 |
PDBsum entry 1vbm
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Structural snapshots of the kmsks loop rearrangement for amino acid activation by bacterial tyrosyl-Trna synthetase.
|
|
|
Authors
|
|
T.Kobayashi,
T.Takimura,
R.Sekine,
V.P.Kelly,
K.Vincent,
K.Kamata,
K.Sakamoto,
S.Nishimura,
S.Yokoyama.
|
|
|
Ref.
|
|
J Mol Biol, 2005,
346,
105-117.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Tyrosyl-tRNA synthetase (TyrRS) has been studied extensively by mutational and
structural analyses to elucidate its catalytic mechanism. TyrRS has the HIGH and
KMSKS motifs that catalyze the amino acid activation with ATP. In the present
study, the crystal structures of the Escherichia coli TyrRS catalytic domain, in
complexes with l-tyrosine and a l-tyrosyladenylate analogue, Tyr-AMS, were
solved at 2.0A and 2.7A resolution, respectively. In the Tyr-AMS-bound
structure, the 2'-OH group and adenine ring of the Tyr-AMS are strictly
recognized by hydrogen bonds. This manner of hydrogen-bond recognition is
conserved among the class I synthetases. Moreover, a comparison between the two
structures revealed that the KMSKS loop is rearranged in response to adenine
moiety binding and hydrogen-bond formation, and the KMSKS loop adopts the more
compact ("semi-open") form, rather than the flexible, open form. The
HIGH motif initially recognizes the gamma-phosphate, and then the alpha and
gamma-phosphates of ATP, with a slight rearrangement of the residues. The other
residues around the substrate also accommodate the Tyr-AMS. This induced-fit
form presents a novel "snapshot" of the amino acid activation step in
the aminoacylation reaction by TyrRS. The present structures and the
T.thermophilus TyrRS ATP-free and bound structures revealed that the extensive
induced-fit conformational changes of the KMSKS loop and the local
conformational changes within the substrate binding site form the basis for
driving the amino acid activation step: the KMSKS loop adopts the open form,
transiently shifts to the semi-open conformation according to the adenosyl
moiety binding, and finally assumes the rigid ATP-bound, closed form. After the
amino acid activation, the KMSKS loop adopts the semi-open form again to accept
the CCA end of tRNA for the aminoacyl transfer reaction.
|
|
|
|
|
|
|
|
Figure 6.
Figure 6. The Tyr-AMP binding sites of the TyrRSs. (a) The
Tyr-AMP-binding site of the E. coli TyrRS·Tyr-AMS
complex. (b) The corresponding view of the B. stearothermophilus
TyrRS·Tyr-AMP complex5 (PDB ID: 3TS1). The carbon atoms
of Tyr-AMS/Tyr-AMP are shown in light blue, and the hydrogen
bonds are indicated by green broken lines. A phosphate atom is
shown in green.
|
|
Figure 8.
Figure 8. Conformational changes of the KMSKS loop. (a)
Open conformation of the KMSKS loop in the E. coli
TyrRS·L-tyrosine structure. (b) Semi-open conformation of
the KMSKS loop in the E. coil TyrRS·Tyr-AMS structure.
The superposition of the open-form KMSKS loop is also shown by a
pink translucent tube. (c) Closed conformation of the KMSKS loop
in the T. thermophilus
TyrRS·ATP·L-tyrosinol·tRNA^Tyr structure13
(PDB ID: 1H3E). The KMSKS loops are shown by orange tubes. The
carbon atoms of L-tyrosine and L-tyrosinol are shown in pink,
and those of Tyr-AMS are shown in light blue, respectively. (d)
The bottleneck of the catalytic site in the T. thermophilus
TyrRS closed form. The surface model of Tyr-AMP phosphate, which
is a landmark of the aminoacyl transfer center, is shown by a
stick model. (e) The 3'-adenosine of the tRNA cannot pass
through the bottleneck of (d). The adenosine moiety is shown by
a CPK model. (f) The exposed catalytic site in the E. coli TyrRS
semi-open form. Tyr-AMS is shown by a stick model. The molecular
surfaces were produced using the program MSMS
(http://www.scripps.edu/mb/olson/people/sanner/html/msms_home.html).
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2005,
346,
105-117)
copyright 2005.
|
|
|
|
|
|
|
