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PDBsum entry 3dmh
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the thermus thermophilus 16 s rrna methyltransferase rsmc in complex with cofactor and substrate guanosine.
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Authors
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H.Demirci,
S.T.Gregory,
A.E.Dahlberg,
G.Jogl.
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Ref.
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J Biol Chem, 2008,
283,
26548-26556.
[DOI no: ]
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PubMed id
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Abstract
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Post-transcriptional modification is a ubiquitous feature of ribosomal RNA in
all kingdoms of life. Modified nucleotides are generally clustered in
functionally important regions of the ribosome, but the functional contribution
to protein synthesis is not well understood. Here we describe high resolution
crystal structures for the N(2)-guanine methyltransferase RsmC that modifies
residue G1207 in 16 S rRNA near the decoding site of the 30 S ribosomal subunit.
RsmC is a class I S-adenosyl-L-methionine-dependent methyltransferase composed
of two methyltransferase domains. However, only one S-adenosyl-L-methionine
molecule and one substrate molecule, guanosine, bind in the ternary complex. The
N-terminal domain does not bind any cofactor. Two structures with bound
S-adenosyl-L-methionine and S-adenosyl-L-homocysteine confirm that the cofactor
binding mode is highly similar to other class I methyltransferases. Secondary
structure elements of the N-terminal domain contribute to cofactor-binding
interactions and restrict access to the cofactor-binding site. The orientation
of guanosine in the active site reveals that G1207 has to disengage from its
Watson-Crick base pairing interaction with C1051 in the 16 S rRNA and flip out
into the active site prior to its modification. Inspection of the 30 S crystal
structure indicates that access to G1207 by RsmC is incompatible with the native
subunit structure, consistent with previous suggestions that this enzyme
recognizes a subunit assembly intermediate.
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Figure 2.
FIGURE 2. Overall structure of RsmC. A, stereo diagram
showing a schematic representation of the overall structure.
Secondary structure elements are colored in orange, yellow, and
red in the N-terminal domain and in blue, cyan, and purple in
the C-terminal domain. AdoMet is shown as yellow sticks with
atoms colored by elements; guanosine is shown as salmon sticks,
and a sulfate molecule bound in the noncatalytic domain is shown
in yellow. B, topology diagram with secondary structure elements
colored as in A. C, least squares superposition of the two
subdomains. The catalytic domain is shown in magenta, and the
N-terminal domain is shown in yellow. AdoMet and guanosine bound
to the catalytic subdomain are shown as sticks.
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Figure 3.
FIGURE 3. The RsmC active site. A, AdoMet binding in the
active site. AdoMet and guanosine are shown as yellow and salmon
sticks, respectively. Solvent water molecules are shown as red
spheres. B, final SigmaA-weighted 2F[o] - F[c] electron density
map of the active site region contoured at 1  . C, guanosine binding
in the active site. D, comparison of side chain orientation in
the noncatalytic N-terminal domain with the active site region
of the catalytic domain. Residues in the N-terminal domain are
colored red and yellow. The C-terminal domain and AdoMet bound
in the catalytic domain are shown in gray for reference.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2008,
283,
26548-26556)
copyright 2008.
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