PDBsum entry 1vdd

Recombination

PDB id: 1vdd

Contents

Protein chains

199 a.a. *

Ligands

IMD ×5

Metals

_ZN ×4

Waters ×65

* Residue conservation analysis

PDB id:

1vdd

Name:

Recombination

Title:

Crystal structure of recombinational repair protein recr

Structure:

Recombination protein recr. Chain: a, b, c, d. Fragment: residues 1-199. Engineered: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Gene: recr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Octamer (from PQS)

Resolution:

2.50Å R-factor: 0.233 R-free: 0.301

Authors:

B.I.Lee,K.H.Kim,S.W.Suh

Key ref:

B.I.Lee et al. (2004). Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair. EMBO J, 23, 2029-2038. PubMed id: 15116069 DOI: 10.1038/sj.emboj.7600222

Date:

20-Mar-04 Release date: 18-May-04

Protein chains

Q9ZNA2  (RECR_DEIRA) -  Recombination protein RecR from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 220 a.a.

Struc: 199 a.a.

DOI no: 10.1038/sj.emboj.7600222

EMBO J 23:2029-2038 (2004)

PubMed id: 15116069

Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair.

B.I.Lee, K.H.Kim, S.J.Park, S.H.Eom, H.K.Song, S.W.Suh.

ABSTRACT

RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway of homologous recombinational DNA repair in procaryotes. The human Rad52 protein is a functional counterpart of RecFOR. We present here the crystal structure of RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a two-domain structure: the N-terminal domain with a helix-hairpin-helix (HhH) motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222 symmetry with a central hole of 30-35 angstroms diameter. In the crystal, two tetramers are concatenated, implying that the RecR tetramer is capable of opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA, and that its HhH motif is essential for DNA binding.

Selected figure(s)

Figure 3.
Figure 3 Detailed views of domains/motifs in DR RecR. (A) HhH motifs from two monomers are swapped. Gly21, Arg23 and Lys27 are shown. Primed residues belong to the second subunit B in Figure 2C. (B) Cys[4] zinc-finger motif. (C) Toprim domain with residues Glu86, Asp90 and Glu146. Corresponding positions (142 and 144) of the 'DxD' sequence are indicated by red balls. (D) The C-terminal regions from two monomers are swapped. Arg167 and Asp182 are the fingerprint residues of the canonical Walker B motif. Double-primed residues belong to the third subunit C. The orientations of domains/motifs are roughly similar to those in subunits B (colored in white green), D (purple) and C (white blue) in Figure 2C.

Figure 5.
Figure 5 A possible DNA clamp model for RecR. (A) Comparison of DR RecR with DNA clamp proteins. Ribbon diagrams and electrostatic potential at the molecular surface are shown for DR RecR, E. coli DNA polymerase III subunit, T4 gp45 and human PCNA. The diameter of the central hole is about 30 -35 Å for DR RecR and about 35 Å for other clamp proteins. The molecular surface was colored according to the electrostatic potential: blue, 10 kT; white, 0 kT; red, -10 kT. (B) Conserved residues of DR RecR located in the putative DNA-binding region of the central hole (left). Strictly conserved residues are colored in green and semiconserved residues in yellow, as deduced by aligning 14 RecR sequences in Figure 1. Negatively charged residues of the Toprim domain and the Walker B motif that may play a role in Mg2+-enhanced DNA binding (right). (C) Model for dsDNA binding by DR RecR.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2029-2038) copyright 2004.

Figures were selected by an automated process.