4D99

Salmonella typhimurium D-Cysteine desulfhydrase with L-ser bound non-covalently at the active site

4D99 の概要

• エントリーDOI: 10.2210/pdb4d99/pdb
• 関連するPDBエントリー: 4D8T 4D8U 4D8W 4D92 4D96 4D97 4D9B 4D9C 4D9E 4D9F
• 分子名称: D-cysteine desulfhydrase, BENZAMIDINE, SERINE, ... (5 entities in total)
• 機能のキーワード: fold type ii plp-dependent enzyme, tryptophan synthase beta subunit-like plp-dependent enzymes superfamily, lyase
• 由来する生物種: Salmonella typhimurium
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 147919.19

構造登録者

Bharath, S.R.,Shveta, B.,Rajesh, K.H.,Savithri, H.S.,Murthy, M.R.N. (登録日: 2012-01-11, 公開日: 2012-05-30, 最終更新日: 2023-12-06)

主引用文献

Bharath, S.R.,Bisht, S.,Harijan, R.K.,Savithri, H.S.,Murthy, M.R.N.
Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase.
Plos One, 7:e36267-e36267, 2012

PubMed Abstract: Salmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H(2)S and pyruvate. It also efficiently degrades β-chloro-D-alanine (βCDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, βCDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 Å. The polypeptide fold of StDCyD consisting of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and βCDA show the product, pyruvate, bound at a site 4.0-6.0 Å away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at Cα proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for Cα proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed.

PubMed: 22574144
DOI: 10.1371/journal.pone.0036267

実験手法

X-RAY DIFFRACTION (2.01 Å)