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PDBsum entry 2i4l
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References listed in PDB file
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Key reference
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Title
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Structures of two bacterial prolyl-Trna synthetases with and without a cis-Editing domain.
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Authors
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T.Crepin,
A.Yaremchuk,
M.Tukalo,
S.Cusack.
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Ref.
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Structure, 2006,
14,
1511-1525.
[DOI no: ]
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PubMed id
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Abstract
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Prolyl-tRNA synthetases (ProRSs) are unique among synthetases in that they have
diverse architectures, notably the variable presence of a cis-editing domain
homologous to the freestanding deacylase proteins YbaK and ProX. Here, we
describe crystal structures of two bacterial ProRSs from the pathogen
Enterococcus faecalis, which possesses an editing domain, and from
Rhodopseudomonas palustris, which does not. We compare the overall structure and
binding mode of ATP and prolyl-adenylate with those of the
archael/eukaryote-type ProRS from Thermus thermophilus. Although structurally
more homologous to YbaK, which preferentially hydrolyzes Cys-tRNA(Pro), the
editing domain of E. faecalis ProRS possesses key elements similar to ProX, with
which it shares the activity of hydrolyzing Ala-tRNA(Pro). The structures give
insight into the complex evolution of ProRSs, the mechanism of editing, and
structural differences between prokaryotic- and eukaryotic-type ProRSs that can
be exploited for antibiotic design.
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Figure 3.
Figure 3. Interactions of ProRSs with ATP
(A–C) Active
sites of (A) R. palustris, (B) E. faecalis, and (C) T.
thermophilus ProRS with bound ATP (predominantly pink molecule),
showing hydrogen bonds with key interacting residues. The
insertion domains are in magenta (in [A] and [B]), and the
eukaryote/archae-type-specific C-terminal domain is in yellow
(in [C]). Note the functionally equivalent roles of Glu218 in
PrsRp and PrsEf with the conserved carboxy terminus (Tyr477) in
PrsTt. In each case, the proline-binding loop is in the open
conformation.
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Figure 4.
Figure 4. Interactions of ProRSs with the Prolyl-Adenylate
Analog, ProAMS
(A–C) ProAMS (predominantly gray molecule)
bound in the active sites of (A) R. palustris, (B) E. faecalis,
and (C) T. thermophilus ProRS, showing key hydrogen bonds to the
proline and sulfate moieties. Class II synthetase conserved
motifs 1, 2, and 3 are shown in green, cyan, and red,
respectively, and the TXE loop is shown in gold. On the
proline-binding loop (violet), which is in the closed
conformation, hydrophobic residues Ile202, Met202, and Phe205
play equivalent roles in PrsRp, PrsEf, and PrsTt, respectively.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2006,
14,
1511-1525)
copyright 2006.
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