PDBsum entry 2gxu

Hydrolase

PDB id: 2gxu

Contents

Protein chain

207 a.a. *

Ligands

PO4

Waters ×229

* Residue conservation analysis

PDB id:

2gxu

Name:

Hydrolase

Title:

Hera n-terminal domain in complex with orthophosphate, crystal form 1

Structure:

Heat resistant RNA dependent atpase. Chain: a. Fragment: n-terminal domain. Engineered: yes

Source:

Thermus thermophilus hb27. Organism_taxid: 262724. Strain: hb-27. Gene: hera. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.67Å R-factor: 0.169 R-free: 0.210

Authors:

M.G.Rudolph,D.Klostermeier

Key ref:

M.G.Rudolph et al. (2006). Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain. J Mol Biol, 361, 731-743. PubMed id: 16890241 DOI: 10.1016/j.jmb.2006.06.065

Date:

09-May-06 Release date: 22-Aug-06

Protein chain

O07897  (O07897_THETH) -  Heat resistant RNA dependent ATPase from Thermus thermophilus

Seq: 510 a.a.

Struc: 207 a.a.

DOI no: 10.1016/j.jmb.2006.06.065

J Mol Biol 361:731-743 (2006)

PubMed id: 16890241

Crystal structure and nucleotide binding of the Thermus thermophilus RNA helicase Hera N-terminal domain.

M.G.Rudolph, R.Heissmann, J.G.Wittmann, D.Klostermeier.

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.

Selected figure(s)

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.

Figures were selected by the author.