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PDBsum entry 3dig
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References listed in PDB file
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Key reference
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Title
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Structural insights into amino acid binding and gene control by a lysine riboswitch.
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Authors
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A.Serganov,
L.Huang,
D.J.Patel.
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Ref.
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Nature, 2008,
455,
1263-1267.
[DOI no: ]
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PubMed id
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Abstract
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In bacteria, the intracellular concentration of several amino acids is
controlled by riboswitches. One of the important regulatory circuits involves
lysine-specific riboswitches, which direct the biosynthesis and transport of
lysine and precursors common for lysine and other amino acids. To understand the
molecular basis of amino acid recognition by riboswitches, here we present the
crystal structure of the 174-nucleotide sensing domain of the Thermotoga
maritima lysine riboswitch in the lysine-bound (1.9 ångström (A)) and free
(3.1 A) states. The riboswitch features an unusual and intricate architecture,
involving three-helical and two-helical bundles connected by a compact
five-helical junction and stabilized by various long-range tertiary
interactions. Lysine interacts with the junctional core of the riboswitch and is
specifically recognized through shape-complementarity within the elongated
binding pocket and through several direct and K(+)-mediated hydrogen bonds to
its charged ends. Our structural and biochemical studies indicate preformation
of the riboswitch scaffold and identify conformational changes associated with
the formation of a stable lysine-bound state, which prevents alternative folding
of the riboswitch and facilitates formation of downstream regulatory elements.
We have also determined several structures of the riboswitch bound to different
lysine analogues, including antibiotics, in an effort to understand the
ligand-binding capabilities of the lysine riboswitch and understand the nature
of antibiotic resistance. Our results provide insights into a mechanism of
lysine-riboswitch-dependent gene control at the molecular level, thereby
contributing to continuing efforts at exploration of the pharmaceutical and
biotechnological potential of riboswitches.
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Figure 1.
Figure 1: Overall structure and long-range tertiary interactions
of the lysine-bound T. maritima riboswitch. a, Schematic of
the riboswitch fold observed in the crystal structure of the
complex. The bound lysine is in red. The RNA domains are
depicted in colours used for subsequent figures. Base-specific
tertiary contacts and long-range stacking interactions are shown
as thin green and thick blue dashed lines, respectively.
Nucleotides invariant in known lysine riboswitches are boxed. b,
c, Overall lysine riboswitch structure in a ribbon
representation showing front (b) and rotated by  60°
(c) views. d, The L2–L3 kissing loop interaction is formed by
six base pairs, supplemented by interstrand stacking
interactions between A42 and C95, G43 and U94, and G44 and G101.
Hydrogen bonds between interstrand base pairs and orthogonally
aligned G43 and U94 bases are depicted by dashed lines. e, The
L4-loop–P2-helix interaction formed by an insertion of the
A126–A127–A129 stack of L4 into the RNA groove of P2
distorted by non-canonical base pairs.
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Figure 2.
Figure 2: Structure and interactions in the junctional region of
the lysine riboswitch. a, Stereo view of the junction with
bound lysine. Green sphere depicts a K^+ cation. b, Details of
riboswitch lysine interactions. Lysine is positioned within the
omit F[o] - F[c] electron density map contoured at 3.5  level.
Water molecules are shown as light blue spheres. K^+ cation
coordination and hydrogen bonds are depicted by dashed lines. c,
Direct and water-mediated interactions involving  -ammonium
group of lysine. d, e, Interactions in the top (d) and middle
(e) junctional layers.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2008,
455,
1263-1267)
copyright 2008.
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Headers
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