PDBsum entry 2hjv

Hydrolase

PDB id: 2hjv

Contents

Protein chains

158 a.a. *

Waters ×163

* Residue conservation analysis

PDB id:

2hjv

Name:

Hydrolase

Title:

Structure of the second domain (residues 207-368) of the bacillus subtilis yxin protein

Structure:

Atp-dependent RNA helicase dbpa. Chain: a, b. Fragment: bacillus subtilis yxin domain 2 (residues 207-368). Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: dbpa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Monomer (from PQS)

Resolution:

1.95Å R-factor: 0.209 R-free: 0.247

Authors:

D.B.Mckay,J.M.Caruthers

Key ref:

J.M.Caruthers et al. (2006). Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN. Acta Crystallograph Sect F Struct Biol Cryst Commun, 62, 1191-1195. PubMed id: 17142894 Ref: Full text

Date:

02-Jul-06 Release date: 12-Dec-06

Protein chains

P42305  (DBPA_BACSU) -  ATP-dependent RNA helicase DbpA from Bacillus subtilis (strain 168)

Seq: 479 a.a.

Struc: 158 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Full text	Acta Crystallograph Sect F Struct Biol Cryst Commun 62:1191-1195 (2006)
PubMed id: 17142894

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

J.M.Caruthers, Y.Hu, D.B.McKay.

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.

Selected figure(s)

Figure 1.
Structure of YxiN(207 --368). (a) Ribbon diagram of protomer A. [beta]-Strands and selected [alpha]-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[[alpha]] trace is shown as a smoothed coil. The backbones of segments of peptide where C[[alpha]] positions differ by <0.5 A are shown in yellow for both protomers; segments where C[[alpha]] positions differ by >0.5 A 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[deg] 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). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 December 1; 62(Pt 12): 1191–1195. Published online 2006 November 30. doi: 10.1107/S1744309106044642. Copyright [copyright] International Union of Crystallography 2006

Figure 2.
Stereo diagram of an isoleucine/leucine/valine 'stack' of the [beta]-sheet in protomer A. The side chains of adjacent residues of one stack, as well as a C[[alpha] backbone and ribbon drawing of five-residue segments of the [beta]-strands, are shown. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 December 1; 62(Pt 12): 1191–1195. Published online 2006 November 30. doi: 10.1107/S1744309106044642. Copyright [copyright] International Union of Crystallography 2006

The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallograph Sect F Struct Biol Cryst Commun (2006, 62, 1191-1195) copyright 2006.