 |
PDBsum entry 2gxu
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Crystal structure and nucleotide binding of the thermus thermophilus RNA helicase hera n-Terminal domain.
|
|
|
Authors
|
|
M.G.Rudolph,
R.Heissmann,
J.G.Wittmann,
D.Klostermeier.
|
|
|
Ref.
|
|
J Mol Biol, 2006,
361,
731-743.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
DEAD box RNA helicases use the energy of ATP hydrolysis to unwind
double-stranded RNA regions or to disrupt RNA/protein complexes. A minimal RNA
helicase comprises nine conserved motifs distributed over two RecA-like domains.
The N-terminal domain contains all motifs involved in nucleotide binding, namely
the Q-motif, the DEAD box, and the P-loop, as well as the SAT motif, which has
been implicated in the coordination of ATP hydrolysis and RNA unwinding. We
present here the crystal structure of the N-terminal domain of the Thermus
thermophilus RNA helicase Hera in complex with adenosine monophosphate (AMP).
Upon binding of AMP the P-loop adopts a partially collapsed or half-open
conformation that is still connected to the DEAD box motif, and the DEAD box in
turn is linked to the SAT motif via hydrogen bonds. This network of interactions
communicates changes in the P-loop conformation to distant parts of the
helicase. The affinity of AMP is comparable to that of ADP and ATP,
substantiating that the binding energy from additional phosphate moieties is
directly converted into conformational changes of the entire helicase.
Importantly, the N-terminal Hera domain forms a dimer in the crystal similar to
that seen in another thermophilic prokaryote. It is possible that this mode of
dimerization represents the prototypic architecture in RNA helicases of
thermophilic origin.
|
|
|
|
|
|
|
|
Figure 3.
Figure 3. Details of the AMP/phosphate binding site. (a)
Stereo image of the chemical environment of AMP. Residues
directly contacting the nucleotide are shown as stick models.
Water molecules are drawn as orange spheres and hydrogen bonds
are shown as broken blue lines. (b) The superposition of the AMP
(yellow) and orthophosphate-bound (grey) TthDEAD structures
reveals that an isolated phosphate ion (blue) is not a good
mimic for the nucleotide as several hydrogen bonds of AMP (shown
in blue) are lost in the orthophosphate complex due to a
rotation of orthophosphate relative to the AMP α-phosphate. (c)
90° rotation of the view in (b) showing subtle
rearrangements of the P-loop due to the absence of the base and
ribose moieties. The σ[A]-weighted mF[o]-DF[c] omit electron
density map of orthophospate is contoured in black at 3σ.
|
|
Figure 5.
Figure 5. Dimer structure. (a) Structure of the TthDEAD
dimer found in the asymmetric unit of crystal form 2. The
monomers are related by an approximate 2-fold (176.5°)
rotation. Helices and β-strands are colored orange and blue,
respectively. Much of the interface is created by an
intermolecular 14-stranded β-sheet, which is an antiparallel
arrangement of the parallel sheets in each monomer. (b) Rotation
of the view in (a) by 90° around the horizontal axis to
highlight additional interactions between the N termini, parts
of the Q-motifs, and the α2 helices of both monomers. (c)
Magnification of the TthDEAD dimer interface in the same
orientation as in (a). The five hydrogen bonds between the β7
strands are shown as broken blue lines. Residues involved in van
der Waals contacts are colored green (molecule A) and cyan
(molecule B). (d) Superposition of the TthDEAD (colored) and
MjaDEAD (grey) dimers. The first molecules of each dimer were
aligned to highlight differences in the other monomers. The mode
of dimerization is similar in both cases via β-strand 7 but the
dimer interface is more extensive in TthDEAD. Note the
difference in tilt between the monomers of each complex (arrow).
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
361,
731-743)
copyright 2006.
|
|
|
|
|
|
|
