5b55 | pdb_00005b55

Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form

spinqualitylabelsall models 5b55, resolution 2.14Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5b55 is a 2 chain structure with sequence from Fusobacterium nucleatum subsp. nucleatum ATCC 25586. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 0JO, MLY, PEG, PLP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q8REP3_FUSNN Publication Abstract from PubMed Hydrogen sulfide (H2S) plays important roles in the pathogenesis of periodontitis. Oral pathogens typically produce H2S from L-cysteine in addition to pyruvate and NH4(+) However, fn1055 from Fusobacterium nucleatum subsp. nucleatum ATCC 25586 encodes a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the production of H2S and L-serine from L-cysteine and H2O, an unusual cysteine (hydroxyl) lyase reaction (beta-replacement reaction). To reveal the reaction mechanism, the crystal structure of substrate-free Fn1055 was determined. Based on this structure, a model of the L-cysteine-PLP Schiff base suggested that the thiol group forms hydrogen bonds with Asp(232) and Ser(74), and the substrate alpha-carboxylate interacts with Thr(73) and Gln(147) Asp(232) is a unique residue to Fn1055 and its substitution to asparagine (D232N) resulted in almost complete loss of beta-replacement activity. The D232N structure obtained in the presence of L-cysteine contained the alpha-aminoacrylate-PLP Schiff base in the active site, indicating that Asp(232) is essential for the addition of water to the alpha-aminoacrylate to produce the L-serine-PLP Schiff base. Rapid scan stopped-flow kinetic analyses showed an accumulation of the alpha-aminoacrylate intermediate during the reaction cycle, suggesting that water addition mediated by Asp(232) is the rate-limiting step. In contrast, mutants containing substitutions of other active-site residues (Ser(74), Thr(73), and Gln(147)) exhibited reduced beta-replacement activity by more than 100-fold. Finally, based on the structural and biochemical analyses, we propose a mechanism of the cysteine (hydroxyl) lyase reaction by Fn1055. This study leads to elucidation of the H2S-producing mechanism in F. nucleatum. Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen-sulfide producing oral pathogen, Fusobacterium nucleatum.,Kezuka Y, Ishida T, Yoshida Y, Nonaka T Biochem J. 2018 Jan 17. pii: BCJ20170838. doi: 10.1042/BCJ20170838. PMID:29343611 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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