Figure 1.

(a) Sequence alignment between pPS10 RepA, ScOrc4p, and PaCdc6p shows similarities between these DNA replication initiators. Identical residues (*) and conservative changes (+) in RepA vs. ScOrc4p alignment are shown. Residues in PaCdc6p found to be identical (24%) in RepA and/or ScOrc4p (black squares). Secondary structural elements are labeled according to the crystal structures of a Rep-type monomer (24) and PaCdc6p (28): the two WH domains in RepA are colored red (WH1) and blue (WH2), whereas that in PaCdc6p is in green. The conserved hydrophobic heptads in the two N-terminal α-helices and Trp-94 (RepA)/Trp-451 (ScOrc4p) are boxed in orange. The alignment between RepA and ScOrc4p was generated with clustalw (29), with minor manual adjustments. After the yeast sequence was shuffled 1,000 times (http://www.ch.embnet.org/software/PRSS_form.html), the probability of a better alignment (score ≥ 294) between RepA and a sequence of the randomized population was 0.0108. Once the sequence of PaCdc6p was available (28), it was included using the alignment as a profile (29). European Molecular Biology Laboratory database accession numbers: RepA, X58896; ScOrc4p, SC34862. (b) Least-squares superposition of the peptide backbones of the WH domains from the RepA homologue RepE54 (24) (Protein Data Bank entry 1REP) and PaCdc6p (28) (1FNN). Forty-one Cα atoms from both three-helix bundle cores (α2-α4 and α16-α18, respectively) were fit with a rms deviation of 2.14 Å. Coordinate transformation was performed with o (30) and displayed with molscript (31).