Antisera raised to a 109 kDa wall-associated protein (WAP) of Bacillus subtilis 168 cross-reacts with two other WAPs of 220 and 58 kDa. The structural gene for the 109 kDa WAP (designated wapA) was cloned, sequenced, mapped at around 340 degrees on the B. subtilis 168 chromosome and found to encode a precursor of all three wall-bound forms (2334 amino acids and 258,329 Da). The protein has two ligand-binding domains; the N-terminal domain has three direct repeats of 102 residues with 40% identity, which are responsible for wall binding. The C-terminal domain consists of two blocks of residues with a conserved motif repeated a total of 31 times. The motif consensus sequence GXXXX(Y,F)XYDXXG is almost identical to that of the Escherichia coli rearrangement hot spot family and shows similarity to a carbohydrate-binding motif of a number of Gram-positive secreted proteins. A mutant insertionally inactivated in the wapA gene had no distinguishable phenotype apart from lacking the three WAPs. The possible role of WAPA and its two-domain relationship with other ligand-binding proteins is discussed.