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PDBsum entry 2du7
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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 the first step of RNA-Dependent cysteine biosynthesis in archaea.
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Authors
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R.Fukunaga,
S.Yokoyama.
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Ref.
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Nat Struct Biol, 2007,
14,
272-279.
[DOI no: ]
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PubMed id
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Abstract
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Cysteine is ligated to tRNA(Cys) by cysteinyl-tRNA synthetase in most organisms.
However, in methanogenic archaea lacking cysteinyl-tRNA synthetase,
O-phosphoserine is ligated to tRNA(Cys) by O-phosphoseryl-tRNA synthetase
(SepRS), and the phosphoseryl-tRNA(Cys) is converted to cysteinyl-tRNA(Cys). In
this study, we determined the crystal structure of the SepRS tetramer in complex
with tRNA(Cys) and O-phosphoserine at 2.6-A resolution. The catalytic domain of
SepRS recognizes the negatively charged side chain of O-phosphoserine at a
noncanonical site, using the dipole moment of a conserved alpha-helix. The
unique C-terminal domain specifically recognizes the anticodon GCA of tRNA(Cys).
On the basis of the structure, we engineered SepRS to recognize tRNA(Cys)
mutants with the anticodons UCA and CUA and clarified the anticodon recognition
mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for
translational incorporation of O-phosphoserine into proteins in response to the
stop codons UGA and UAG.
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Figure 2.
(a) Superposition of the catalytic domains of SepRS (pink)
and PheRS (light blue). Cyan ball-and-stick model,
O-phosphoserine; gray ball-and-stick, phenylalanine; dark blue,
magenta and violet tubes, motifs 1, 2 and 3, respectively, which
are characteristic of class II aaRSs; dark green, central helix
and the preceding loop. (b) The catalytic site in the A.
fulgidus SepRS–tRNA^Cys–O-phosphoserine complex. Yellow,
O-phosphoserine carbons; cyan, O-phosphoserine phosphorus atoms.
SepRS is colored as in a. (c) The catalytic site in the T.
thermophilus PheRS–phenylalanine complex, colored as in b. (d)
Schematic representation of the unique recognition mechanism for
O-phosphoserine by SepRS.
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Figure 3.
(a) Structure of the anticodon-binding domain (stereo view).
Green, helices; blue,  -strands;
yellow, tRNA; red, anticodon nucleotides; ball-and-stick models,
Glu418 and Glu420. (b) The recognition of the tRNA^Cys anticodon
loop in the SepRS–tRNA^Cys–O-phosphoserine complex (stereo
view). Pink and green mesh, |F[o] - F[c]| simulated-annealing
omit electron density maps (3.0  )
for the tRNA anticodon loop nucleotides and the SepRS
recognition residues, respectively. (c) Recognition of A36, G37
and A38. (d) Recognition of G34 and C35. Pink, the two residues
(Glu418 and Glu420) that were mutated for engineering.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2007,
14,
272-279)
copyright 2007.
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