Crystal Structure of Archaeal Recombinase RadA Yan Wu, Yujiong He, Ignace A Moya, Xinguo Qian, Yu Luo  Molecular Cell  Volume 15, Issue 3, Pages 423-435 (August 2004) DOI: 10.1016/j.molcel.2004.07.014 Copyright © 2004 Cell Press Terms and Conditions

Figure 1 ATPase Activity of RadA in the Presence of PEG (A) The initial turnover rates of the ATPase reaction are plotted against PEG concentration. (B) Phosphate release over time in the presence of 35% PEG 400 or 15% PEG 3350. Results of parallel experiments at room temperature and 37°C are shown. Molecular Cell 2004 15, 423-435DOI: (10.1016/j.molcel.2004.07.014) Copyright © 2004 Cell Press Terms and Conditions

Figure 2 Sequence Alignment and Architecture of RadA (A) Sequence alignment of RadA homologs from M. voltae (MvRadA), P. furiosus (PfRad51), H. sapiens (HsRad51 and HsDMC1), S. cerevisiae (ScRad51 and ScDMC1), M. smegmatis (MsRecA), M. tuberculosis (MtRecA), and E. coli (EcRecA). The three RecA sequences and the six non-RecA sequences were aligned in separate groups by ClustalW (Pearson and Lipman, 1988). The two groups of recombinases were aligned by CE (Shindyalov and Bourne, 1998) using the representative structures of EcRecA and MvRadA. The non-RecA recombinases have similar N-terminal domains. The C-terminal domain and extra sequences upstream of a conserved polymerization motif of the three RecA proteins have been removed for clarity. Sequences, secondary structures, and sequence numbers of MvRadA and EcRecA are colored in red and blue, respectively. The N-terminal domain and the ATPase core are labeled in salmon and cyan, respectively. The polymerization motif and its interaction partner are labeled as “zip” (beet). The Walker A and B motifs and a newly identified ATP cap are highlighted in green. The L1 and L2 regions are highlighted in gold and cornflower blue, respectively. The HhH motif is highlighted in blue. This alignment figure is generated by Alscript (Barton, 1993). (B) Subunit architecture of MvRadA in stereo. Each subunit has two half-sites for binding to the AMP-PNP (magenta). Molecular Cell 2004 15, 423-435DOI: (10.1016/j.molcel.2004.07.014) Copyright © 2004 Cell Press Terms and Conditions

Figure 3 ATP-Mediated Subunit Interface (A) Electron density maps at the ATP binding site in stereo. The refined model of the AMP-PNP, Thr-112, and the magnesium site are shown. A 2.0 Å resolution omit difference electron density map is contoured at 3.0 σ (purple). A 2.6 Å resolution anomalous difference map were generated using model phases retarded by 90 degrees. The anomalous map is contoured at 6.0 σ (red). The peak in the anomalous map supports the location of a divalent cation. (B) The solvent-filled subunit interface. Each subunit is shown in alternating light blue and lavender. Red and yellow spheres are solvent molecules and magnesium ions, respectively. The helical axis is shown in cyan. Solvent molecules are concentrated at the subunit interface. (C) A ball-and-stick model of the ATP binding site. Oxygen, nitrogen, and phosphorous atoms are shown in red, blue, and yellow, respectively. Carbon atoms from the two adjacent subunits of MvRadA and the AMP-PNP are colored in green, lavender, and yellow, respectively. The magnesium ion and the solvent molecules are shown in gold and purple spheres, respectively. The putative hydrolyzing water is shown in a larger sphere. Selected hydrogen bonds are shown in dashed brown lines. The Walker A motif interacts with the triphosphate, while the ATP cap interacts with the base and ribose moieties of the ATP analog. Molecular Cell 2004 15, 423-435DOI: (10.1016/j.molcel.2004.07.014) Copyright © 2004 Cell Press Terms and Conditions

Figure 4 Structural Comparison of RadA and Rad51 Recombinases The nucleotide is shown in ball-and-stick model. (A) Superimposed structures of MvRadA and PfRad51. MvRadA is colored by domain. PfRad51 is colored in lavender. Both proteins have two similar domains with noticeably different disposition. (B) A conserved polymerization motif. The solvent accessible surface of MvRadA with green-colored hydrophobic patches is generated by GRASP (Nicholls et al., 1991). Cα trace of residues 63-68 and stick model of side chain atoms of Phe-64 of MvRadA (beet) and their counterparts in PfRad51 (blue), BRCA2 (gold), and EcRecA (cyan) are shown. The 6-residue fragments in the four known structures were superposed by structural alignment of their noncovalently associated ATPase cores. (C) Comparison of the two interacting ATPase cores of MvRadA and those of PfRad51. The bottom ATPase cores are superimposed. MvRadA has a closed ATP binding site. The disposition of adjacent L2 regions is different between the two homologs. Molecular Cell 2004 15, 423-435DOI: (10.1016/j.molcel.2004.07.014) Copyright © 2004 Cell Press Terms and Conditions

Figure 5 Subunit Interface of RecA Models Two interacting ATPase cores of EcRecA models are shown in ribbons along with ball-and-stick models of the AMP-PNP. (A) EM model of the EcRecA active filament. (B) Model of the EcRecA active filament based on the crystal structure of MvRadA. (C) Crystal structure of EcRecA. The EM and MvRadA-based models resemble each other in the ATP-mediated interface and the disposition of adjacent L2 regions. The crystal structure of EcRecA is distinctive from the other two models. Molecular Cell 2004 15, 423-435DOI: (10.1016/j.molcel.2004.07.014) Copyright © 2004 Cell Press Terms and Conditions

Figure 6 Comparison between Filamentous Structures of MvRadA and EcRecA The L1 and L2 regions are highlighted in yellow and red, respectively. The L2 regions in both proteins and the L1 region in EcRecA are disordered in their respective crystal structures. These loops are modeled based on the crystal structure of MsRecA using ordered elbow regions (blue) as guides for rigid-body translocation. (A) Extended filament of MvRadA. The HhH motif is also shown (salmon). (B) Compact filament of EcRecA. In the structure of MvRadA, the L1 and L2 regions are placed closer to the helical axis (vertical line). Molecular Cell 2004 15, 423-435DOI: (10.1016/j.molcel.2004.07.014) Copyright © 2004 Cell Press Terms and Conditions