Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN

Abstract

The Bacillus subtilis RNA helicase YxiN is a modular three-domain protein. The first two domains form a conserved helicase core that couples an ATPase activity to an RNA duplex-destabilization activity, while the third domain recognizes a stem-loop of 23S ribosomal RNA with high affinity and specificity. The structure of the second domain, amino-acid residues 207-368, has been solved to 1.95 A resolution, revealing a parallel alphabeta-fold. The crystallographic asymmetric unit contains two protomers; superposition shows that they differ substantially in two segments of peptide that overlap the conserved helicase sequence motifs V and VI, while the remainder of the domain is isostructural. The conformational variability of these segments suggests that induced fit is intrinsic to the recognition of ligands (ATP and RNA) and the coupling of the ATPase activity to conformational changes.

Figure 1

Structure of YxiN(207–368). (a) Ribbon diagram of protomer A. β-Strands and selected α-helices are numbered sequentially. The motif V and VI loops are labeled. (b) Superposition of the two protomers in the asymmetric unit. A stereo diagram of the C_α trace is shown as a smoothed coil. The backbones of segments of peptide where C_α positions differ by <0.5 Å are shown in yellow for both protomers; segments where C_α positions differ by >0.5 Å are shown in magenta (protomer A) and cyan (protomer B). The side chains of selected residues of helicase motifs V and VI, as well as Asp298, are shown for protomer A. The orientation of the figure is rotated approximately 180° around a vertical axis relative to the schematic drawing in (a). (c) Crystal-packing interactions involving residues from motifs V and VI. Only the side chains of residues from motifs V and VI that are involved in intermolecular interactions are shown. Protomer A, red; protomer B, blue; symmetry-related A, magenta; symmetry-related B, cyan. All figures were produced using PyMOL (http://www.pymol.org).

Figure 2

Stereo diagram of an isoleucine/leucine/valine ‘stack’ of the β-sheet in protomer A. The side chains of adjacent residues of one stack, as well as a C_α backbone and ribbon drawing of five-residue segments of the β-strands, are shown.