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PDBsum entry 1l2q
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References listed in PDB file
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Key reference
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Title
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A new uag-Encoded residue in the structure of a methanogen methyltransferase.
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Authors
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B.Hao,
W.Gong,
T.K.Ferguson,
C.M.James,
J.A.Krzycki,
M.K.Chan.
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Ref.
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Science, 2002,
296,
1462-1466.
[DOI no: ]
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PubMed id
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Abstract
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Genes encoding methanogenic methylamine methyltransferases all contain an
in-frame amber (UAG) codon that is read through during translation. We have
identified the UAG-encoded residue in a 1.55 angstrom resolution structure of
the Methanosarcina barkeri monomethylamine methyltransferase (MtmB). This
structure reveals a homohexamer comprised of individual subunits with a TIM
barrel fold. The electron density for the UAG-encoded residue is distinct from
any of the 21 natural amino acids. Instead it appears consistent with a lysine
in amide-linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate. We suggest
that this amino acid be named l-pyrrolysine.
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Figure 2.
Fig. 2. (A) Fit of
(4R,5R)-4-substituted-pyrroline-5-carboxylate to the 2F[O] -
F[C] 3  density of
the NaCl crystal form (orientation 1). The substituent attached
to the C-4 carbon is shown as a methyl, but it could also be an
ammonium or hydroxyl group. (B) Stick-diagram of proposed
L-pyrrolysine amino acid. (C) Residual F[O] - F[C] difference
map of NH[4]SO[4] crystal form after incorporation of a 40%
occupancy model consisting of L-pyrrolysine in orientation 1 and
an exogenous ammonium ion. This remaining omit density suggests
that L-pyrrolysine adopts a different orientation (orientation
2) at 60% occupancy in NH[4]SO[4] with an amine added to the C-2
carbon of the pyrroline ring. These figures were prepared with
the programs XtalView, MOLSCRIPT, and Raster3D (22-24).
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Figure 3.
Fig. 3. Stereoview of primary forms of the active site around
the amber-encoded ligand: (A) NaCl crystals; (B) (NH[4])[2]SO[4]
crystals, 40% occupancy orientation that is similar to NaCl
crystals; (C) (NH[4])[2]SO[4] crystals, 60% occupancy
orientation with amine added to ring. These figures were
prepared with the programs XtalView, MOLSCRIPT, and Raster3D.
(22-24).
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The above figures are
reprinted
by permission from the AAAs:
Science
(2002,
296,
1462-1466)
copyright 2002.
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