7P81 | pdb_00007p81

Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compact state)

PDB DOI: https://doi.org/10.2210/pdb7P81/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-21 Released: 2022-06-29
Deposition Author(s): Lee, B.-G., Kim, L., Kim, M.K., Kwon, D.H., Song, H.K.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.290 (Depositor), 0.290 (DCC)
R-Value Work:
0.235 (Depositor), 0.235 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis.

Kim, L., Lee, B.G., Kim, M., Kim, M.K., Kwon, D.H., Kim, H., Brotz-Oesterhelt, H., Roh, S.H., Song, H.K.

(2022) EMBO J 41: e109755-e109755

PubMed: 35593068 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.15252/embj.2021109755
Primary Citation Related Structures:
7FEP, 7FEQ, 7FER, 7FES, 7P80, 7P81

PubMed Abstract:
The ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause the dysregulation and activation of ClpP without ATPases and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed its structural details, conformational changes, and activation mechanism. Although product release through side exit pores has been proposed, the detailed driving force for product release remains elusive. Herein, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures of BsClpP revealed various conformational states under different pH conditions. To understand the conformational change required for product release, we investigated the relationship between substrate hydrolysis and the pH-lowering process. The production of hydrolyzed peptides from acidic and basic substrates by proteinase K and BsClpP lowered the pH values. Our data, together with those of previous findings, provide insight into the molecular mechanism of product release by the ClpP self-compartmentalizing protease.

Organizational Affiliation

Department of Life Sciences, Korea University, Seoul, South Korea.

Macromolecule Content

Total Structure Weight: 633.55 kDa
Atom Count: 38,248
Modeled Residue Count: 4,944
Deposited Residue Count: 5,712
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	199	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: clpP, yvdN, BSU34540 EC: 3.4.21.92
UniProt
Find proteins for P80244 (Bacillus subtilis (strain 168)) Explore P80244 Go to UniProtKB: P80244
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80244
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADEP2	CA [auth c] DA [auth d] EA [auth e] FA [auth f] GA [auth g] CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth t], TA [auth u], UA [auth v], VA [auth w]	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MP8 Query on MP8	CA [auth c] DA [auth d] EA [auth e] FA [auth f] GA [auth g] CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth t], TA [auth u], UA [auth v], VA [auth w]	L-PEPTIDE LINKING	C₆ H₁₁ N O₂		PRO
WFP Query on WFP	CA [auth c] DA [auth d] EA [auth e] FA [auth f] GA [auth g] CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth t], TA [auth u], UA [auth v], VA [auth w]	L-PEPTIDE LINKING	C₉ H₉ F₂ N O₂		PHE
YCP Query on YCP	CA [auth c] DA [auth d] EA [auth e] FA [auth f] GA [auth g] CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth t], TA [auth u], UA [auth v], VA [auth w]	L-PEPTIDE LINKING	C₆ H₁₁ N O₂		--

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000504 Query on PRD_000504	CA [auth c] DA [auth d] EA [auth e] FA [auth f] GA [auth g] CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth t], TA [auth u], UA [auth v], VA [auth w]	ADEP2	Cyclic depsipeptide / Antibiotic		Interactions Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth t] Focus chain TA [auth u] Focus chain UA [auth v] Focus chain VA [auth w] Interactions & Density Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth t] Focus chain TA [auth u] Focus chain UA [auth v] Focus chain VA [auth w]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.290 (Depositor), 0.290 (DCC)
R-Value Work: 0.235 (Depositor), 0.235 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.979	α = 90
b = 173.075	β = 91.66
c = 160.001	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1A2C3008285
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1A5A1019023
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021M3A9I4030068