PDBsum entry: 1z3i

Recombination/DNA binding

PDB-id: 1z3i

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

644 a.a. *

Ligands

SO4 ×9

Metal ions

_ZN

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, dimer
(*as deduced by PQS)

PDB id:

1z3i

Name:

Recombination/DNA binding

Title:

Structure of the swi2/snf2 chromatin remodeling domain of eukaryotic rad54

Structure:

Similar to rad54-like. Chain: x. Fragment: proteolytic fragment. Engineered: yes

Source:

Danio rerio. Zebrafish. Organism_taxid: 7955. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108

Biological unit:

Dimer (from PQS)

UniProt:

Q7ZV09 (Q7ZV09_DANRE)

Seq:

Struc:

Seq:

Struc:

Seq:

738 a.a.

Struc:

644 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure

Resolution:

3.00Å

R-factor:

0.200

R-free:

0.234

Authors:

N.H.Thoma,B.K.Czyzewski,A.A.Alexeev,A.V.Mazin, S.C.Kowalczykowski,N.P.Pavletich

Key ref:

N.H.Thomä et al. (2005). Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54.. Nat Struct Mol Biol, 12, 350-356. [PubMed id: 15806108] [DOI: 10.1038/nsmb919]

Date:

12-Mar-05

Release date:

05-Apr-05

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1038/nsmb919

Nat Struct Mol Biol 12:350-356 (2005)

PubMed id: 15806108

Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54.

N.H.Thomä, B.K.Czyzewski, A.A.Alexeev, A.V.Mazin, S.C.Kowalczykowski, N.P.Pavletich.

ABSTRACT

SWI2/SNF2 chromatin-remodeling proteins mediate the mobilization of nucleosomes and other DNA-associated proteins. SWI2/SNF2 proteins contain sequence motifs characteristic of SF2 helicases but do not have helicase activity. Instead, they couple ATP hydrolysis with the generation of superhelical torsion in DNA. The structure of the nucleosome-remodeling domain of zebrafish Rad54, a protein involved in Rad51-mediated homologous recombination, reveals that the core of the SWI2/SNF2 enzymes consist of two alpha/beta-lobes similar to SF2 helicases. The Rad54 helicase lobes contain insertions that form two helical domains, one within each lobe. These insertions contain SWI2/SNF2-specific sequence motifs likely to be central to SWI2/SNF2 function. A broad cleft formed by the two lobes and flanked by the helical insertions contains residues conserved in SWI2/SNF2 proteins and motifs implicated in DNA-binding by SF2 helicases. The Rad54 structure suggests that SWI2/SNF2 proteins use a mechanism analogous to helicases to translocate on dsDNA.

Selected figure(s)

Figure 4.
Figure 4. The position of canonical helicase motifs and SWI2/SNF2-specific helicase motifs in Rad54. (a) The canonical motifs Ia, II, III, IV, V and VI are yellow, while the SWI/SNF-specific motifs A,B,C and D are brown and red. (b) Motifs involved in DNA binding are green, while those mainly involved in ATP binding are blue. A sulfate ion bound to the ATP-binding site is shown in both panels in ball-and-stick.

Figure 5.
Figure 5. Juxtapositions of nucleic acid -bound RecG and HCV NS3 with the structure of Rad54. The first helicase lobe in RecG, Rad54 and HCV NS3 is blue, the second lobe is red. The double-stranded DNA in RecG and the single-stranded RNA in HCV NS3 are orange. The proposed dsDNA-binding site in Rad54 is shown with an orange line depicting the DNA strand contacting the motifs, while its complementary strand is shown in gray. The dsDNA axis is indicated with a dotted line. Inset, a close-up view of the DNA-binding site and the conserved arginine and lysine residues involved.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 350-356) copyright 2005.

Figures were selected by an automated process.