Volume 11, Issue 12, Pages 1557-1567 (December 2003) The Structure of Escherichia coli RusA Endonuclease Reveals a New Holliday Junction DNA Binding Fold  John B Rafferty, Edward L Bolt, Tatyana A Muranova, Svetlana E Sedelnikova, Philip Leonard, Alessandra Pasquo, Patrick J Baker, David W Rice, Gary J Sharples, Robert G Lloyd  Structure  Volume 11, Issue 12, Pages 1557-1567 (December 2003) DOI: 10.1016/j.str.2003.11.004

Figure 1 The Fold of E. coli RusA (A) A monomer of RusA with α helices and β strands shown as coils (red) and arrows (blue), respectively. The secondary structure elements and the termini are marked. The flexible loop region in monomer A (that is disordered in monomer B) is colored yellow. (B) A dimer of RusA viewed along its 2-fold axis into the face containing the catalytically important residues (shown in green). (C) Electron density from the final 2|Fo-Fc| map with the refined coordinates of the model. (D) The region around the catalytically critical residues whose side chains are shown and colored by atom type. Hydrogen bonds are shown as dotted lines. (E) A stereo view of the α carbon backbone trace of the RusA dimer with every tenth residue labeled (the asterisk is used to differentiate the monomers). Structure 2003 11, 1557-1567DOI: (10.1016/j.str.2003.11.004)

Figure 2 Alignment of the Most Diverse Representatives of the RusA Family of Proteins Structural elements (β strands as arrows and α helices as cylinders) are illustrated above the RusA sequence with a dashed black line indicating the disordered loop found in one of the subunits. The aligned sequences are numbered according to the corresponding position on the 120 residue E. coli RusA protein. Functionally related residues present in the majority of sequences are highlighted: indigo, basic (K/R/H); red, acidic (D/E); green, hydrophobic (A/F/I/L/M/V/W/Y); and cyan, other conserved residues (including Q/N and S/T). The RusA sequences of bacterial and phage sources are from Escherichia coli cryptic prophage DLP12 (Eco); E. coli O157:H7 prophage CP933 (CP933); Listeria monocytogenes phage A118 (A118); Shigella flexneri phage V (SflV1); Legionella pneumophila (Lpn); Salmonella paratyphi (Spa); lambdoid phages HK97 and HK022 (HK); Neisseria gonorrhoeae (Ngo); Aquifex aeolicus (Aae); Clostridium acetobutylicum (Cac); Bacillus subtilis plasmid pLS32 (pLS); Streptococcus thermophilus phage 7201 (7201); Enterococcus faecalis (Efa); Streptococcus pyogenes (Spy1 and Spy2); Listeria innocua (Lin); Staphylococcus aureus phage φPVL (PVL); Bacillus subtilis skin prophage (Bsu); Mycobacteriophage TM4 (TM4); and Lactococcus lactis phage r1t (r1t). For clarity, three residues located after position 75 in the RusA from phage A118 are excluded from the alignment, and other residues omitted are indicated at gaps in the alignment. Structure 2003 11, 1557-1567DOI: (10.1016/j.str.2003.11.004)

Figure 3 DNA Binding Interface of RusA and a Model for Its Interaction with a Distorted Holliday Junction (A and B) The surface of a RusA dimer that has been modeled to be symmetric using the coordinates of subunit A fitted to subunit B and including all residue side chains. The surface is colored by electrostatic potential (red, ≤−10 kcal(mol·e)−1; blue, ≥10 kcal(mol·e)−1). The view in (A) is that in Figure 1B, and in (B) is that of the opposite face of the dimer. The residues mentioned in the text are labeled, and the asterisk is used to differentiate between the monomers. (C) A stereo view of a model for a RusA dimer bound to a pseudo-tetrahedral Holliday junction. The protein is shown in red, with the catalytically critical residues (D70, D72, K76, and D91) shown in green. The four strands of the DNA phosphate backbone of the Holliday junction are shown as colored tubes with the positions of the scissile bonds marked in yellow, and the bases are shown as a surface representation in gray. Structure 2003 11, 1557-1567DOI: (10.1016/j.str.2003.11.004)