8E5W

Crystal structure of dehydroalanine Hip1

8E5W の概要

• エントリーDOI: 10.2210/pdb8e5w/pdb
• 関連するPDBエントリー: 5BKM 5UNO
• 分子名称: Protease, PALMITIC ACID, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: serine protease hip1, hydrolase
• 由来する生物種: Mycobacterium tuberculosis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 52782.08

構造登録者

Goldfarb, N.E.,Brooks, C.L.,Ostrov, D.A. (登録日: 2022-08-22, 公開日: 2022-12-07, 最終更新日: 2023-10-25)

主引用文献

Brooks, C.L.,Ostrov, D.A.,Schumann, N.C.,Kakkad, S.,Li, D.,Pena, K.,Williams, B.P.,Goldfarb, N.E.
2.1 angstrom crystal structure of the Mycobacterium tuberculosis serine hydrolase, Hip1, in its anhydro-form (Anhydrohip1).
Biochem.Biophys.Res.Commun., 630:57-63, 2022

PubMed Abstract: The 2.6 Å crystal structure of the apo form of Hip1 (hydrolase important for pathogenesis) has been previously reported. However, very little is known about the active site architecture of this M. tuberculosis (Mtb), serine hydrolase drug target. To begin mapping the active site of Hip1, we cocrystallized Hip1 with the irreversible serine protease inhibitor, 4-(2-aminoethyl)-benzenesulfonylfluoride (AEBSF). We chose AEBSF for cocrystallization with Hip1 since the similar inhibitor, phenylmethylsulfonyl fluoride (PMSF), interestingly exhibited no activity against Hip1. We obtained crystals that diffracted to 2.1 Å but to our bewilderment, we did not observe any electron density for the inhibitor in the omit map for the Hip1-AEBSF complex. Rather, in the active site, dehydroalanine (dAla) was found to occupy the expected position of the catalytic Ser228, thus yielding anhydrohip1. Here we present a comparative analysis of the crystal structures of anhydrohip1 and Hip1 and provide a mechanism for the conversion of the enzyme to the anhydro-form through reaction with AEBSF. With the aid of molecular docking, we propose an explanation for the differential inhibition of Hip1 by AEBSF and PMSF. We also present a preliminary definition of the S1 and S2 pockets of the protease's active site and propose a mechanism for a ligand-induced conformational change within the S2 pocket. Finally, we expand upon the previous demarcation of the putative lipid binding pocket in the α-domain of the enzyme. We believe that this detailed analysis of the structures of anhydrohip1 and Hip1 provides valuable information useful for the structure-based drug design of novel Hip1-directed Mtb therapeutics.

PubMed: 36148729
DOI: 10.1016/j.bbrc.2022.09.021

実験手法

X-RAY DIFFRACTION (2.15 Å)