7OB1

OLIGOPEPTIDASE B FROM S. PROTEOMACULANS WITH MODIFIED HINGE

「6TF5」から置き換えられました

7OB1 の概要

• エントリーDOI: 10.2210/pdb7ob1/pdb
• 分子名称: Oligopeptidase B, SPERMINE (3 entities in total)
• 機能のキーワード: peptidase, hydrolase
• 由来する生物種: Serratia proteamaculans
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 79471.55

構造登録者

Petrenko, D.E.,Nikolaeva, A.Y.,Lazarenko, V.A.,Dorovatovskiy, P.V.,Vlaskina, A.V.,Korzhenevskiy, D.A.,Mikhailova, A.G.,Rakitina, T.V.,Timofeev, V.I. (登録日: 2021-04-20, 公開日: 2021-05-19, 最終更新日: 2024-01-31)

主引用文献

Petrenko, D.E.,Timofeev, V.I.,Britikov, V.V.,Britikova, E.V.,Kleymenov, S.Y.,Vlaskina, A.V.,Kuranova, I.P.,Mikhailova, A.G.,Rakitina, T.V.
First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine.
Biology (Basel), 10:-, 2021

PubMed Abstract: Oligopeptidase B (OpB) is a two-domain, trypsin-like serine peptidase belonging to the S9 prolyloligopeptidase (POP) family. Two domains are linked by a hinge region that participates in the transition of the enzyme between two major states-closed and open-in which domains and residues of the catalytic triad are located close to each other and separated, respectively. In this study, we described, for the first time, a structure of OpB from bacteria obtained for an enzyme from with a modified hinge region (PSPmod). PSPmod was crystallized in a conformation characterized by a disruption of the catalytic triad together with a domain arrangement intermediate between open and closed states found in crystals of ligand-free and inhibitor-bound POP, respectively. Two additional derivatives of PSPmod were crystallized in the same conformation. Neither wild-type PSP nor its corresponding mutated variants were susceptible to crystallization, indicating that the hinge region modification was key in the crystallization process. The second key factor was suggested to be polyamine spermine since all crystals were grown in its presence. The influences of the hinge region modification and spermine on the conformational state of PSP in solution were evaluated by small-angle X-ray scattering. SAXS showed that, in solution, wild-type PSP adopted the open state, spermine caused the conformational transition to the intermediate state, and spermine-free PSPmod contained molecules in the open and intermediate conformations in dynamic equilibrium.

PubMed: 34681120
DOI: 10.3390/biology10101021

実験手法

X-RAY DIFFRACTION (2 Å)