PDBsum entry 1hqc

Hydrolase

PDB id: 1hqc

Contents

Protein chains

314 a.a. *

Ligands

ADE ×2

Metals

_MG ×2

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the holliday junction migration motor protein ruvb from thermus thermophilus hb8.

Authors

K.Yamada, N.Kunishima, K.Mayanagi, T.Ohnishi, T.Nishino, H.Iwasaki, H.Shinagawa, K.Morikawa.

Ref.

Proc Natl Acad Sci U S A, 2001, 98, 1442-1447. [DOI no: 10.1073/pnas.031470598]

PubMed id

11171970

Abstract

We report here the crystal structure of the RuvB motor protein from Thermus thermophilus HB8, which drives branch migration of the Holliday junction during homologous recombination. RuvB has a crescent-like architecture consisting of three consecutive domains, the first two of which are involved in ATP binding and hydrolysis. DNA is likely to interact with a large basic cleft, which encompasses the ATP-binding pocket and domain boundaries, whereas the junction-recognition protein RuvA may bind a flexible beta-hairpin protruding from the N-terminal domain. The structures of two subunits, related by a noncrystallographic pseudo-2-fold axis, imply that conformational changes of motor protein coupled with ATP hydrolysis may reflect motility essential for its translocation around double-stranded DNA.

Figure 2.
Fig. 2. Electron density maps and ribbon models of nucleotide-binding sites in the two ncs subunits. Possible residues that interact with nucleotides are depicted: Y14, I15, Y168, R179, and D180 are in contact with the adenine bases; K51 and T52 (Walker A), D97 (Walker B), T146 (Sensor I), and R205 (Sensor II) may interact with the phosphate groups. The stick models of (a) AMPPNP and (b) ADP were represented with corresponding simulated annealed F[o] F[c] omit maps at a 1.5 contour. The nucleotide atoms were omitted from the map calculation. Ribbons corresponding to the two sensor motifs and the two Walker motifs are indicated by the same color as in Fig. 1c. (c) Structural differences between the "A" (blue) and "B" (yellow) forms. Here, only the C backbones of domain N (ATPase domain) were superimposed between the two ncs molecules.

Figure 4.
Fig. 4. Comparison of the hypothetical hexamer model of RuvB with the electron microscopic image. (a) Projection image (Left) of negative stained RuvB complexed with a 30-bp DNA, obtained by averaging 140 top views in our previous work (15). The resolution of the averaged image was 30.0 Å. The top views of the hexamer model (Center and Right) were constructed by superimposing each ATPase domain of RuvB (AMPPNP form) (blue region) onto the corresponding regions of HslU crystal structure (25) and the NSF crystal structure (23), respectively. The domains N, M, C, labeled residues, and the bound nucleotides are represented with the same color code as defined in Fig. 1. (b) Projection image (Left) of RuvB-DNA obtained by averaging 266 side views. This image of the single ring was taken from one-half of the double ring, which encircles duplex DNA. The resolution of the averaged image was 34.3 Å. Side view of the hexamer model (Right). [Reproduced with permission from ref. 15 (Copyright 2000, Academic Press).