PDBsum entry 2bke

DNA binding protein

PDB id: 2bke

Contents

Protein chain

293 a.a. *

Metals

_CL

Waters ×40

* Residue conservation analysis

PDB id:

2bke

Name:

DNA binding protein

Title:

Conformational flexibility revealed by the crystal structure of a crenarchaeal rada

Structure:

DNA repair and recombination protein rada. Chain: a. Synonym: rada. Engineered: yes. Other_details: selenomethionine derivative

Source:

Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.20Å R-factor: 0.178 R-free: 0.240

Authors:

A.Ariza,D.L.Richard,M.F.White,C.S.Bond

Key ref:

A.Ariza et al. (2005). Conformational flexibility revealed by the crystal structure of a crenarchaeal RadA. Nucleic Acids Res, 33, 1465-1473. PubMed id: 15755748

Date:

15-Feb-05 Release date: 16-Mar-05

Protein chain

Q55075  (RADA_SULSO) -  DNA repair and recombination protein RadA from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 324 a.a.

Struc: 293 a.a.

Nucleic Acids Res 33:1465-1473 (2005)

PubMed id: 15755748

Conformational flexibility revealed by the crystal structure of a crenarchaeal RadA.

A.Ariza, D.J.Richard, M.F.White, C.S.Bond.

ABSTRACT

Homologous recombinational repair is an essential mechanism for repair of double-strand breaks in DNA. Recombinases of the RecA-fold family play a crucial role in this process, forming filaments that utilize ATP to mediate their interactions with single- and double-stranded DNA. The recombinase molecules present in the archaea (RadA) and eukaryota (Rad51) are more closely related to each other than to their bacterial counterpart (RecA) and, as a result, RadA makes a suitable model for the eukaryotic system. The crystal structure of Sulfolobus solfataricus RadA has been solved to a resolution of 3.2 A in the absence of nucleotide analogues or DNA, revealing a narrow filamentous assembly with three molecules per helical turn. As observed in other RecA-family recombinases, each RadA molecule in the filament is linked to its neighbour via interactions of a short beta-strand with the neighbouring ATPase domain. However, despite apparent flexibility between domains, comparison with other structures indicates conservation of a number of key interactions that introduce rigidity to the system, allowing allosteric control of the filament by interaction with ATP. Additional analysis reveals that the interaction specificity of the five human Rad51 paralogues can be predicted using a simple model based on the RadA structure.

Selected figure(s)

Figure 2.
The oligomerization strand. (a) {sigma} ; purple mesh) of the region surrounding Phe73. Atoms from different monomers are coloured differently (grey/blue). (b) A cluster of salt bridges stabilizes the SsRadA oligomerization motif. (c) Superposition of the oligomerization strands of SsRadA (blue), EcRecA (green) and HsRad51/BRCA2 (magenta). The common ATPase domain of the interacting subunit is shown as a grey surface. (d and e) Conserved interactions between the N-terminal domain of SsRadA, MvRadA and ScRad51, with the neighbouring ATPase domain.

Figure 3.
Interactions between ATPase subunits for SsRadA (blue), ScRad51 (red) and PfRadA (green). Structures were superimposed on one subunit (shown as backbone trace). The neighbouring subunits are shown as semi-transparent surfaces, with a solid cartoon representation of residues between helices {alpha} 10 and {alpha} 12. (a) Side view. (b) Top view.

The above figures are reprinted from an Open Access publication published by Oxford University Press: Nucleic Acids Res (2005, 33, 1465-1473) copyright 2005.

Figures were selected by an automated process.