Figure 2.

Alignment of the HKD motifs found in Tdp1 orthologs with the HKD motifs of a representative member from each PLD superfamily class. The program clustalw with additional manual modifications was used to create the alignment. Proteins that possess only one HKD motif are grouped with the N-terminal motifs of the proteins containing two HKD motifs. Highlighted in gray are key residues that fall into one of the three categories established by Ponting and Kerr (1) for the members of the PLD superfamily: hydrophobic residues (A, C, I, L, V, M, F, Y, W), small residues (G, A, S), and acidic and amides of acidic residues (D, E, N, Q). Black boxes indicate the most conserved amino acids in the motif. * marks positions that were mutated in human Tdp1. Numbers flanking the sequences indicate the positions of the first and last amino acids shown in that protein sequence. Numbers in brackets represent the numbers of amino acids not shown in the alignment. Accession codes and sequences represented are the same as in Fig. 1 for the Tdp1 orthologs. Representatives of the other PLD superfamily classes are [roman numerals indicate the class according to Ponting and Kerr (1)]: PLD_cb (I, castor bean PLD, PIR: A54850), Toxin_yp (II, Y. pestis murine toxin, GenPept: CAA63386), CLS_ec (III, E. coli cardiolipin synthase, SWISS-PROT: P31071), PSS_ec (IV, E. coli phosphatidylserine synthase, SWISS-PROT: P23830), orf_ssp (VI, Synchocystis sp. product of comE ORF1, GenPept: BAA10416), nuc_st (VII, S. typhimurium Nuc protein precursor, PIR: S41475), o338_ec (VIII, E. coli hypothetical 38-kDa protein in FEC1-FIMB intergenic region, SWISS-PROT: P39369), p37K_vv (V, Vaccinia virus p37K major envelope protein, SWISS-PROT: P20638).