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PDBsum entry 2e7i
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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 second step of RNA-Dependent cysteine biosynthesis in archaea: crystal structure of sep-Trna:cys-Trna synthase from archaeoglobus fulgidus.
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Authors
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R.Fukunaga,
S.Yokoyama.
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Ref.
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J Mol Biol, 2007,
370,
128-141.
[DOI no: ]
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PubMed id
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Abstract
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In the ancient organisms, methanogenic archaea, lacking the canonical
cysteinyl-tRNA synthetase, Cys-tRNA(Cys) is produced by an indirect pathway, in
which O-phosphoseryl-tRNA synthetase ligates O-phosphoserine (Sep) to tRNA(Cys)
and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to
Cys-tRNA(Cys). In this study, the crystal structure of SepCysS from
Archaeoglobus fulgidus has been determined at 2.4 A resolution. SepCysS forms a
dimer, composed of monomers bearing large and small domains. The large domain
harbors the seven-stranded beta-sheet, which is typical of the pyridoxal
5'-phosphate (PLP)-dependent enzymes. In the active site, which is located near
the dimer interface, PLP is covalently bound to the side-chain of the conserved
Lys209. In the proximity of PLP, a sulfate ion is bound by the side-chains of
the conserved Arg79, His103, and Tyr104 residues. The active site is located
deep within the large, basic cleft to accommodate Sep-tRNA(Cys). On the basis of
the surface electrostatic potential, the amino acid residue conservation
mapping, the position of the bound sulfate ion, and the substrate amino acid
binding manner in other PLP-dependent enzymes, a binding model of Sep-tRNA(Cys)
to SepCysS was constructed. One of the three strictly conserved Cys residues
(Cys39, Cys42, or Cys247), of one subunit may play a crucial role in the
catalysis in the active site of the other subunit.
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Figure 4.
Figure 4. The internal aldimine Lys209-PLP and the sulfate
ion in the active site. (a) Architecture of the active site
(stereo view). The main-chain traces of subunits A and B are
shown by light blue and light green tubes, respectively. The
internal aldimine Lys209-PLP (cyan) and the sulfate ion are
shown by ball and stick models. Hydrogen bonds are shown as pink
broken lines. (b) The |F[o]–F[c]| simulated-annealing omit
electron density maps (3.0σ) for Lys209-PLP and the sulfate ion
are shown in blue and green, respectively. (c) The |F[o]–F[c]|
simulated-annealing omit electron density maps (3.0σ) for
Lys209 and the sulfate ion are shown in blue and green,
respectively, in the active site of molecule B of the SeMet
SepCysS structure.
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Figure 8.
Figure 8. Active site comparison between SepCysS and CsdB and
the Sep-Ado76 binding model. (a) Architecture of the SepCysS
active site (stereo view). The main-chain traces are colored as
in Figure 7(a). The internal aldimine Lys209-PLP (cyan) and the
sulfate ion are shown by ball and stick models. (b) Architecture
of the CsdB active site (PDB ID, 1KMK) (stereo view). The
main-chain traces are colored as in Figure 7(b). The internal
aldimine Lys226-PLP and the selenocysteine are shown by cyan and
pink ball and stick models, respectively. The Cys364 side-chain
is perselenided. The coordinates of one of the oxygen atoms in
the α-COO^− group of the selenocysteine is missing in PDB ID,
1KMK. (c) Sep-Ado76 binding model. Sep-Ado76 is shown by a pink
ball and stick model. (d) Sep-Ado76 binding model on the
conservation mapping shown in Figure 6.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
370,
128-141)
copyright 2007.
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