FIG. 1.

Type-specific signature sequences in L. lactis ClpC and ClpE. (A) The class 1 Clp proteins contain N-terminal and C-terminal domains (white bars), two highly conserved ATP binding domains (ATP-1 and ATP-2, shaded bars), and a variably sized middle domain (white bars in center). The presence of signature sequences is indicated by black boxes and numbering as described previously (31). (B) Comparison of the amino acid sequences of the L. lactis ClpC and ClpE proteins with those of homologous proteins from various organisms (GenBank accession numbers): ClpC—A. aeolicus (AE000733), S. hyodysenteriae (X73140), and B. subtilis (D26185); ClpE—B. subtilis (BSUB0008) and L. sake (OrfX; partial sequence, U82366). The ClpC and ClpE sequences are aligned with signature sequences I, II, and III and with the consensus sequence of a domain present in both the UvrB and the UvrC proteins from a variety of bacteria (24). A putative coiled-coil heptad motif (abcdefg) in which the first and fourth amino acids are hydrophobic (bold) is indicated. Also shown is the ClpE-specific signature sequence (El) and a PDZ-like domain (believed to be involved in protein-protein interactions) deduced from the E. coli ClpA (M31045) and ClpB (M29364) proteins and from the S. cerevisiae Hsp104 (M67479) and Hsp78 (L16533) proteins (21). Residues identical to the signature sequences are indicated by gray shading, whereas amino acids matching the UvrB or UvrC sequences or the PDZ-like consensus sequence are in boldface. h, hydrophobic amino acid; e, D or E; t, S or T.