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PDBsum entry 2nxn
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References listed in PDB file
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Key reference
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Title
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Recognition of ribosomal protein l11 by the protein trimethyltransferase prma.
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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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EMBO J, 2007,
26,
567-577.
[DOI no: ]
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PubMed id
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Abstract
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Bacterial ribosomal protein L11 is post-translationally trimethylated at
multiple residues by a single methyltransferase, PrmA. Here, we describe four
structures of PrmA from the extreme thermophile Thermus thermophilus. Two
apo-PrmA structures at 1.59 and 2.3 A resolution and a third with bound cofactor
S-adenosyl-L-methionine at 1.75 A each exhibit distinct relative positions of
the substrate recognition and catalytic domains, revealing how PrmA can position
the L11 substrate for multiple, consecutive side-chain methylation reactions.
The fourth structure, the PrmA-L11 enzyme-substrate complex at 2.4 A resolution,
illustrates the highly specific interaction of the N-terminal domain with its
substrate and places Lys39 in the PrmA active site. The presence of a unique
flexible loop in the cofactor-binding site suggests how exchange of AdoMet with
the reaction product S-adenosyl-L-homocysteine can occur without necessitating
the dissociation of PrmA from L11. Finally, the mode of interaction of PrmA with
L11 explains its observed preference for L11 as substrate before its assembly
into the 50S ribosomal subunit.
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Figure 4.
Figure 4 The PrmA–L11 complex structure. (A) Cartoon
representation of the overall structure. PrmA and L11 are
colored in salmon and cyan. The Lys39 side chain is shown in a
stick representation. (B) Final 2F[o]-F[c] density for the
active site region contoured at the 1  level.
(C) Ribbon diagram of binding interactions between the PrmA
N-terminal domain and L11. (D) Ribbon diagram of binding
interactions between the PrmA catalytic domain and L11. (E)
Stereo representation comparing the PrmA–L11 complex with the
L11–RNA complex (PDB code 1MMS) after least-squares alignment
of L11. PrmA is colored in salmon and L11 is colored in cyan in
the PrmA complex and in blue in the RNA complex. RNA is shown in
yellow.
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Figure 5.
Figure 5 The active site of PrmA. (A) Stereo representation of
the active site. The position of AdoMet and Phe99 is modeled by
least-squares alignment from the position observed in PrmA3. (B,
C) Comparison of the PrmA surface in the complex structure (B,
flexible loop absent) with the cofactor-bound structure PrmA3
(C, flexible loop present, L11 surface is shown for reference).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2007,
26,
567-577)
copyright 2007.
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