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PDBsum entry 1kuq
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Role of n-Terminal helix in interaction of ribosomal protein s15 with 16s rrna.
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Authors
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S.V.Revtovich,
A.D.Nikulin,
S.V.Nikonov.
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Ref.
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Biochemistry (mosc), 2004,
69,
1319-1323.
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PubMed id
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Abstract
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The position and conformation of the N-terminal helix of free ribosomal protein
S15 was earlier found to be modified under various conditions. This variability
was supposed to provide the recognition by the protein of its specific site on
16S rRNA. To test this hypothesis, we substituted some amino acid residues in
this helix and assessed effects of these substitutions on the affinity of the
protein for 16S rRNA. The crystal structure of the complex of one of these
mutants (Thr3Cys S15) with the 16S rRNA fragment was determined, and a computer
model of the complex containing another mutant (Gln8Met S15) was designed. The
available and new information was analyzed in detail, and the N-terminal helix
was concluded to play no significant role in the specific binding of the S15
protein to its target on 16S rRNA.
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Secondary reference #1
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Title
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Crystal structure of the s15-Rrna complex.
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Authors
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A.Nikulin,
A.Serganov,
E.Ennifar,
S.Tishchenko,
N.Nevskaya,
W.Shepard,
C.Portier,
M.Garber,
B.Ehresmann,
C.Ehresmann,
S.Nikonov,
P.Dumas.
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Ref.
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Nat Struct Biol, 2000,
7,
273-277.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Components of the S15−rRNA complex. a, Sequence
of the Thermus thermophilus S15 protein^17. Colored residues are
>80% conserved among 23 bacterial sequences (green) and
additionally conserved among 55 homologous sequences from
plastids, Archaea and Eukarya (red). Amino acids that interact
with the rRNA fragment are underlined, and the four  -helices
deduced from the crystallographic structure are indicated. b,
Schematic of tertiary structure of the 57 nt RNA corresponding
to nucleotides 584−590/649−667/739−757 of E. coli rRNA as
determined by comparative sequence analysis, and contacts with
protein. Nucleotides within the UUCG loops capping helices 21
and 22 are in italics. Bases in red are >95% conserved in  6,000
prokaryotic sequences. Ribose rings in black are in a C2'-endo
conformation, stacking is shown by hatched lines, and water
molecules are indicated by W. Two alternative conformations of
G664 are shown. Nucleotide C748 is not well defined. Conserved
amino acid residues are colored as in (a), and their contacts
with RNA backbone (phosphate group or 2'-OH) or functional
groups of bases are indicated. Contacts are with amino acid side
chains, with the single exception of Gly 22, which interacts
through the backbone carbonyl.
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Figure 4.
Figure 4. Schematic representation of the recognition by S15 on
rRNA, possible implications in 30S assembly and comparison with
mRNA binding. S15 is schematized in green with its two RNA
binding sites numbered 1 and 2. The first one recognizes a
particular backbone geometry (the three-way junction in rRNA and
the pseudoknot fold in mRNA). The second one recognizes an
analogous G-U/G-C motif in both RNAs. In 16S rRNA, binding
induces a conformational adjustment (widening of the deep
groove), denoted by a red star, that is most likely required for
subsequent 30S assembly steps (for example, S18 binding).
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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