Biomedical Engineering Reference
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Fig. 7.2
Pept-tRNA hydrolysis in termination. (
a
) Schematic of the reaction. Pept-tRNA is
depicted in
green
, RF1/2 in
yellow
. (
b
) Time courses in H
2
O and D
2
O-containing buffers. Catalyzed
(
closed symbols
) and uncatalyzed (
open symbols
) reactions were measured in buffer with either
H
2
O (
fi lled circles
,
open circles
) or D
2
O (
fi lled triangles
,
open triangles
). (
c
) Proton inventories.
n
, mole fractions of D
2
O. For the ribosome-catalyzed reaction (
fi lled circles
), the linear fit yields
an overall KSIE of 4.1; the
dotted line
simulates the rate-limiting simultaneous transfer of two
protons in the TS with a fractionation factor of 0.49 each. In the uncatalyzed reaction (
open circles
),
many protons contribute to the overall KSIE of 7.0; the dashed line simulates the rate-limiting
transfer of three protons. (
d
) TS of the catalyzed reaction. The single low-barrier hydrogen bond
that determines the reaction rate is
encircled
. The possibility of the involvement of another water
molecule and/or residue A2451 of 23S rRNA is indicated
7.5.2
Peptidyl-tRNA Hydrolysis
The second reaction catalyzed by the ribosome is the hydrolysis of pept-tRNA,
which requires the help of the termination (release) factors, RF1 and RF2 in
Escherichia coli
(Fig.
7.2a
). The reaction takes place when the ribosome arrives at a
stop codon in the mRNA. RF1/2 are recruited to the ribosome and, upon stop codon
recognition, undergo a conformational change which places a conserved GGQ
sequence motif of the factors into the catalytic center of the ribosome (Jin et al.
2010
;
Korostelev et al.
2008
; Laurberg et al.
2008
; Weixlbaumer et al.
2008
) . This contact
presumably induces a rearrangement of 23S rRNA that allows for the correct posi-
tioning of the hydrolytic water molecule for the attack on the ester bond (Schmeing
et al.
2005b
). Unlike peptidyl transfer, peptide release is impaired by mutations in
23S rRNA of the active site (Polacek et al.
2003
; Youngman et al.
2004
) , although
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