2IFW

Crystal structure of scytalido-glutamic peptidase with a transition state analog inhibitor

2IFW の概要

• エントリーDOI: 10.2210/pdb2ifw/pdb
• 関連するPDBエントリー: 1S2B 1S2K
• 分子名称: Scytalidopepsin B, Heptapeptide, ACETIC ACID, ... (5 entities in total)
• 機能のキーワード: enzyme-inhibitor complex, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: Scytalidium lignicola
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 45268.26

構造登録者

Pillai, B.,Cherney, M.M.,Hiraga, K.,Takada, K.,Oda, K.,James, M.N. (登録日: 2006-09-21, 公開日: 2006-10-03, 最終更新日: 2023-08-30)

主引用文献

Pillai, B.,Cherney, M.M.,Hiraga, K.,Takada, K.,Oda, K.,James, M.N.
Crystal structure of scytalidoglutamic peptidase with its first potent inhibitor provides insights into substrate specificity and catalysis.
J.Mol.Biol., 365:343-361, 2007

PubMed Abstract: Scytalidoglutamic peptidase (SGP) from Scytalidium lignicolum is the founding member of the newly discovered\ family of peptidases, G1, so far found exclusively in fungi. The crystal structure of SGP revealed a previously undescribed fold for peptidases and a unique catalytic dyad of residues Gln53 and Glu136. Surprisingly, the beta-sandwich structure of SGP is strikingly similar to members of the carbohydrate-binding concanavalin A-like lectins/glucanases superfamily. By analogy with the active sites of aspartic peptidases, a mechanism employing nucleophillic attack by a water molecule activated by the general base functionality of Glu136 has been proposed. Here, we report the first crystal structures of SGP in complex with two transition state peptide analogs designed to mimic the tetrahedral intermediate of the proteolytic reaction. Of these two analogs, the one containing a central S-hydroxyl group is a potent sub-nanomolar inhibitor of SGP. The inhibitor binds non-covalently to the concave surface of the upper beta-sheet and enables delineation of the S4 to S3' substrate specificity pockets of the enzyme. Structural differences in these pockets account for the unique substrate preferences of SGP among peptidases having an acidic pH optimum. Inhibitor binding is accompanied by a structuring of the region comprising residues Tyr71-Gly80 from being mostly disordered in the apoenzyme and leading to positioning of crucial active site residues for establishing enzyme-inhibitor contacts. In addition, conformational rearrangements are seen in a disulfide bridged surface loop (Cys141-Cys148), which moves inwards, partially closing the open substrate binding cleft of the native enzyme. The non-hydrolysable scissile bond analog of the inhibitor is located in the active site forming close contacts with Gln53 and Glu136. The nucleophilic water molecule is displaced and a unique mode of binding is observed with the S-OH of the inhibitor occupying the oxyanion binding site of the proposed tetrahedral intermediate. Details of the enzyme-inhibitor interactions and mechanistic interpretations are discussed.

PubMed: 17069854
DOI: 10.1016/j.jmb.2006.09.058

実験手法

X-RAY DIFFRACTION (2.3 Å)