2QA9

Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2

2QA9 の概要

• エントリーDOI: 10.2210/pdb2qa9/pdb
• 分子名称: Streptogrisin-B, 4-mer peptide DAIY, CHLORIDE ION, ... (7 entities in total)
• 機能のキーワード: chymotrypsin-type serine peptidase, second tetrahedral intermediate, tetrapeptide, beta barrels, alpha helix, hydrolase
• 由来する生物種: Streptomyces griseus; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 19737.14

構造登録者

Lee, T.W.,James, M.N.G. (登録日: 2007-06-14, 公開日: 2007-12-11, 最終更新日: 2024-11-13)

主引用文献

Lee, T.W.,James, M.N.
1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB).
Biochim.Biophys.Acta, 1784:319-334, 2008

PubMed Abstract: Streptogrisin B (SGPB) has served as one of the models for studying the catalytic activities of serine peptidases. Here we report its native crystal structures at pH 4.2 at a resolution of 1.18A, and at pH 7.3 at a resolution of 1.23A. Unexpectedly, outstanding electron density peaks occurred in the active site and the substrate-binding region of SGPB in the computed maps at both pHs. The densities at pH 4.2 were assigned as a tetrapeptide, Asp-Ala-Ile-Tyr, whereas those at pH 7.3 were assigned as a tyrosine molecule and a leucine molecule existing at equal occupancies in both of the SGPB molecules in the asymmetric unit. Refinement with relaxed geometric restraints resulted in molecular structures representing mixtures of the second tetrahedral intermediates and the enzyme-product complexes of SGPB existing in a pH-dependent equilibrium. Structural comparisons with the complexes of SGPB with turkey ovomucoid third domain (OMTKY3) and its variants have shown that, upon the formation of the tetrahedral intermediate, residues Glu192A to Gly193 of SGPB move towards the alpha-carboxylate O of residue P1 of the bound species, and adjustments in the side-chain conformational angles of His57 and Ser195 of SGPB favor the progression of the catalytic mechanism of SGPB.

PubMed: 18157955
DOI: 10.1016/j.bbapap.2007.11.012

実験手法

X-RAY DIFFRACTION (1.18 Å)