 |
PDBsum entry 1pyb
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
RNA binding protein
|
PDB id
|
|
|
|
1pyb
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Crystal structure of trbp111: a structure-Specific tRNA-Binding protein.
|
|
|
Authors
|
|
M.A.Swairjo,
A.J.Morales,
C.C.Wang,
A.R.Ortiz,
P.Schimmel.
|
|
|
Ref.
|
|
EMBO J, 2000,
19,
6287-6298.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Trbp111 is a 111 amino acid Aquifex aeolicus structure-specific tRNA-binding
protein that has homologous counterparts distributed throughout evolution. A
dimer is the functional unit for binding a single tRNA. Here we report the 3D
structures of the A.aeolicus protein and its Escherichia coli homolog at
resolutions of 2.50 and 1.87 A, respectively. The structure shows a symmetrical
dimer of two core domains and a central dimerization domain where the N- and
C-terminal regions of Trbp111 form an extensive dimer interface. The core of the
monomer is a classical oligonucleotide/oligosaccharide-binding (OB) fold with a
five-stranded ss-barrel and a small capping helix. This structure is similar to
that seen in the anticodon-binding domain of three class II tRNA synthetases and
several other proteins. Mutational analysis identified sites important for
interactions with tRNA. These residues line the inner surfaces of two clefts
formed between the ss-barrel of each monomer and the dimer interface. The
results are consistent with a proposed model for asymmetrical docking of the
convex side of tRNA to the dimer.
|
|
|
|
|
|
|
|
Figure 7.
Figure 7 Stereo view of a C[  ]trace
of the Trbp111 dimeric structure with all single site mutations
described in Figure 6 highlighted in ball-and-stick
representation. Side chains of residues found to be important in
tRNA binding are in black (on the top side of the dimer) and are
labeled. Residues at which an alanine substitution did not
correlate with a measurable effect on tRNA binding are shown in
gray (bottom side of the dimer). Loops L2 and L6 are indicated.
The figure was made with MOLSCRIPT (Kraulis, 1991).
|
|
Figure 8.
Figure 8 (A) Highest score docking model of the Trbp111–tRNA
complex showing surface complementarity and tRNA binding mode.
The protein dimer is shown in a Connolly surface representation
(generated in the program InsightII; Molecular Simulations, San
Diego, CA) of all non-hydrogen atoms, superimposed on a C[ ]trace.
The monomers are shown in different colors. tRNA is shown as
sticks. The asterisk denotes the observed cleft (putative
tRNA-binding site). Loop L6 is also labeled. (B) Side view of
(A) looking down the tRNA acceptor stem helix. The surface
electrostatic potential on the Trbp111 dimer is shown. Positive
charge potential is shown in blue and negative charge potential
in red. The surface is superimposed on a ribbon diagram of the
protein. The tRNA is shown in green as a ribbon through the
backbone phosphate groups.
|
|
|
|
|
|
The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2000,
19,
6287-6298)
copyright 2000.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Structure-Specific tRNA-Binding protein from the extreme thermophile aquifex aeolicus.
|
|
|
Authors
|
|
A.J.Morales,
M.A.Swairjo,
P.Schimmel.
|
|
|
Ref.
|
|
Embo J, 1999,
18,
3475-3483.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 2.
Figure 2 Determination of the oligomeric state of Trbp111 in
solution by analytical ultracentrifugation at 4°C.
Sedimentation velocity profile and fit to mol. wt of 23.29 kDa
(solid lines) for Trbp111 (15  M,
pH 7.0) corresponds to a dimer. Fit parameters are as follows: s
= 2.033 +/ 0.002, r.m.s. residual = 1.00241  10^-2.
Data sets were taken  30
min apart. Inset (A) shows the first data set fit to the
expected monomer mol. wt of 12 kDa, and inset (B) shows the
first data set fit to the expected trimer mol. wt (36 kDa).
|
|
Figure 7.
Figure 7 Competition of tRNA[f]^Met with other RNAs. (A) Primary
structure of tRNA[f]^Met and various RNAs used in competition
experiments. Relevant features of the tRNA structure are shown.
(B) Competition of 1–2 nM [5'-^32P] tRNA[f]^Met with RNAs that
resemble individual domains of tRNA[f]^Met. Competition by
single-stranded Poly-A RNA is also shown. (C) Competition of
1–2 nM [5'-^32P] tRNA[f]^Met with X.laevis 5S rRNA.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
|
|
|
|
|
|
|
