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Contents |
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234 a.a.
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206 a.a.
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208 a.a.
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150 a.a.
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101 a.a.
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155 a.a.
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138 a.a.
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127 a.a.
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98 a.a.
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119 a.a.
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124 a.a.
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118 a.a.
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60 a.a.
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88 a.a.
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83 a.a.
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104 a.a.
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73 a.a.
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84 a.a.
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99 a.a.
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24 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Ribosome
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Title:
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Structure of the thermus thermophilus 30s ribosomal subunit in complex with a messenger RNA fragment and cognate transfer RNA anticodon stem-loop bound at the a site and with the antibiotic paromomycin
|
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Structure:
|
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16s ribosomal RNA. Chain: a. P-site messenger RNA fragment. Chain: x. Engineered: yes. Anticodon stem-loop of phenylalanine transfer RNA. Chain: y. Engineered: yes.
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Source:
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Thermus thermophilus. Organism_taxid: 274. Synthetic: yes. Organism_taxid: 274
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Biol. unit:
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24mer (from
)
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Resolution:
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3.11Å
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R-factor:
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0.232
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R-free:
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0.275
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Authors:
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J.M.Ogle,D.E.Brodersen,W.M.Clemons Jr.,M.J.Tarry,A.P.Carter, V.Ramakrishnan
|
Key ref:
|
|
J.M.Ogle
et al.
(2001).
Recognition of cognate transfer RNA by the 30S ribosomal subunit.
Science,
292,
897-902.
PubMed id:
DOI:
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Date:
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28-Mar-01
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Release date:
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04-May-01
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PROCHECK
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Headers
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References
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P80371
(RS2_THET8) -
30S ribosomal protein S2
|
|
|
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Seq:
Struc:
|
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|
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256 a.a.
234 a.a.
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P80372
(RS3_THET8) -
30S ribosomal protein S3
|
|
|
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Seq:
Struc:
|
|
|
|
239 a.a.
206 a.a.
|
|
|
|
|
|
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|
|
|
|
|
|
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P80373
(RS4_THET8) -
30S ribosomal protein S4
|
|
|
|
Seq:
Struc:
|
|
|
|
209 a.a.
208 a.a.
|
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|
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Q5SHQ5
(RS5_THET8) -
30S ribosomal protein S5
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|
|
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Seq:
Struc:
|
|
|
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162 a.a.
150 a.a.
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Q5SLP8
(RS6_THET8) -
30S ribosomal protein S6
|
|
|
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Seq:
Struc:
|
|
|
|
101 a.a.
101 a.a.
|
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|
|
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P17291
(RS7_THET8) -
30S ribosomal protein S7
|
|
|
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Seq:
Struc:
|
|
|
|
156 a.a.
155 a.a.
|
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|
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Q5SHQ2
(RS8_THET8) -
30S ribosomal protein S8
|
|
|
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Seq:
Struc:
|
|
|
|
138 a.a.
138 a.a.
|
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|
|
|
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|
|
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P80374
(RS9_THET8) -
30S ribosomal protein S9
|
|
|
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Seq:
Struc:
|
|
|
|
128 a.a.
127 a.a.*
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|
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Q5SHN7
(RS10_THET8) -
30S ribosomal protein S10
|
|
|
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Seq:
Struc:
|
|
|
|
105 a.a.
98 a.a.
|
|
|
|
|
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|
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|
|
|
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|
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P80376
(RS11_THET8) -
30S ribosomal protein S11
|
|
|
|
Seq:
Struc:
|
|
|
|
129 a.a.
119 a.a.
|
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|
|
|
|
|
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|
|
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|
|
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|
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Q5SHN3
(RS12_THET8) -
30S ribosomal protein S12
|
|
|
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Seq:
Struc:
|
|
|
|
132 a.a.
124 a.a.
|
|
|
|
|
|
|
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|
|
|
|
|
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|
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P80377
(RS13_THET8) -
30S ribosomal protein S13
|
|
|
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Seq:
Struc:
|
|
|
|
126 a.a.
118 a.a.
|
|
|
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|
|
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|
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|
|
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|
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Q5SHQ1
(RS14Z_THET8) -
30S ribosomal protein S14 type Z
|
|
|
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Seq:
Struc:
|
|
|
|
61 a.a.
60 a.a.
|
|
|
|
|
|
|
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|
|
|
|
|
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|
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Q5SJ76
(RS15_THET8) -
30S ribosomal protein S15
|
|
|
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Seq:
Struc:
|
|
|
|
89 a.a.
88 a.a.
|
|
|
|
|
|
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|
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|
|
|
|
|
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Q5SJH3
(RS16_THET8) -
30S ribosomal protein S16
|
|
|
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Seq:
Struc:
|
|
|
|
88 a.a.
83 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Q5SHP7
(RS17_THET8) -
30S ribosomal protein S17
|
|
|
|
Seq:
Struc:
|
|
|
|
105 a.a.
104 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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Q5SLQ0
(RS18_THET8) -
30S ribosomal protein S18
|
|
|
|
Seq:
Struc:
|
|
|
|
88 a.a.
73 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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Q5SHP2
(RS19_THET8) -
30S ribosomal protein S19
|
|
|
|
Seq:
Struc:
|
|
|
|
93 a.a.
84 a.a.
|
|
|
|
|
|
|
|
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|
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|
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Gene Ontology (GO) functional annotation
|
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|
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Cellular component
|
intracellular
|
4 terms
|
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Biological process
|
translation
|
1 term
|
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Biochemical function
|
structural constituent of ribosome
|
6 terms
|
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 |
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|
| |
|
DOI no:
|
Science
292:897-902
(2001)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Recognition of cognate transfer RNA by the 30S ribosomal subunit.
|
|
J.M.Ogle,
D.E.Brodersen,
W.M.Clemons,
M.J.Tarry,
A.P.Carter,
V.Ramakrishnan.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Crystal structures of the 30S ribosomal subunit in complex with messenger RNA
and cognate transfer RNA in the A site, both in the presence and absence of the
antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms
resolution. Cognate transfer RNA (tRNA) binding induces global domain movements
of the 30S subunit and changes in the conformation of the universally conserved
and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact
intimately with the minor groove of the first two base pairs between the codon
and anticodon, thus sensing Watson-Crick base-pairing geometry and
discriminating against near-cognate tRNA. The third, or "wobble,"
position of the codon is free to accommodate certain noncanonical base pairs. By
partially inducing these structural changes, paromomycin facilitates binding of
near-cognate tRNAs.
|
|
|
|
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|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 2.
Fig. 2. Complex of the 30S subunit with mRNA from a U[6]
hexanucleotide and a cognate tRNA-ASL. (A) Overview of the
complex. The 50S interface side of the 30S subunit is facing the
reader, and important elements have been given standard colors
that are used throughout the figures, namely, ASL at the A site
(gold), codon from the U[6] hexanucleotide at the A site
(purple), 3' end of 16S RNA that mimics mRNA at the P site
(green), P site tRNA mimic introduced by helix 6 from a
neighboring molecule (dark blue), and protein S12 (tan). (B)
Stereo view showing details of the A and P sites, colored as in
(A), with, in addition, helix 44 (cyan, right), helix 34 (blue,
left), 530 loop (green, left), and paromomycin (yellow sticks,
within helix 44). The hydrogen bonds responsible for the
codon-anticodon interaction at both the A and P sites are shown
as red lines.
|
|
Figure 3.
Fig. 3. Stereo views showing interactions of the ribosome with
the codon-anticodon base pairs. The tightness of the
interactions is shown by the semitransparent van der Waals
surface. (A) In the first position, A1493 binds in the minor
groove of the A36-U1 base pair. (B) In the second position, G530
and A1492 (both brown) act in concert to monitor the A35-U2 base
pair. (C) The third (wobble) position, showing the G34-U3 base
pair. C1054 stacks against G36 of the ASL. U3 interacts with
G530, and indirectly through a Mg2+ ion (magenta) with C518 and
residue Pro48 (E. coli Pro44) from protein S12 (gray). The base
pair seems closer to Watson-Crick geometry. (D) The third
position in the presence of paromomycin, with the expected GU
wobble pair. The interactions with the ribosome are similar to
those in (C).
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from the AAAs:
Science
(2001,
292,
897-902)
copyright 2001.
|
|
| |
Figures were
selected
by the author.
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 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
A.B.Mentewab,
M.J.Jacobsen,
and
R.A.Flowers
(2011).
Incomplete homogenization of 18 S ribosomal DNA coding regions in Arabidopsis thaliana.
|
| |
BMC Res Notes, 4,
93.
|
|
|
|
|
|
|
B.P.Klaholz
(2011).
Molecular recognition and catalysis in translation termination complexes.
|
| |
Trends Biochem Sci, 36,
282-292.
|
|
|
|
|
|
|
C.Y.Liu,
M.T.Qureshi,
and
T.H.Lee
(2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
|
| |
Biophys J, 100,
2201-2208.
|
|
|
|
|
|
|
G.D.Wright
(2011).
Molecular mechanisms of antibiotic resistance.
|
| |
Chem Commun (Camb), 47,
4055-4061.
|
|
|
|
|
|
|
M.Ouberai,
F.El Garch,
A.Bussiere,
M.Riou,
D.Alsteens,
L.Lins,
I.Baussanne,
Y.F.Dufrêne,
R.Brasseur,
J.L.Decout,
and
M.P.Mingeot-Leclercq
(2011).
The Pseudomonas aeruginosa membranes: A target for a new amphiphilic aminoglycoside derivative?
|
| |
Biochim Biophys Acta, 1808,
1716-1727.
|
|
|
|
|
|
|
T.Cottin,
C.Pyrkotis,
C.I.Stathakis,
I.Mavridis,
I.A.Katsoulis,
P.Anastasopoulou,
G.Kythreoti,
A.L.Zografos,
V.R.Nahmias,
A.Papakyriakou,
and
D.Vourloumis
(2011).
Designed spiro-bicyclic analogues targeting the ribosomal decoding center.
|
| |
Chembiochem, 12,
71-87.
|
|
|
|
|
|
|
T.M.Schmeing,
R.M.Voorhees,
A.C.Kelley,
and
V.Ramakrishnan
(2011).
How mutations in tRNA distant from the anticodon affect the fidelity of decoding.
|
| |
Nat Struct Mol Biol, 18,
432-436.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
X.Agirrezabala,
E.Schreiner,
L.G.Trabuco,
J.Lei,
R.F.Ortiz-Meoz,
K.Schulten,
R.Green,
and
J.Frank
(2011).
Structural insights into cognate versus near-cognate discrimination during decoding.
|
| |
EMBO J, 30,
1497-1507.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Ben-Shem,
L.Jenner,
G.Yusupova,
and
M.Yusupov
(2010).
Crystal structure of the eukaryotic ribosome.
|
| |
Science, 330,
1203-1209.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.L.Ng,
K.Lang,
N.A.Meenan,
A.Sharma,
A.C.Kelley,
C.Kleanthous,
and
V.Ramakrishnan
(2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
|
| |
Nat Struct Mol Biol, 17,
1241-1246.
|
|
|
|
|
|
|
G.De Pascale,
and
G.D.Wright
(2010).
Antibiotic resistance by enzyme inactivation: from mechanisms to solutions.
|
| |
Chembiochem, 11,
1325-1334.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
I.Wohlgemuth,
C.Pohl,
and
M.V.Rodnina
(2010).
Optimization of speed and accuracy of decoding in translation.
|
| |
EMBO J, 29,
3701-3709.
|
|
|
|
|
|
|
J.A.Dunkle,
and
J.H.Cate
(2010).
Ribosome structure and dynamics during translocation and termination.
|
| |
Annu Rev Biophys, 39,
227-244.
|
|
|
|
|
|
|
J.Frank,
and
R.L.Gonzalez
(2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
|
| |
Annu Rev Biochem, 79,
381-412.
|
|
|
|
|
|
|
J.Sund,
M.Andér,
and
J.Aqvist
(2010).
Principles of stop-codon reading on the ribosome.
|
| |
Nature, 465,
947-950.
|
|
|
|
|
|
|
K.D.Green,
W.Chen,
J.L.Houghton,
M.Fridman,
and
S.Garneau-Tsodikova
(2010).
Exploring the substrate promiscuity of drug-modifying enzymes for the chemoenzymatic generation of N-acylated aminoglycosides.
|
| |
Chembiochem, 11,
119-126.
|
|
|
|
|
|
|
L.B.Jenner,
N.Demeshkina,
G.Yusupova,
and
M.Yusupov
(2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
|
| |
Nat Struct Mol Biol, 17,
555-560.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.Jenner,
N.Demeshkina,
G.Yusupova,
and
M.Yusupov
(2010).
Structural rearrangements of the ribosome at the tRNA proofreading step.
|
| |
Nat Struct Mol Biol, 17,
1072-1078.
|
|
|
|
|
|
|
M.S.Ramirez,
and
M.E.Tolmasky
(2010).
Aminoglycoside modifying enzymes.
|
| |
Drug Resist Updat, 13,
151-171.
|
|
|
|
|
|
|
M.V.Rodnina,
and
W.Wintermeyer
(2010).
The ribosome goes Nobel.
|
| |
Trends Biochem Sci, 35,
1-5.
|
|
|
|
|
|
|
P.Khade,
and
S.Joseph
(2010).
Functional interactions by transfer RNAs in the ribosome.
|
| |
FEBS Lett, 584,
420-426.
|
|
|
|
|
|
|
P.Shah,
and
M.A.Gilchrist
(2010).
Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.
|
| |
PLoS Genet, 6,
0.
|
|
|
|
|
|
|
R.E.Stanley,
G.Blaha,
R.L.Grodzicki,
M.D.Strickler,
and
T.A.Steitz
(2010).
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
|
| |
Nat Struct Mol Biol, 17,
289-293.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.M.Voorhees,
T.M.Schmeing,
A.C.Kelley,
and
V.Ramakrishnan
(2010).
The mechanism for activation of GTP hydrolysis on the ribosome.
|
| |
Science, 330,
835-838.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.L.He,
and
R.Green
(2010).
Visualization of codon-dependent conformational rearrangements during translation termination.
|
| |
Nat Struct Mol Biol, 17,
465-470.
|
|
|
|
|
|
|
S.M.Dibrov,
J.Parsons,
and
T.Hermann
(2010).
A model for the study of ligand binding to the ribosomal RNA helix h44.
|
| |
Nucleic Acids Res, 38,
4458-4465.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
W.E.Running,
and
J.P.Reilly
(2010).
Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH.
|
| |
Proteomics, 10,
3669-3687.
|
|
|
|
|
|
|
X.Agirrezabala,
and
J.Frank
(2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
|
| |
Hum Genomics, 4,
226-237.
|
|
|
|
|
|
|
Y.Xie,
A.V.Dix,
and
Y.Tor
(2010).
Antibiotic selectivity for prokaryotic vs. eukaryotic decoding sites.
|
| |
Chem Commun (Camb), 46,
5542-5544.
|
|
|
|
|
|
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