3B1C

Crystal structure of betaC-S lyase from Streptococcus anginosus: Internal aldimine form

3B1C の概要

• エントリーDOI: 10.2210/pdb3b1c/pdb
• 関連するPDBエントリー: 3B1D 3B1E
• 分子名称: BetaC-S lyase, PYRIDOXAL-5'-PHOSPHATE, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: lyase
• 由来する生物種: Streptococcus anginosus
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 181451.50

構造登録者

Kezuka, Y.,Yoshida, Y.,Nonaka, T. (登録日: 2011-06-29, 公開日: 2012-06-27, 最終更新日: 2025-03-26)

主引用文献

Kezuka, Y.,Yoshida, Y.,Nonaka, T.
Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus
Proteins, 80:2447-2458, 2012

PubMed Abstract: Hydrogen sulfide (H(2)S) is a causative agent of oral malodor and may play an important role in the pathogenicity of oral bacteria such as Streptococcus anginosus. In this microorganism, H(2)S production is associated with βC-S lyase (Lcd) encoded by lcd gene, which is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the α,β-elimination of sulfur-containing amino acids. When Lcd acts on L-cysteine, H(2)S is produced along with pyruvate and ammonia. To understand the H(2)S-producing mechanism of Lcd in detail, we determined the crystal structures of substrate-free Lcd (internal aldimine form) and two reaction intermediate complexes (external aldimine and α-aminoacrylate forms). The formation of intermediates induced little changes in the overall structure of the enzyme and in the active site residues, with the exception of Lys234, a PLP-binding residue. Structural and mutational analyses highlighted the importance of the active site residues Tyr60, Tyr119, and Arg365. In particular, Tyr119 forms a hydrogen bond with the side chain oxygen atom of L-serine, a substrate analog, in the external aldimine form suggesting its role in the recognition of the sulfur atom of the true substrate (L-cysteine). Tyr119 also plays a role in fixing the PLP cofactor at the proper position during catalysis through binding with its side chain. Finally, we partly modified the catalytic mechanism known for cystalysin, a βC-S lyase from Treponema denticola, and proposed an improved mechanism, which seems to be common to the βC-S lyases from oral bacteria.

PubMed: 22674431
DOI: 10.1002/prot.24129

実験手法

X-RAY DIFFRACTION (1.93 Å)