PDBsum entry 2i1q

Recombination

PDB id: 2i1q

Contents

Protein chain

311 a.a. *

Ligands

ANP

Metals

_MG

_CA ×3

_NA

Waters ×149

* Residue conservation analysis

PDB id:

2i1q

Name:

Recombination

Title:

Rada recombinase in complex with calcium

Structure:

DNA repair and recombination protein rada. Chain: a. Engineered: yes. Mutation: yes

Source:

Methanococcus voltae. Organism_taxid: 2188. Gene: rada. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.191 R-free: 0.211

Authors:

X.Qian,Y.He,X.Ma,M.N.Fodje,P.Grochulski,Y.Luo

Key ref:

X.Qian et al. (2006). Calcium stiffens archaeal Rad51 recombinase from Methanococcus voltae for homologous recombination. J Biol Chem, 281, 39380-39387. PubMed id: 17050545 DOI: 10.1074/jbc.M607785200

Date:

14-Aug-06 Release date: 24-Oct-06

Protein chain

O73948  (RADA_METVO) -  DNA repair and recombination protein RadA from Methanococcus voltae

Seq: 322 a.a.

Struc: 311 a.a.

DOI no: 10.1074/jbc.M607785200

J Biol Chem 281:39380-39387 (2006)

PubMed id: 17050545

Calcium stiffens archaeal Rad51 recombinase from Methanococcus voltae for homologous recombination.

X.Qian, Y.He, X.Ma, M.N.Fodje, P.Grochulski, Y.Luo.

ABSTRACT

Archaeal RadA or Rad51 recombinases are close homologues of eukaryal Rad51 and DMC1. These and bacterial RecA orthologues play a key role in DNA repair by forming helical nucleoprotein filaments in which a hallmark strand exchange reaction between homologous DNA substrates occurs. Recent studies have discovered the stimulatory role by calcium on human and yeast recombinases. Here we report that the strand exchange activity but not the ATPase activity of an archaeal RadA/Rad51 recombinase from Methanococcus voltae (MvRadA) is also subject to calcium stimulation. Crystallized MvRadA filaments in the presence of CaCl(2) resemble that of the recently reported ATPase active form in the presence of an activating dose of KCl. At the ATPase center, one Ca(2+) ion takes the place of two K(+) ions in the K(+)-bound form. The terminal phosphate of the nonhydrolyzable ATP analogue is in a staggered conformation in the Ca(2+)-bound form. In comparison, an eclipsed conformation was seen in the K(+)-bound form. Despite the changes in the ATPase center, both forms harbor largely ordered L2 regions in essentially identical conformations. These data suggest a unified stimulation mechanism by potassium and calcium because of the existence of a conserved ATPase center promiscuous in binding cations.

Selected figure(s)

Figure 3.
FIGURE 3. ATPase center of MvRadA in stereo. The view is rotated from that in Fig. 2 by 90°. Two MvRadA subunits are in yellow and gray, respectively. Ca^2+ and K^+ ions are in salmon and red, respectively. Mg^2+ ions and water molecules are blue and green, respectively. The putative hydrolysis water is highlighted in a larger sphere. A, Ca^2+-bound form. B, previously reported K^+-bound form (Protein Data Bank entry code 2FPM). The L2 regions are in essentially identical conformations in both forms. Ca^2+ and K^+ are bound in a conserved cavity lined by the tip of the nucleotide cofactor, the catalytic Glu-151, Asp-302 in the ATP cap, and the C terminus of a short helix in the L2 region. The terminal phosphate is in a staggered conformation in the Ca^2+-bound form but in an eclipsed conformation in the K^+-bound form.

Figure 5.
FIGURE 5. Ca^2+-triggered conformational change in the L2 region in stereo. The views cover 12 consecutive subunits of MvRadA or two helical turns of the crystallized filaments. The filament axes are shown as vertical lines. The ordered residues in the L1 regions (residues 218-230) and L2 regions (residues 256-285) are shown in green and gold, respectively. The ATP analogues, Mg^2+ ions and Ca^2+ ions are shown in cyan, blue, and magenta, respectively. A, structure in the absence of Ca^2+. The structure of Protein Data Bank entry 1T4G is shown (13). B,Ca^2+-bound form. Binding of a Ca^2+ ion in every ATPase center triggers a disorder-order transformation in the DNA-interacting L2 region. The largely ordered structure in the presence of stimulatory K^+ and Ca^2+ ions appears correlated with strand exchange activity of MvRadA.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 39380-39387) copyright 2006.

Figures were selected by the author.

Author's comment

Calcium as well as other cations such as potassium stabilize an active conformation of the DNA-interacting loop L2 in recombinase RadA, a prototype of human Rad51 and DMC1.