PDBsum entry: 1l8d

Replication

PDB id: 1l8d

Contents

Protein chains

103 a.a. *

Ligands

PO4 ×6

CIT

Metals

_HG

Waters ×124

* Residue conservation analysis

PDB id:

1l8d

Name:

Replication

Title:

Rad50 coiled-coil zn hook

Structure:

DNA double-strand break repair rad50 atpase. Chain: a, b. Fragment: rad50 coiled-coil fragment containing the cxxc motif, rad50 molecular hook. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.225 R-free: 0.278

Authors:

K.P.Hopfner,J.A.Tainer

Key ref:

K.P.Hopfner et al. (2002). The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature, 418, 562-566. PubMed id: 12152085 DOI: 10.1038/nature00922

Date:

20-Mar-02 Release date: 28-Aug-02

Protein chains

P58301  (RAD50_PYRFU) -  DNA double-strand break repair Rad50 ATPase

Seq: 882 a.a.

Struc: 103 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: DNA repair (1 term)
• Biochemical function: nuclease activity (3 terms)

DOI no: 10.1038/nature00922

Nature 418:562-566 (2002)

PubMed id: 12152085

The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair.

K.P.Hopfner, L.Craig, G.Moncalian, R.A.Zinkel, T.Usui, B.A.Owen, A.Karcher, B.Henderson, J.L.Bodmer, C.T.McMurray, J.P.Carney, J.H.Petrini, J.A.Tainer.

ABSTRACT

The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. These functions all imply that the linked binding of two DNA substrates occurs, although the molecular basis for this process remains unknown. Here we present a 2.2 A crystal structure of the Rad50 coiled-coil region that reveals an unexpected dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn(2+) ion. Biochemical, X-ray and electron microscopy data indicate that these hooks can join oppositely protruding Rad50 coiled-coil domains to form a flexible bridge of up to 1,200 A. This suggests a function for the long insertion in the Rad50 ABC-ATPase domain. The Rad50 hook is functional, because mutations in this motif confer radiation sensitivity in yeast and disrupt binding at the distant Mre11 nuclease interface. These data support an architectural role for the Rad50 coiled coils in forming metal-mediated bridging complexes between two DNA-binding heads. The resulting assemblies have appropriate lengths and conformational properties to link sister chromatids in homologous recombination and DNA ends in non-homologous end-joining.

Selected figure(s)

Figure 2.
Figure 2: Crystal structures of the central portion of the Rad50 coiled coil reveal a dimerization motif mediated by a single Zn2+-binding site. a, Two pfRad50-CXXC molecules (yellow and orange) form a composite Zn2+-binding site at the dimer interface. Each pfRad50-CXXC contributes two cysteines (green) to tetrahedrally coordinate the metal (Zn2+ or Hg2+, magenta sphere). The interaction is stabilized by two main-chain hydrogen bonds (white dots). b, Fold and assembly of the metal-bound pfRad50-CXXC dimer. Each of the two pfRad50-CXXC molecules forms an antiparallel coiled coil around a 14-residue non-helical hook-shaped region, which encompasses the CXXC motif and folds into the Zn2+-binding hook. The coiled coils extend from the composite Zn2+-binding site in opposite directions, which allows them to link two distinct Mre11 complexes. The dimer on the right is rotated 90° relative to the one on the left. c, Stereo view of the Rad50-CXXC dimer interface showing the two cysteine hooks, bound metal ion and hydrophobic interactions. Hydrophobic side chains are labelled and coloured pink for one pfRad50-CXXC and blue for the other. Additional hydrogen bonds and salt bridges are indicated by white dots.

Figure 3.
Figure 3: Negatively stained electron micrographs of human and P. furiosus Mre11 complexes reveal conformational properties of the component domains including Zn2+-mediated tail-to-tail linkages between individual coiled-coil arms of Rad50. a, c, Human M2R2 tetramer; b, d, P. furiosus M2R2 tetramer; e, f, hook-linked human (M2R2)[2] octamer; g, hook-linked P. furiosus (M2R2)[2] octamer; h, single-linkage (M2R2)[2] octamer; i, circular human M2R2 tetramer; j, circular P. furiosus M2R2 tetramer; k, circular P. furiosus M2R2 tetramer bound to DNA. hd, head domain comprising two Rad50 ATPases (red and yellow spheres in the diagrams) and two Mre11 molecules (blue spheres); cc, coiled coil (single red or yellow line); hk, Zn2+-hook. l, Architecture of the Zn2+-linked (M2R2)[2] Mre11 complex and its interaction with DNA. An Mre11 dimer (blue spheres) binds to the coiled coils of two Rad50 molecules adjacent to the ATPase domains (red/yellow spheres), forming the DNA-binding head of the Mre11 complex. The two binding heads are joined by a Zn2+-mediated tail-to-tail linkage between the coiled-coil hooks of Rad50, providing a bridge between sister chromatids before recombination. Zn2+ is shown as a magenta sphere.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2002, 418, 562-566) copyright 2002.

Figures were selected by an automated process.