrolide polyketides containing D-angolosamine and D-mycaminose moieties.
|
| |
Org Biomol Chem,
6,
3315-3327.
|
|
|
|
|
|
|
A.L.Manuell,
J.Quispe,
and
S.P.Mayfield
(2007).
Structure of the chloroplast ribosome: novel domains for translation regulation.
|
| |
PLoS Biol,
5,
e209.
|
|
|
|
|
|
|
A.Yassin,
and
A.S.Mankin
(2007).
Potential new antibiotic sites in the ribosome revealed by deleterious mutations in RNA of the large ribosomal subunit.
|
| |
J Biol Chem,
282,
24329-24342.
|
|
|
|
|
|
|
D.Liang,
and
J.Qiao
(2007).
Phylogenetic analysis of antibiotic glycosyltransferases.
|
| |
J Mol Evol,
64,
342-353.
|
|
|
|
|
|
|
E.S.Burgie,
and
H.M.Holden
(2007).
Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine.
|
| |
Biochemistry,
46,
8999-9006.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
F.Franceschi
(2007).
Back to the future: the ribosome as an antibiotic target.
|
| |
Future Microbiol,
2,
571-574.
|
|
|
|
|
|
|
F.Leontiadou,
A.Tsagkalia,
and
T.Choli-Papadopoulou
(2007).
Thermus thermophilus L4 ribosomal protein: purification and sensitivity alteration against erythromycin of E. coli cells harboring a single amino acid mutant of TthL4 within its extended loop.
|
| |
Amino Acids,
33,
463-468.
|
|
|
|
|
|
|
G.A.Korshunova,
N.V.Sumbatian,
N.V.Fedorova,
I.V.Kuznetsova,
A.V.Shishkina,
and
A.A.Bogdanov
(2007).
[Peptide derivatives of tylosin-related macrolides]
|
| |
Bioorg Khim,
33,
235-244.
|
|
|
|
|
|
|
J.S.Weinger,
and
S.A.Strobel
(2007).
Exploring the mechanism of protein synthesis with modified substrates and novel intermediate mimics.
|
| |
Blood Cells Mol Dis,
38,
110-116.
|
|
|
|
|
|
|
K.L.Leach,
S.M.Swaney,
J.R.Colca,
W.G.McDonald,
J.R.Blinn,
L.M.Thomasco,
R.C.Gadwood,
D.Shinabarger,
L.Xiong,
and
A.S.Mankin
(2007).
The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria.
|
| |
Mol Cell,
26,
393-402.
|
|
|
|
|
|
|
M.Kopp,
C.Rupprath,
H.Irschik,
A.Bechthold,
L.Elling,
and
R.Müller
(2007).
SorF: a glycosyltransferase with promiscuous donor substrate specificity in vitro.
|
| |
Chembiochem,
8,
813-819.
|
|
|
|
|
|
|
M.S.Chae,
C.C.Lin,
K.E.Kessler,
C.E.Nargang,
L.L.Tanton,
L.B.Hahn,
and
F.E.Nargang
(2007).
Identification of an alternative oxidase induction motif in the promoter region of the aod-1 gene in Neurospora crassa.
|
| |
Genetics,
175,
1597-1606.
|
|
|
|
|
|
|
M.Schlitzer
(2007).
Malaria Chemotherapeutics Part I: History of Antimalarial Drug Development, Currently Used Therapeutics, and Drugs in Clinical Development.
|
| |
ChemMedChem,
2,
944-986.
|
|
|
|
|
|
|
M.V.Rodnina,
M.Beringer,
and
W.Wintermeyer
(2007).
How ribosomes make peptide bonds.
|
| |
Trends Biochem Sci,
32,
20-26.
|
|
|
|
|
|
|
P.C.Bevilacqua,
A.L.Cerrone-Szakal,
and
N.A.Siegfried
(2007).
Insight into the functional versatility of RNA through model-making with applications to data fitting.
|
| |
Q Rev Biophys,
40,
55-85.
|
|
|
|
|
|
|
R.Binet,
and
A.T.Maurelli
(2007).
Frequency of development and associated physiological cost of azithromycin resistance in Chlamydia psittaci 6BC and C. trachomatis L2.
|
| |
Antimicrob Agents Chemother,
51,
4267-4275.
|
|
|
|
|
|
|
R.M.Anderson,
M.Kwon,
and
S.A.Strobel
(2007).
Toward ribosomal RNA catalytic activity in the absence of protein.
|
| |
J Mol Evol,
64,
472-483.
|
|
|
|
|
|
|
S.J.Schroeder,
G.Blaha,
J.Tirado-Rives,
T.A.Steitz,
and
P.B.Moore
(2007).
The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole.
|
| |
J Mol Biol,
367,
1471-1479.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.M.Toh,
L.Xiong,
C.A.Arias,
M.V.Villegas,
K.Lolans,
J.Quinn,
and
A.S.Mankin
(2007).
Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid.
|
| |
Mol Microbiol,
64,
1506-1514.
|
|
|
|
|
|
|
S.Zaman,
M.Fitzpatrick,
L.Lindahl,
and
J.Zengel
(2007).
Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli.
|
| |
Mol Microbiol,
66,
1039-1050.
|
|
|
|
|
|
|
Y.Tanrikulu,
M.Nietert,
U.Scheffer,
E.Proschak,
K.Grabowski,
P.Schneider,
M.Weidlich,
M.Karas,
M.Göbel,
and
G.Schneider
(2007).
Scaffold hopping by "fuzzy" pharmacophores and its application to RNA targets.
|
| |
Chembiochem,
8,
1932-1936.
|
|
|
|
|
|
|
A.R.Kwon,
Y.H.Min,
E.J.Yoon,
J.A.Kim,
M.J.Shim,
and
E.C.Choi
(2006).
ErmK leader peptide : amino acid sequence critical for induction by erythromycin.
|
| |
Arch Pharm Res,
29,
1154-1157.
|
|
|
|
|
|
|
A.Serganov,
A.Polonskaia,
A.T.Phan,
R.R.Breaker,
and
D.J.Patel
(2006).
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch.
|
| |
Nature,
441,
1167-1171.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.Hyeon,
R.I.Dima,
and
D.Thirumalai
(2006).
Size, shape, and flexibility of RNA structures.
|
| |
J Chem Phys,
125,
194905.
|
|
|
|
|
|
|
D.A.Thayer,
and
C.H.Wong
(2006).
Vancomycin analogues containing monosaccharides exhibit improved antibiotic activity: a combined one-pot enzymatic glycosylation and chemical diversification strategy.
|
| |
Chem Asian J,
1,
445-452.
|
|
|
|
|
|
|
D.H.Sherman,
S.Li,
L.V.Yermalitskaya,
Y.Kim,
J.A.Smith,
M.R.Waterman,
and
L.M.Podust
(2006).
The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae.
|
| |
J Biol Chem,
281,
26289-26297.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.C.Böttger
(2006).
The ribosome as a drug target.
|
| |
Trends Biotechnol,
24,
145-147.
|
|
|
|
|
|
|
E.C.Kouvela,
A.D.Petropoulos,
and
D.L.Kalpaxis
(2006).
Unraveling new features of clindamycin interaction with functional ribosomes and dependence of the drug potency on polyamines.
|
| |
J Biol Chem,
281,
23103-23110.
|
|
|
|
|
|
|
F.von Nussbaum,
M.Brands,
B.Hinzen,
S.Weigand,
and
D.Häbich
(2006).
Antibacterial natural products in medicinal chemistry--exodus or revival?
|
| |
Angew Chem Int Ed Engl,
45,
5072-5129.
|
|
|
|
|
|
|
G.G.Zhanel,
T.Hisanaga,
A.Wierzbowski,
and
D.J.Hoban
(2006).
Telithromycin in the treatment of acute bacterial sinusitis, acute exacerbations of chronic bronchitis, and community-acquired pneumonia.
|
| |
Ther Clin Risk Manag,
2,
59-75.
|
|
|
|
|
|
|
G.Papadopoulos,
S.Grudinin,
D.L.Kalpaxis,
and
T.Choli-Papadopoulou
(2006).
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis.
|
| |
Eur Biophys J,
35,
675-683.
|
|
|
|
|
|
|
G.Rosenbaum,
R.W.Alkire,
G.Evans,
F.J.Rotella,
K.Lazarski,
R.G.Zhang,
S.L.Ginell,
N.Duke,
I.Naday,
J.Lazarz,
M.J.Molitsky,
L.Keefe,
J.Gonczy,
L.Rock,
R.Sanishvili,
M.A.Walsh,
E.Westbrook,
and
A.Joachimiak
(2006).
The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.
|
| |
J Synchrotron Radiat,
13,
30-45.
|
|
|
|
|
|
|
H.Yoneyama,
and
R.Katsumata
(2006).
Antibiotic resistance in bacteria and its future for novel antibiotic development.
|
| |
Biosci Biotechnol Biochem,
70,
1060-1075.
|
|
|
|
|
|
|
J.Donarski,
C.Shammas,
R.Banks,
and
V.Ramesh
(2006).
NMR and molecular modelling studies of the binding of amicetin antibiotic to conserved secondary structural motifs of 23S ribosomal RNAs.
|
| |
J Antibiot (Tokyo),
59,
177-183.
|
|
|
|
|
|
|
J.Mengel-Jørgensen,
S.S.Jensen,
A.Rasmussen,
J.Poehlsgaard,
J.J.Iversen,
and
F.Kirpekar
(2006).
Modifications in Thermus thermophilus 23 S ribosomal RNA are centered in regions of RNA-RNA contact.
|
| |
J Biol Chem,
281,
22108-22117.
|
|
|
|
|
|
|
J.Qiu,
D.Zhou,
L.Qin,
Y.Han,
X.Wang,
Z.DU,
Y.Song,
and
R.Yang
(2006).
Microarray expression profiling of Yersinia pestis in response to chloramphenicol.
|
| |
FEMS Microbiol Lett,
263,
26-31.
|
|
|
|
|
|
|
K.S.Long,
J.Poehlsgaard,
C.Kehrenberg,
S.Schwarz,
and
B.Vester
(2006).
The Cfr rRNA methyltransferase confers resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibiotics.
|
| |
Antimicrob Agents Chemother,
50,
2500-2505.
|
|
|
|
|
|
|
K.Yan,
L.Madden,
A.E.Choudhry,
C.S.Voigt,
R.A.Copeland,
and
R.R.Gontarek
(2006).
Biochemical characterization of the interactions of the novel pleuromutilin derivative retapamulin with bacterial ribosomes.
|
| |
Antimicrob Agents Chemother,
50,
3875-3881.
|
|
|
|
|
|
|
M.A.Fischbach,
H.Lin,
D.R.Liu,
and
C.T.Walsh
(2006).
How pathogenic bacteria evade mammalian sabotage in the battle for iron.
|
| |
Nat Chem Biol,
2,
132-138.
|
|
|
|
|
|
|
M.Hallier,
J.Desreac,
and
B.Felden
(2006).
Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation.
|
| |
Nucleic Acids Res,
34,
1935-1943.
|
|
|
|
|
|
|
M.Lovmar,
K.Nilsson,
V.Vimberg,
T.Tenson,
M.Nervall,
and
M.Ehrenberg
(2006).
The molecular mechanism of peptide-mediated erythromycin resistance.
|
| |
J Biol Chem,
281,
6742-6750.
|
|
|
|
|
|
|
P.Imming,
C.Sinning,
and
A.Meyer
(2006).
Drugs, their targets and the nature and number of drug targets.
|
| |
Nat Rev Drug Discov,
5,
821-834.
|
|
|
|
|
|
|
R.Berisio,
N.Corti,
P.Pfister,
A.Yonath,
and
E.C.Böttger
(2006).
23S rRNA 2058A-->G alteration mediates ketolide resistance in combination with deletion in L22.
|
| |
Antimicrob Agents Chemother,
50,
3816-3823.
|
|
|
|
|
|
|
S.A.Borisova,
C.Zhang,
H.Takahashi,
H.Zhang,
A.W.Wong,
J.S.Thorson,
and
H.W.Liu
(2006).
Substrate specificity of the macrolide-glycosylating enzyme pair DesVII/DesVIII: opportunities, limitations, and mechanistic hypotheses.
|
| |
Angew Chem Int Ed Engl,
45,
2748-2753.
|
|
|
|
|
|
|
S.M.Halling,
and
A.E.Jensen
(2006).
Intrinsic and selected resistance to antibiotics binding the ribosome: analyses of Brucella 23S rrn, L4, L22, EF-Tu1, EF-Tu2, efflux and phylogenetic implications.
|
| |
BMC Microbiol,
6,
84.
|
|
|
|
|
|
|
T.Morimura,
N.Noda,
Y.Kato,
T.Watanabe,
T.Saitoh,
T.Yamazaki,
K.Takada,
S.Aoki,
K.Ohta,
M.Ohshige,
K.Sakaguchi,
and
F.Sugawara
(2006).
Identification of antibiotic clarithromycin binding peptide displayed by T7 phage particles.
|
| |
J Antibiot (Tokyo),
59,
625-632.
|
|
|
|
|
|
|
T.Tenson,
and
A.Mankin
(2006).
Antibiotics and the ribosome.
|
| |
Mol Microbiol,
59,
1664-1677.
|
|
|
|
|
|
|
A.T.Descheneau,
I.A.Cleary,
and
F.E.Nargang
(2005).
Genetic evidence for a regulatory pathway controlling alternative oxidase production in Neurospora crassa.
|
| |
Genetics,
169,
123-135.
|
|
|
|
|
|
|
A.Tsagkalia,
F.Leontiadou,
M.A.Xaplanteri,
G.Papadopoulos,
D.L.Kalpaxis,
and
T.Choli-Papadopoulou
(2005).
Ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus display multiple defects in ribosomal functions and sensitivity against erythromycin.
|
| |
RNA,
11,
1633-1639.
|
|
|
|
|
|
|
A.Yonath
(2005).
Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation.
|
| |
Annu Rev Biochem,
74,
649-679.
|
|
|
|
|
|
|
C.Kehrenberg,
S.Schwarz,
L.Jacobsen,
L.H.Hansen,
and
B.Vester
(2005).
A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: methylation of 23S ribosomal RNA at A2503.
|
| |
Mol Microbiol,
57,
1064-1073.
|
|
|
|
|
|
|
C.M.Wu,
H.Wu,
Y.Ning,
J.Wang,
X.Du,
and
J.Shen
(2005).
Induction of macrolide resistance in Mycoplasma gallisepticum in vitro and its resistance-related mutations within domain V of 23S rRNA.
|
| |
FEMS Microbiol Lett,
247,
199-205.
|
|
|
|
|
|
|
C.T.Madsen,
L.Jakobsen,
K.Buriánková,
F.Doucet-Populaire,
J.L.Pernodet,
and
S.Douthwaite
(2005).
Methyltransferase Erm(37) slips on rRNA to confer atypical resistance in Mycobacterium tuberculosis.
|
| |
J Biol Chem,
280,
38942-38947.
|
|
|
|
|
|
|
D.E.Brodersen,
and
P.Nissen
(2005).
The social life of ribosomal proteins.
|
| |
FEBS J,
272,
2098-2108.
|
|
|
|
|
|
|
D.N.Wilson,
F.Schluenzen,
J.M.Harms,
T.Yoshida,
T.Ohkubo,
R.Albrecht,
J.Buerger,
Y.Kobayashi,
and
P.Fucini
(2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
|
| |
EMBO J,
24,
251-260.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.N.Wilson,
J.M.Harms,
K.H.Nierhaus,
F.Schlünzen,
and
P.Fucini
(2005).
Species-specific antibiotic-ribosome interactions: implications for drug development.
|
| |
Biol Chem,
386,
1239-1252.
|
|
|
|
|
|
|
D.N.Wilson,
and
K.H.Nierhaus
(2005).
Ribosomal proteins in the spotlight.
|
| |
Crit Rev Biochem Mol Biol,
40,
243-267.
|
|
|
|
|
|
|
D.Tu,
G.Blaha,
P.B.Moore,
and
T.A.Steitz
(2005).
Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.
|
| |
Cell,
121,
257-270.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.E.Nagiec,
L.Wu,
S.M.Swaney,
J.G.Chosay,
D.E.Ross,
J.K.Brieland,
and
K.L.Leach
(2005).
Oxazolidinones inhibit cellular proliferation via inhibition of mitochondrial protein synthesis.
|
| |
Antimicrob Agents Chemother,
49,
3896-3902.
|
|
|
|
|
|
|
F.Schlünzen,
D.N.Wilson,
P.Tian,
J.M.Harms,
S.J.McInnes,
H.A.Hansen,
R.Albrecht,
J.Buerger,
S.M.Wilbanks,
and
P.Fucini
(2005).
The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction.
|
| |
Structure,
13,
1685-1694.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.A.Silvers,
and
W.S.Champney
(2005).
Accumulation and turnover of 23S ribosomal RNA in azithromycin-inhibited ribonuclease mutant strains of Escherichia coli.
|
| |
Arch Microbiol,
184,
66-77.
|
|
|
|
|
|
|
J.A.Sutcliffe
(2005).
Improving on nature: antibiotics that target the ribosome.
|
| |
Curr Opin Microbiol,
8,
534-542.
|
|
|
|
|
|
|
J.Kleinjung,
and
F.Fraternali
(2005).
POPSCOMP: an automated interaction analysis of biomolecular complexes.
|
| |
Nucleic Acids Res,
33,
W342-W346.
|
|
|
|
|
|
|
J.Poehlsgaard,
P.Pfister,
E.C.Böttger,
and
S.Douthwaite
(2005).
Molecular mechanisms by which rRNA mutations confer resistance to clindamycin.
|
| |
Antimicrob Agents Chemother,
49,
1553-1555.
|
|
|
|
|
|
|
J.Poehlsgaard,
and
S.Douthwaite
(2005).
The bacterial ribosome as a target for antibiotics.
|
| |
Nat Rev Microbiol,
3,
870-881.
|
|
|
|
|
|
|
J.T.Lin,
M.B.Connelly,
C.Amolo,
S.Otani,
and
D.S.Yaver
(2005).
Global transcriptional response of Bacillus subtilis to treatment with subinhibitory concentrations of antibiotics that inhibit protein synthesis.
|
| |
Antimicrob Agents Chemother,
49,
1915-1926.
|
|
|
|
|
|
|
K.A.Nash,
Y.Zhang,
B.A.Brown-Elliott,
and
R.J.Wallace
(2005).
Molecular basis of intrinsic macrolide resistance in clinical isolates of Mycobacterium fortuitum.
|
| |
J Antimicrob Chemother,
55,
170-177.
|
|
|
|
|
|
|
K.Yan,
E.Hunt,
J.Berge,
E.May,
R.A.Copeland,
and
R.R.Gontarek
(2005).
Fluorescence polarization method to characterize macrolide-ribosome interactions.
|
| |
Antimicrob Agents Chemother,
49,
3367-3372.
|
|
|
|
|
|
|
L.L.Shen,
C.Black-Schaefer,
Y.Cai,
P.J.Dandliker,
and
B.A.Beutel
(2005).
Mechanism of action of a novel series of naphthyridine-type ribosome inhibitors: enhancement of tRNA footprinting at the decoding site of 16S rRNA.
|
| |
Antimicrob Agents Chemother,
49,
1890-1897.
|
|
|
|
|
|
|
L.Palenzuela,
N.M.Hahn,
R.P.Nelson,
J.N.Arno,
C.Schobert,
R.Bethel,
L.A.Ostrowski,
M.R.Sharma,
P.P.Datta,
R.K.Agrawal,
J.E.Schwartz,
and
M.Hirano
(2005).
Does linezolid cause lactic acidosis by inhibiting mitochondrial protein synthesis?
|
| |
Clin Infect Dis,
40,
e113-e116.
|
|
|
|
|
|
|
L.Xiong,
Y.Korkhin,
and
A.S.Mankin
(2005).
Binding site of the bridged macrolides in the Escherichia coli ribosome.
|
| |
Antimicrob Agents Chemother,
49,
281-288.
|
|
|
|
|
|
|
M.Sumita,
J.P.Desaulniers,
Y.C.Chang,
H.M.Chui,
L.Clos,
and
C.S.Chow
(2005).
Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA.
|
| |
RNA,
11,
1420-1429.
|
|
|
|
|
|
|
N.Polacek,
and
A.S.Mankin
(2005).
The ribosomal peptidyl transferase center: structure, function, evolution, inhibition.
|
| |
Crit Rev Biochem Mol Biol,
40,
285-311.
|
|
|
|
|
|
|
N.Woodford
(2005).
Biological counterstrike: antibiotic resistance mechanisms of Gram-positive cocci.
|
| |
Clin Microbiol Infect,
11,
2.
|
|
|
|
|
|
|
P.Kamra,
R.S.Gokhale,
and
D.Mohanty
(2005).
SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites.
|
| |
Nucleic Acids Res,
33,
W220-W225.
|
|
|
|
|
|
|
P.Pfister,
N.Corti,
S.Hobbie,
C.Bruell,
R.Zarivach,
A.Yonath,
and
E.C.Böttger
(2005).
23S rRNA base pair 2057-2611 determines ketolide susceptibility and fitness cost of the macrolide resistance mutation 2058A-->G.
|
| |
Proc Natl Acad Sci U S A,
102,
5180-5185.
|
|
|
|
|
|
|
S.Douthwaite,
J.Jalava,
and
L.Jakobsen
(2005).
Ketolide resistance in Streptococcus pyogenes correlates with the degree of rRNA dimethylation by Erm.
|
| |
Mol Microbiol,
58,
613-622.
|
|
|
|
|
|
|
S.T.Gregory,
J.F.Carr,
D.Rodriguez-Correa,
and
A.E.Dahlberg
(2005).
Mutational analysis of 16S and 23S rRNA genes of Thermus thermophilus.
|
| |
J Bacteriol,
187,
4804-4812.
|
|
|
|
|
|
|
T.Auerbach-Nevo,
R.Zarivach,
M.Peretz,
and
A.Yonath
(2005).
Reproducible growth of well diffracting ribosomal crystals.
|
| |
Acta Crystallogr D Biol Crystallogr,
61,
713-719.
|
|
|
|
|
|
|
T.Hermann
(2005).
Drugs targeting the ribosome.
|
| |
Curr Opin Struct Biol,
15,
355-366.
|
|
|
|
|
|
|
W.E.Steinmetz,
A.Sparrow,
and
M.Somsouk
(2005).
Determination of the three-dimensional, solution-phase structure of the macrolide antibiotic oxolide in CD2Cl2 and D2O from NMR constraints.
|
| |
Magn Reson Chem,
43,
16-20.
|
|
|
|
|
|
|
Y.Yuan,
H.S.Chung,
C.Leimkuhler,
C.T.Walsh,
D.Kahne,
and
S.Walker
(2005).
In vitro reconstitution of EryCIII activity for the preparation of unnatural macrolides.
|
| |
J Am Chem Soc,
127,
14128-14129.
|
|
|
|
|
|
|
A.D.Petropoulos,
M.A.Xaplanteri,
G.P.Dinos,
D.N.Wilson,
and
D.L.Kalpaxis
(2004).
Polyamines affect diversely the antibiotic potency: insight gained from kinetic studies of the blasticidin S AND spiramycin interactions with functional ribosomes.
|
| |
J Biol Chem,
279,
26518-26525.
|
|
|
|
|
|
|
A.Raja,
J.Lebbos,
and
P.Kirkpatrick
(2004).
Telithromycin.
|
| |
Nat Rev Drug Discov,
3,
733-734.
|
|
|
|
|
|
|
A.Sievers,
M.Beringer,
M.V.Rodnina,
and
R.Wolfenden
(2004).
The ribosome as an entropy trap.
|
| |
Proc Natl Acad Sci U S A,
101,
7897-7901.
|
|
|
|
|
|
|
A.Yonath,
and
A.Bashan
(2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
|
| |
Annu Rev Microbiol,
58,
233-251.
|
|
|
|
|
|
|
B.Hutter,
C.Fischer,
A.Jacobi,
C.Schaab,
and
H.Loferer
(2004).
Panel of Bacillus subtilis reporter strains indicative of various modes of action.
|
| |
Antimicrob Agents Chemother,
48,
2588-2594.
|
|
|
|
|
|
|
C.A.Woolhead,
P.J.McCormick,
and
A.E.Johnson
(2004).
Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins.
|
| |
Cell,
116,
725-736.
|
|
|
|
|
|
|
C.D.Reeves,
S.L.Ward,
W.P.Revill,
H.Suzuki,
M.Marcus,
O.V.Petrakovsky,
S.Marquez,
H.Fu,
S.D.Dong,
and
L.Katz
(2004).
Production of hybrid 16-membered macrolides by expressing combinations of polyketide synthase genes in engineered Streptomyces fradiae hosts.
|
| |
Chem Biol,
11,
1465-1472.
|
|
|
|
|
|
|
F.S.Liang,
S.K.Wang,
T.Nakatani,
and
C.H.Wong
(2004).
Targeting RNAs with tobramycin analogues.
|
| |
Angew Chem Int Ed Engl,
43,
6496-6500.
|
|
|
|
|
|
|
F.Schlünzen,
E.Pyetan,
P.Fucini,
A.Yonath,
and
J.M.Harms
(2004).
Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin.
|
| |
Mol Microbiol,
54,
1287-1294.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.Maravić,
J.M.Bujnicki,
and
M.Flögel
(2004).
Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC'.
|
| |
Folia Microbiol (Praha),
49,
3-7.
|
|
|
|
|
|
|
G.W.Novotny,
L.Jakobsen,
N.M.Andersen,
J.Poehlsgaard,
and
S.Douthwaite
(2004).
Ketolide antimicrobial activity persists after disruption of interactions with domain II of 23S rRNA.
|
| |
Antimicrob Agents Chemother,
48,
3677-3683.
|
|
|
|
|
|
|
H.B.Kim,
B.Lee,
H.C.Jang,
S.H.Kim,
C.I.Kang,
Y.J.Choi,
S.W.Park,
B.S.Kim,
E.C.Kim,
M.D.Oh,
and
K.W.Choe
(2004).
A high frequency of macrolide-lincosamide-streptogramin resistance determinants in Staphylococcus aureus isolated in South Korea.
|
| |
Microb Drug Resist,
10,
248-254.
|
|
|
|
|
|
|
H.Engelberg-Kulka,
B.Sat,
M.Reches,
S.Amitai,
and
R.Hazan
(2004).
Bacterial programmed cell death systems as targets for antibiotics.
|
| |
Trends Microbiol,
12,
66-71.
|
|
|
|
|
|
|
H.Nakatogawa,
and
K.Ito
(2004).
Intraribosomal regulation of expression and fate of proteins.
|
| |
Chembiochem,
5,
48-51.
|
|
|
|
|
|
|
H.Yoshida,
H.Yamamoto,
T.Uchiumi,
and
A.Wada
(2004).
RMF inactivates ribosomes by covering the peptidyl transferase centre and entrance of peptide exit tunnel.
|
| |
Genes Cells,
9,
271-278.
|
|
|
|
|
|
|
J.M.Harms,
F.Schlünzen,
P.Fucini,
H.Bartels,
and
A.Yonath
(2004).
Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin.
|
| |
BMC Biol,
2,
4.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Spízek,
and
T.Rezanka
(2004).
Lincomycin, clindamycin and their applications.
|
| |
Appl Microbiol Biotechnol,
64,
455-464.
|
|
|
|
|
|
|
J.Thompson,
C.A.Pratt,
and
A.E.Dahlberg
(2004).
Effects of a number of classes of 50S inhibitors on stop codon readthrough during protein synthesis.
|
| |
Antimicrob Agents Chemother,
48,
4889-4891.
|
|
|
|
|
|
|
K.Das,
T.Acton,
Y.Chiang,
L.Shih,
E.Arnold,
and
G.T.Montelione
(2004).
Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site.
|
| |
Proc Natl Acad Sci U S A,
101,
4041-4046.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.Cochella,
and
R.Green
(2004).
Isolation of antibiotic resistance mutations in the rRNA by using an in vitro selection system.
|
| |
Proc Natl Acad Sci U S A,
101,
3786-3791.
|
|
|
|
|
|
|
M.Liu,
G.W.Novotny,
and
S.Douthwaite
(2004).
Methylation of 23S rRNA nucleotide G745 is a secondary function of the RlmAI methyltransferase.
|
| |
RNA,
10,
1713-1720.
|
|
|
|
|
|
|
M.Lovmar,
T.Tenson,
and
M.Ehrenberg
(2004).
Kinetics of macrolide action: the josamycin and erythromycin cases.
|
| |
J Biol Chem,
279,
53506-53515.
|
|
|
|
|
|
|
M.Pringle,
J.Poehlsgaard,
B.Vester,
and
K.S.Long
(2004).
Mutations in ribosomal protein L3 and 23S ribosomal RNA at the peptidyl transferase centre are associated with reduced susceptibility to tiamulin in Brachyspira spp. isolates.
|
| |
Mol Microbiol,
54,
1295-1306.
|
|
|
|
|
|
|
O.Y.Misyurina,
E.V.Chipitsyna,
Y.P.Finashutina,
V.N.Lazarev,
T.A.Akopian,
A.M.Savicheva,
and
V.M.Govorun
(2004).
Mutations in a 23S rRNA gene of Chlamydia trachomatis associated with resistance to macrolides.
|
| |
Antimicrob Agents Chemother,
48,
1347-1349.
|
|
|
|
|
|
|
P.S.Klosterman,
D.K.Hendrix,
M.Tamura,
S.R.Holbrook,
and
S.E.Brenner
(2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
|
| |
Nucleic Acids Res,
32,
2342-2352.
|
|
|
|
|
|
|
R.J.Gilbert,
P.Fucini,
S.Connell,
S.D.Fuller,
K.H.Nierhaus,
C.V.Robinson,
C.M.Dobson,
and
D.I.Stuart
(2004).
Three-dimensional structures of translating ribosomes by Cryo-EM.
|
| |
Mol Cell,
14,
57-66.
|
|
|
|
|
|
|
R.R.Breaker
(2004).
Natural and engineered nucleic acids as tools to explore biology.
|
| |
Nature,
432,
838-845.
|
|
|
|
|
|
|
S.L.Ward,
Z.Hu,
A.Schirmer,
R.Reid,
W.P.Revill,
C.D.Reeves,
O.V.Petrakovsky,
S.D.Dong,
and
L.Katz
(2004).
Chalcomycin biosynthesis gene cluster from Streptomyces bikiniensis: novel features of an unusual ketolide produced through expression of the chm polyketide synthase in Streptomyces fradiae.
|
| |
Antimicrob Agents Chemother,
48,
4703-4712.
|
|
|
|
|
|
|
S.Pereyre,
C.Guyot,
H.Renaudin,
A.Charron,
C.Bébéar,
and
C.M.Bébéar
(2004).
In vitro selection and characterization of resistance to macrolides and related antibiotics in Mycoplasma pneumoniae.
|
| |
Antimicrob Agents Chemother,
48,
460-465.
|
|
|
|
|
|
|
S.Schwarz,
C.Kehrenberg,
B.Doublet,
and
A.Cloeckaert
(2004).
Molecular basis of bacterial resistance to chloramphenicol and florfenicol.
|
| |
FEMS Microbiol Rev,
28,
519-542.
|
|
|
|
|
|
|
T.Auerbach,
A.Bashan,
and
A.Yonath
(2004).
Ribosomal antibiotics: structural basis for resistance, synergism and selectivity.
|
| |
Trends Biotechnol,
22,
570-576.
|
|
|
|
|
|
|
V.Vimberg,
L.Xiong,
M.Bailey,
T.Tenson,
and
A.Mankin
(2004).
Peptide-mediated macrolide resistance reveals possible specific interactions in the nascent peptide exit tunnel.
|
| |
Mol Microbiol,
54,
376-385.
|
|
|
|
|
|
|
Y.Wang,
N.B.Shoemaker,
and
A.A.Salyers
(2004).
Regulation of a Bacteroides operon that controls excision and transfer of the conjugative transposon CTnDOT.
|
| |
J Bacteriol,
186,
2548-2557.
|
|
|
|
|
|
|
Z.Druzina,
and
B.S.Cooperman
(2004).
Photolabile anticodon stem-loop analogs of tRNAPhe as probes of ribosomal structure and structural fluctuation at the decoding center.
|
| |
RNA,
10,
1550-1562.
|
|
|
|
|
|
|
A.Bashan,
I.Agmon,
R.Zarivach,
F.Schluenzen,
J.Harms,
R.Berisio,
H.Bartels,
F.Franceschi,
T.Auerbach,
H.A.Hansen,
E.Kossoy,
M.Kessler,
and
A.Yonath
(2003).
Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression.
|
| |
Mol Cell,
11,
91.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Bashan,
R.Zarivach,
F.Schluenzen,
I.Agmon,
J.Harms,
T.Auerbach,
D.Baram,
R.Berisio,
H.Bartels,
H.A.Hansen,
P.Fucini,
D.Wilson,
M.Peretz,
M.Kessler,
and
A.Yonath
(2003).
Ribosomal crystallography: peptide bond formation and its inhibition.
|
| |
Biopolymers,
70,
19-41.
|
|
|
|
|
|
|
A.Yonath
(2003).
Ribosomal tolerance and peptide bond formation.
|
| |
Biol Chem,
384,
1411-1419.
|
|
|
|
|
|
|
A.Yonath
(2003).
Structural insight into functional aspects of ribosomal RNA targeting.
|
| |
Chembiochem,
4,
1008-1017.
|
|
|
|
|
|
|
C.M.Duarte,
L.M.Wadley,
and
A.M.Pyle
(2003).
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.
|
| |
Nucleic Acids Res,
31,
4755-4761.
|
|
|
|
|
|
|
C.T.Madsen,
J.Mengel-Jørgensen,
F.Kirpekar,
and
S.Douthwaite
(2003).
Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry.
|
| |
Nucleic Acids Res,
31,
4738-4746.
|
|
|
|
|
|
|
C.Walsh
(2003).
Where will new antibiotics come from?
|
| |
Nat Rev Microbiol,
1,
65-70.
|
|
|
|
|
|
|
D.Abbanat,
M.Macielag,
and
K.Bush
(2003).
Novel antibacterial agents for the treatment of serious Gram-positive infections.
|
| |
Expert Opin Investig Drugs,
12,
379-399.
|
|
|
|
|
|
|
D.J.Farrell,
S.Douthwaite,
I.Morrissey,
S.Bakker,
J.Poehlsgaard,
L.Jakobsen,
and
D.Felmingham
(2003).
Macrolide resistance by ribosomal mutation in clinical isolates of Streptococcus pneumoniae from the PROTEKT 1999-2000 study.
|
| |
Antimicrob Agents Chemother,
47,
1777-1783.
|
|
|
|
|
|
|
F.Schlünzen,
J.M.Harms,
F.Franceschi,
H.A.Hansen,
H.Bartels,
R.Zarivach,
and
A.Yonath
(2003).
Structural basis for the antibiotic activity of ketolides and azalides.
|
| |
Structure,
11,
329-338.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.G.Zhanel,
T.Hisanaga,
K.Nichol,
A.Wierzbowski,
and
D.J.Hoban
(2003).
Ketolides: an emerging treatment for macrolide-resistant respiratory infections, focusing on S. pneumoniae.
|
| |
Expert Opin Emerg Drugs,
8,
297-321.
|
|
|
|
|
|
|
G.Villescas-Diaz,
and
M.Zacharias
(2003).
Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis.
|
| |
Biophys J,
85,
416-425.
|
|
|
|
|
|
|
I.Agmon,
T.Auerbach,
D.Baram,
H.Bartels,
A.Bashan,
R.Berisio,
P.Fucini,
H.A.Hansen,
J.Harms,
M.Kessler,
M.Peretz,
F.Schluenzen,
A.Yonath,
and
R.Zarivach
(2003).
On peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. Derived on 20 October 2002 at the 28th FEBS Meeting in Istanbul.
|
| |
Eur J Biochem,
270,
2543-2556.
|
|
|
|
|
|
|
I.G.Boneca,
and
G.Chiosis
(2003).
Vancomycin resistance: occurrence, mechanisms and strategies to combat it.
|
| |
Expert Opin Ther Targets,
7,
311-328.
|
|
|
|
|
|
|
I.Lebars,
S.Yoshizawa,
A.R.Stenholm,
E.Guittet,
S.Douthwaite,
and
D.Fourmy
(2003).
Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII.
|
| |
EMBO J,
22,
183-192.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.R.Colca,
W.G.McDonald,
D.J.Waldon,
L.M.Thomasco,
R.C.Gadwood,
E.T.Lund,
G.S.Cavey,
W.R.Mathews,
L.D.Adams,
E.T.Cecil,
J.D.Pearson,
J.H.Bock,
J.E.Mott,
D.L.Shinabarger,
L.Xiong,
and
A.S.Mankin
(2003).
Cross-linking in the living cell locates the site of action of oxazolidinone antibiotics.
|
| |
J Biol Chem,
278,
21972-21979.
|
|
|
|
|
|
|
K.B.Waites,
D.M.Crabb,
and
L.B.Duffy
(2003).
In vitro activities of ABT-773 and other antimicrobials against human mycoplasmas.
|
| |
Antimicrob Agents Chemother,
47,
39-42.
|
|
|
|
|
|
|
K.Fredrick,
and
H.F.Noller
(2003).
Catalysis of ribosomal translocation by sparsomycin.
|
| |
Science,
300,
1159-1162.
|
|
|
|
|
|
|
K.S.Long,
and
B.T.Porse
(2003).
A conserved chloramphenicol binding site at the entrance to the ribosomal peptide exit tunnel.
|
| |
Nucleic Acids Res,
31,
7208-7215.
|
|
|
|
|
|
|
L.R.Cruz-Vera,
E.Hernandez-Ramon,
B.Perez-Zamorano,
and
G.Guarneros
(2003).
The rate of peptidyl-tRNA dissociation from the ribosome during minigene expression depends on the nature of the last decoding interaction.
|
| |
J Biol Chem,
278,
26065-26070.
|
|
|
|
|
|
|
M.A.Xaplanteri,
A.Andreou,
G.P.Dinos,
and
D.L.Kalpaxis
(2003).
Effect of polyamines on the inhibition of peptidyltransferase by antibiotics: revisiting the mechanism of chloramphenicol action.
|
| |
Nucleic Acids Res,
31,
5074-5083.
|
|
|
|
|
|
|
M.Machius
(2003).
Structural biology: a high-tech tool for biomedical research.
|
| |
Curr Opin Nephrol Hypertens,
12,
431-438.
|
|
|
|
|
|
|
N.B.Leontis,
and
E.Westhof
(2003).
Analysis of RNA motifs.
|
| |
Curr Opin Struct Biol,
13,
300-308.
|
|
|
|
|
|
|
N.Piganeau,
and
R.Schroeder
(2003).
Aptamer structures: a preview into regulatory pathways?
|
| |
Chem Biol,
10,
103-104.
|
|
|
|
|
|
|
P.B.Moore,
and
T.A.Steitz
(2003).
The structural basis of large ribosomal subunit function.
|
| |
Annu Rev Biochem,
72,
813-850.
|
|
|
|
|
|
|
P.Pfister,
M.Risch,
D.E.Brodersen,
and
E.C.Böttger
(2003).
Role of 16S rRNA Helix 44 in Ribosomal Resistance to Hygromycin B.
|
| |
Antimicrob Agents Chemother,
47,
1496-1502.
|
|
|
|
|
|
|
Q.Vicens,
and
E.Westhof
(2003).
RNA as a drug target: the case of aminoglycosides.
|
| |
Chembiochem,
4,
1018-1023.
|
|
|
|
|
|
|
R.Berisio,
F.Schluenzen,
J.Harms,
A.Bashan,
T.Auerbach,
D.Baram,
and
A.Yonath
(2003).
Structural insight into the role of the ribosomal tunnel in cellular regulation.
|
| |
Nat Struct Biol,
10,
366-370.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Berisio,
J.Harms,
F.Schluenzen,
R.Zarivach,
H.A.Hansen,
P.Fucini,
and
A.Yonath
(2003).
Structural insight into the antibiotic action of telithromycin against resistant mutants.
|
| |
J Bacteriol,
185,
4276-4279.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Joseph
(2003).
After the ribosome structure: how does translocation work?
|
| |
RNA,
9,
160-164.
|
|
|
|
|
|
|
T.A.Steitz,
and
P.B.Moore
(2003).
RNA, the first macromolecular catalyst: the ribosome is a ribozyme.
|
| |
Trends Biochem Sci,
28,
411-418.
|
|
|
|
|
|
|
T.Hermann
(2003).
Chemical and functional diversity of small molecule ligands for RNA.
|
| |
Biopolymers,
70,
4.
|
|
|
|
|
|
|
W.L.Ng,
K.M.Kazmierczak,
G.T.Robertson,
R.Gilmour,
and
M.E.Winkler
(2003).
Transcriptional regulation and signature patterns revealed by microarray analyses of Streptococcus pneumoniae R6 challenged with sublethal concentrations of translation inhibitors.
|
| |
J Bacteriol,
185,
359-370.
|
|
|
|
|
|
|
Y.Tor
(2003).
Targeting RNA with small molecules.
|
| |
Chembiochem,
4,
998.
|
|
|
|
|
|
|
A.Dömling
(2002).
Recent advances in isocyanide-based multicomponent chemistry.
|
| |
Curr Opin Chem Biol,
6,
306-313.
|
|
|
|
|
|
|
A.Yonath
(2002).
The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states.
|
| |
Annu Rev Biophys Biomol Struct,
31,
257-273.
|
|
|
|
|
|
|
D.Mandelman,
P.Gonzalo,
J.P.Lavergne,
C.Corbier,
J.P.Reboud,
and
R.Haser
(2002).
Crystallization and preliminary X-ray study of an N-terminal fragment of rat liver ribosomal P2 protein.
|
| |
Acta Crystallogr D Biol Crystallogr,
58,
668-671.
|
|
|
|
|
|
|
G.G.Zhanel,
and
D.J.Hoban
(2002).
Ketolides in the treatment of respiratory infections.
|
| |
Expert Opin Pharmacother,
3,
277-297.
|
|
|
|
|
|
|
J.L.Hansen,
J.A.Ippolito,
N.Ban,
P.Nissen,
P.B.Moore,
and
T.A.Steitz
(2002).
The structures of four macrolide antibiotics bound to the large ribosomal subunit.
|
| |
Mol Cell,
10,
117-128.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Carriere,
V.Vijayabaskar,
D.Applefield,
I.Harvey,
P.Garneau,
J.Lorsch,
A.Lapidot,
and
J.Pelletier
(2002).
Inhibition of protein synthesis by aminoglycoside-arginine conjugates.
|
| |
RNA,
8,
1267-1279.
|
|
|
|
|
|
|
M.Liu,
and
S.Douthwaite
(2002).
Activity of the ketolide telithromycin is refractory to Erm monomethylation of bacterial rRNA.
|
| |
Antimicrob Agents Chemother,
46,
1629-1633.
|
|
|
|
|
|
|
M.Liu,
and
S.Douthwaite
(2002).
Resistance to the macrolide antibiotic tylosin is conferred by single methylations at 23S rRNA nucleotides G748 and A2058 acting in synergy.
|
| |
Proc Natl Acad Sci U S A,
99,
14658-14663.
|
|
|
|
|
|
|
M.Liu,
and
S.Douthwaite
(2002).
Methylation at nucleotide G745 or G748 in 23S rRNA distinguishes Gram-negative from Gram-positive bacteria.
|
| |
Mol Microbiol,
44,
195-204.
|
|
|
|
|
|
|
N.Böddeker,
G.Bahador,
C.Gibbs,
E.Mabery,
J.Wolf,
L.Xu,
and
J.Watson
(2002).
Characterization of a novel antibacterial agent that inhibits bacterial translation.
|
| |
RNA,
8,
1120-1128.
|
|
|
|
|
|
|
N.B.Leontis,
J.Stombaugh,
and
E.Westhof
(2002).
The non-Watson-Crick base pairs and their associated isostericity matrices.
|
| |
Nucleic Acids Res,
30,
3497-3531.
|
|
|
|
|
|
|
O.Kristensen,
and
M.Laurberg
(2002).
Expression, refolding and crystallization of Aquifex aeolicus elongation factor P.
|
| |
Acta Crystallogr D Biol Crystallogr,
58,
1039-1041.
|
|
|
|
|
|
|
P.Sander,
L.Belova,
Y.G.Kidan,
P.Pfister,
A.S.Mankin,
and
E.C.Böttger
(2002).
Ribosomal and non-ribosomal resistance to oxazolidinones: species-specific idiosyncrasy of ribosomal alterations.
|
| |
Mol Microbiol,
46,
1295-1304.
|
|
|
|
|
|
|
R.Leclercq,
and
P.Courvalin
(2002).
Resistance to macrolides and related antibiotics in Streptococcus pneumoniae.
|
| |
Antimicrob Agents Chemother,
46,
2727-2734.
|
|
|
|
|
|
|
S.Pereyre,
P.Gonzalez,
B.De Barbeyrac,
A.Darnige,
H.Renaudin,
A.Charron,
S.Raherison,
C.Bébéar,
and
C.M.Bébéar
(2002).
Mutations in 23S rRNA account for intrinsic resistance to macrolides in Mycoplasma hominis and Mycoplasma fermentans and for acquired resistance to macrolides in M. hominis.
|
| |
Antimicrob Agents Chemother,
46,
3142-3150.
|
|
|
|
|
|
|
V.Ramakrishnan
(2002).
Ribosome structure and the mechanism of translation.
|
| |
Cell,
108,
557-572.
|
|
|
|
|
|
|
A.Bashan,
I.Agmon,
R.Zarivach,
F.Schluenzen,
J.Harms,
M.Pioletti,
H.Bartels,
M.Gluehmann,
H.Hansen,
T.Auerbach,
F.Franceschi,
and
A.Yonath
(2001).
High-resolution structures of ribosomal subunits: initiation, inhibition, and conformational variability.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
43-56.
|
|
|
|
|
|
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.
|
 |
|
Links
