PDBsum entry 1ixr

Hydrolase

PDB id: 1ixr

Contents

Protein chains

135 a.a. *

191 a.a. *

308 a.a. *

Ligands

ANP

* Residue conservation analysis

PDB id:

1ixr

Name:

Hydrolase

Title:

Ruva-ruvb complex

Structure:

Holliday junction DNA helicase ruva. Chain: a, b. Engineered: yes. Ruvb. Chain: c. Fragment: residues 1-312. Engineered: yes. Mutation: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Gene: ruva. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ruvb.

Biol. unit:

Dodecamer (from PDB file)

Resolution:

3.30Å R-factor: 0.268 R-free: 0.335

Authors:

K.Yamada,T.Miyata,D.Tsuchiya,T.Oyama,Y.Fujiwara,T.Ohnishi,H.Iwasaki, H.Shinagawa,M.Ariyoshi,K.Mayanagi,K.Morikawa

Key ref:

K.Yamada et al. (2002). Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery. Mol Cell, 10, 671-681. PubMed id: 12408833 DOI: 10.1016/S1097-2765(02)00641-X

Date:

04-Jul-02 Release date: 06-Nov-02

Protein chain

Q9F1Q3  (RUVA_THET8) -  Holliday junction branch migration complex subunit RuvA from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 191 a.a.

Struc: 135 a.a.

Protein chain

Q9F1Q3  (RUVA_THET8) -  Holliday junction branch migration complex subunit RuvA from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 191 a.a.

Struc: 191 a.a.

Protein chain

Q5SL87  (RUVB_THET8) -  Holliday junction branch migration complex subunit RuvB from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 324 a.a.

Struc: 308 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chain C: E.C.3.6.4.- - ?????

DOI no: 10.1016/S1097-2765(02)00641-X

Mol Cell 10:671-681 (2002)

PubMed id: 12408833

Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery.

K.Yamada, T.Miyata, D.Tsuchiya, T.Oyama, Y.Fujiwara, T.Ohnishi, H.Iwasaki, H.Shinagawa, M.Ariyoshi, K.Mayanagi, K.Morikawa.

ABSTRACT

We present the X-ray structure of the RuvA-RuvB complex, which plays a crucial role in ATP-dependent branch migration. Two RuvA tetramers form the symmetric and closed octameric shell, where four RuvA domain IIIs spring out in the two opposite directions to be individually caught by a single RuvB. The binding of domain III deforms the protruding beta hairpin in the N-terminal domain of RuvB and thereby appears to induce a functional and less symmetric RuvB hexameric ring. The model of the RuvA-RuvB junction DNA ternary complex, constructed by fitting the X-ray structure into the averaged electron microscopic images of the RuvA-RuvB junction, appears to be more compatible with the branch migration mode of a fixed RuvA-RuvB interaction than with a rotational interaction mode.

Selected figure(s)

Figure 4.
Figure 4. Averaged Electron Microscopic Image of the RuvA-RuvB-Holliday Junction Ternary Complex and the Corresponding Functional Atomic ModelThe IMAGIC program package (van Heel et al., 1996) was used to cluster particle images and to obtain class averages. The hypothetical model was constructed by fitting the RuvA octameric core structure (yellow) and the RuvB hexamer models (blue) into the averaged images, referring to the hexameric oligomerization of the HslU protein similar to RuvB (Sousa et al., 2000). One pair of subunits related in each hexameric ring by the central 2-fold axis was replaced by the two domain III (orange)-RuvB (magenta) complexes (see text). Averaged electron microscopic images correspond to two orthogonal views of the ternary complex. The 858 original images were grouped into three major classes of averaged images, and only two of them, (A) and (B), averaged from 171 and 370 electron microscopic images, are shown here. Note the good coincidence of the images with the side (A) and end views (B) of the RuvA octameric core structure. The resolutions of the averaged images of (A) and (B) were estimated at 34 and 31 Å, respectively, from differential phase residuals. The scale bar represents 100 Å.

Figure 5.
Figure 5. Model of the Loading Process of the RuvA-RuvB Complex on a Holliday JunctionEach of the three components in this process was determined by X-ray analyses (forms I, II, and III) or by an electron microscopic study (form IV). The RuvA core region and domain III are colored by yellow and orange, respectively. The RuvB subunit is depicted by a blue oval. Red-trimmed ovals represent domain III bound to the RuvB subunit. The RuvA-RuvB complex (form III) is regarded as the preloading complex before forming the functional complex on a Holliday junction (form IV). During the conversion from form III to IV, the RuvB subunit that was previously connected with the RuvA octameric core is no longer replaced by other partners.

The above figures are reprinted by permission from Cell Press: Mol Cell (2002, 10, 671-681) copyright 2002.

Figures were selected by an automated process.