CDP-6-deoxy-L-threo-D-glycero-4-hexulose 3-dehydrase (E1) purified from Yersinia pseudotuberculosis is a pyridoxamine 5'-phosphate (PMP) dependent iron-sulfur-containing enzyme which catalyzes the C-O bond cleavage at C-3 of its substrate leading to the formation of 3,6-dideoxyhexose. This enzyme is rapidly inactivated by diethyl pyrocarbonate (DEP) at pH 6.0 and 25 degrees C. The inactivation of E1 by DEP, which is reversible upon treatment of hydroxylamine, appears to be attributable solely to the modification of histidine residues. The fact that coincubation of E1 with its substrate gave almost total protection against DEP inactivation and that only one less histidine residue was modified in the presence of substrate strongly suggested that inactivation is due to the modification of only one reactive histidine residue which resides in or near the active site of E1 and is critical for E1's activity. Sequence alignment between the translated ascC (E1) gene and several representative pyridoxal 5'-phosphate (PLP)/PMP dependent enzymes revealed that three of the four invariant residues, glycine, aspartate, and arginine found in all other aminotransferases, are conserved in the E1 sequence (G169, D191, and R403). However, the highly conserved lysine is replaced by a histidine residue (H220) in E1. In order to test whether H220 plays an essential role in E1 catalysis, H220N mutant was constructed and the encoding protein was found to exhibit nearly identical physical characteristics as the wild-type E1. Interestingly, the mutant protein had lost most of its catalytic activity, and one less histidine residue was modified upon treatment of H220N-mutated protein with DEP. Such a single-point mutation also impaired E1's capability of catalyzing the solvent hydrogen exchange at C-4' position of the PMP coenzyme. Our findings strongly suggested that H220 is most likely the active-site base which abstracts the C-4' proton from the PMP-substrate adduct and initiates the catalysis. Furthermore, E1's preservation of other invariant residues found in many PLP/PMP dependent enzymes allowed a speculation of their roles in E1 catalysis.(ABSTRACT TRUNCATED AT 400 WORDS)