Hydrogen sulfide (H2S) is one of the predominant volatile sulfur compounds that are primarily responsible for oral malodor and contribute to the progress of periodontal disease. H2S in the human oral cavity is generally produced by enzymatic actions of oral bacteria.Fusobacterium nucleatum, a Gram negative periodontal pathogen, is known to be one of the heaviest H2S producers [1]. For now, four genes (fn0625,fn1055,fn1220, andfn1419) encoding pyridoxal-5′-phosphate (PLP)-dependent H2S-producing enzymes have been identified and characterized inF. nucleatumATCC 25586. Of the four enzymes, Fn1055 protein is a unique H2S-producing enzyme, which produces H2S and L-serine from L-cysteine [2]. Therefore, Fn1055 might play important roles in L-serine biosynthesis in addition to H2S production in this periodontal pathogen. Crystal structures of recombinant Fn1055 and its site-directed mutant complex with L-cysteine (a substrate) were determined at 2.1 Å resolution. The enzyme forms a homodimer whose subunits are related by a two-fold axis. The subunit is composed of two domains with α/β structure. The PLP cofactor forms a covalent internal aldimine linkage with the ε-amino group of Lys46 at the bottom of active site cleft between the domains, in the absence of substrate. On the other hand, in the cocrystal of mutant with L-cysteine, the introduced L-cysteine was found to be covalently bound to PLP, instead of Lys46. This covalent intermediate was identified as an α-aminoacrylate, which is the key species of PLP-dependent-enzyme catalysis, by spectrophotometric measurement. Along with the intermediate formation, closure of active site cleft was also observed. Furthermore, we found an amino acid residue acting as a base and confirmed its indispensability for catalysis by enzymatic analyses. These results support that H2S production by Fn1055 proceeds through the β-elimination of L-cysteine, and enable us to propose a detailed catalytic mechanism of Fn1055.
X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase