5DZK

Crystal structure of the active form of the proteolytic complex clpP1 and clpP2

5DZK の概要

• エントリーDOI: 10.2210/pdb5dzk/pdb
• 関連するBIRD辞書のPRD_ID: PRD_002200
• 分子名称: ATP-dependent Clp protease proteolytic subunit 2, BEZ-LEU-LEU, ATP-dependent Clp protease proteolytic subunit 1, ... (4 entities in total)
• 機能のキーワード: hydrolase
• 由来する生物種: Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh); 詳細
• 細胞内の位置: Cytoplasm : P9WPC2 P9WPC4
• タンパク質・核酸の鎖数: 56
• 化学式量合計: 643822.09

構造登録者

LI, M.,Wlodawer, A.,Maurizi, M. (登録日: 2015-09-25, 公開日: 2016-02-17, 最終更新日: 2025-04-02)

主引用文献

Li, M.,Kandror, O.,Akopian, T.,Dharkar, P.,Wlodawer, A.,Maurizi, M.R.,Goldberg, A.L.
Structure and Functional Properties of the Active Form of the Proteolytic Complex, ClpP1P2, from Mycobacterium tuberculosis.
J.Biol.Chem., 291:7465-7476, 2016

PubMed Abstract: The ClpP protease complex and its regulatory ATPases, ClpC1 and ClpX, inMycobacterium tuberculosis(Mtb) are essential and, therefore, promising drug targets. TheMtbClpP protease consists of two heptameric rings, one composed of ClpP1 and the other of ClpP2 subunits. Formation of the enzymatically active ClpP1P2 complex requires binding of N-blocked dipeptide activators. We have found a new potent activator, benzoyl-leucine-leucine (Bz-LL), that binds with higher affinity and promotes 3-4-fold higher peptidase activity than previous activators. Bz-LL-activated ClpP1P2 specifically stimulates the ATPase activity ofMtbClpC1 and ClpX. The ClpC1P1P2 and ClpXP1P2 complexes exhibit 2-3-fold enhanced ATPase activity, peptide cleavage, and ATP-dependent protein degradation. The crystal structure of ClpP1P2 with bound Bz-LL was determined at a resolution of 3.07 Å and with benzyloxycarbonyl-Leu-Leu (Z-LL) bound at 2.9 Å. Bz-LL was present in all 14 active sites, whereas Z-LL density was not resolved. Surprisingly, Bz-LL adopts opposite orientations in ClpP1 and ClpP2. In ClpP1, Bz-LL binds with the C-terminal leucine side chain in the S1 pocket. One C-terminal oxygen is close to the catalytic serine, whereas the other contacts backbone amides in the oxyanion hole. In ClpP2, Bz-LL binds with the benzoyl group in the S1 pocket, and the peptide hydrogen bonded between parallel β-strands. The ClpP2 axial loops are extended, forming an open axial channel as has been observed with bound ADEP antibiotics. Thus occupancy of the active sites of ClpP allosterically alters sites on the surfaces thereby affecting the association of ClpP1 and ClpP2 rings, interactions with regulatory ATPases, and entry of protein substrates.

PubMed: 26858247
DOI: 10.1074/jbc.M115.700344

実験手法

X-RAY DIFFRACTION (3.07 Å)