8OLL | pdb_00008oll

Staphylococcus aureus ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.7 A resolution

PDB DOI: https://doi.org/10.2210/pdb8OLL/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-30 Released: 2023-12-06
Deposition Author(s): Illigmann, A., Vielberg, M.-T., Lakemeyer, M., Wolf, F., Staudt, N., Dema, T., Stange, P., Malik, I., Grond, S., Sieber, S.A., Groll, M., Kaysser, L., Broetz-Oesterhelt, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.258 (Depositor), 0.259 (DCC)
R-Value Work:
0.224 (Depositor), 0.226 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of Staphylococcus aureus ClpP Bound to the Covalent Active-Site Inhibitor Cystargolide A.

Illigmann, A., Vielberg, M.T., Lakemeyer, M., Wolf, F., Dema, T., Stange, P., Kuttenlochner, W., Liebhart, E., Kulik, A., Staudt, N.D., Malik, I., Grond, S., Sieber, S.A., Kaysser, L., Groll, M., Brotz-Oesterhelt, H.

(2024) Angew Chem Int Ed Engl 63: e202314028-e202314028

PubMed: 38029352 Search on PubMed
DOI: https://doi.org/10.1002/anie.202314028
Primary Citation Related Structures:
8OLL, 8OLR, 8R03, 8R04, 8R05

PubMed Abstract:
The caseinolytic protease is a highly conserved serine protease, crucial to prokaryotic and eukaryotic protein homeostasis, and a promising antibacterial and anticancer drug target. Herein, we describe the potent cystargolides as the first natural β-lactone inhibitors of the proteolytic core ClpP. Based on the discovery of two clpP genes next to the cystargolide biosynthetic gene cluster in Kitasatospora cystarginea, we explored ClpP as a potential cystargolide target. We show the inhibition of Staphylococcus aureus ClpP by cystargolide A and B by different biochemical methods in vitro. Synthesis of semisynthetic derivatives and probes with improved cell penetration allowed us to confirm ClpP as a specific target in S. aureus cells and to demonstrate the anti-virulence activity of this natural product class. Crystal structures show cystargolide A covalently bound to all 14 active sites of ClpP from S. aureus, Aquifex aeolicus, and Photorhabdus laumondii, and reveal the molecular mechanism of ClpP inhibition by β-lactones, the predominant class of ClpP inhibitors.

Organizational Affiliation

Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.

Macromolecule Content

Total Structure Weight: 642.63 kDa
Atom Count: 40,791
Modeled Residue Count: 5,156
Deposited Residue Count: 5,684
Unique protein chains: 1

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	203	Staphylococcus aureus	Mutation(s): 0 Gene Names: clpP, SAR0823 EC: 3.4.21.92
UniProt
Find proteins for Q2G036 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G036 Go to UniProtKB: Q2G036
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G036
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VSZ (Subject of Investigation/LOI) Query on VSZ Download:Ideal Coordinates CCD File SDF format, chain AB [auth Y] SDF format, chain BB [auth Z] SDF format, chain CA [auth A] SDF format, chain CB [auth a] SDF format, chain DA [auth B] SDF format, chain DB [auth b] SDF format, chain EA [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth F] SDF format, chain IA [auth G] SDF format, chain JA [auth H] SDF format, chain KA [auth I] SDF format, chain LA [auth J] SDF format, chain MA [auth K] SDF format, chain NA [auth L] SDF format, chain OA [auth M] SDF format, chain PA [auth N] SDF format, chain QA [auth O] SDF format, chain RA [auth P] SDF format, chain SA [auth Q] SDF format, chain TA [auth R] SDF format, chain UA [auth S] SDF format, chain VA [auth T] SDF format, chain WA [auth U] SDF format, chain XA [auth V] SDF format, chain YA [auth W] SDF format, chain ZA [auth X] MOL2 format, chain AB [auth Y] MOL2 format, chain BB [auth Z] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth a] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth b] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain MA [auth K] MOL2 format, chain NA [auth L] MOL2 format, chain OA [auth M] MOL2 format, chain PA [auth N] MOL2 format, chain QA [auth O] MOL2 format, chain RA [auth P] MOL2 format, chain SA [auth Q] MOL2 format, chain TA [auth R] MOL2 format, chain UA [auth S] MOL2 format, chain VA [auth T] MOL2 format, chain WA [auth U] MOL2 format, chain XA [auth V] MOL2 format, chain YA [auth W] MOL2 format, chain ZA [auth X] mmCIF format, chain AB [auth Y] mmCIF format, chain BB [auth Z] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth a] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth b] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth J] mmCIF format, chain MA [auth K] mmCIF format, chain NA [auth L] mmCIF format, chain OA [auth M] mmCIF format, chain PA [auth N] mmCIF format, chain QA [auth O] mmCIF format, chain RA [auth P] mmCIF format, chain SA [auth Q] mmCIF format, chain TA [auth R] mmCIF format, chain UA [auth S] mmCIF format, chain VA [auth T] mmCIF format, chain WA [auth U] mmCIF format, chain XA [auth V] mmCIF format, chain YA [auth W] mmCIF format, chain ZA [auth X]	AB [auth Y] BB [auth Z] CA [auth A] CB [auth a] DA [auth B] AB [auth Y], BB [auth Z], CA [auth A], CB [auth a], DA [auth B], DB [auth b], EA [auth C], FA [auth D], GA [auth E], HA [auth F], IA [auth G], JA [auth H], KA [auth I], LA [auth J], MA [auth K], NA [auth L], OA [auth M], PA [auth N], QA [auth O], RA [auth P], SA [auth Q], TA [auth R], UA [auth S], VA [auth T], WA [auth U], XA [auth V], YA [auth W], ZA [auth X]	Cystargolide A (bound) C₁₈ H₃₂ N₂ O₆ NPCIMWWVLQVJPA-YYFQZIEXSA-N		Interactions Focus chain AB [auth Y] Focus chain BB [auth Z] Focus chain CA [auth A] Focus chain CB [auth a] Focus chain DA [auth B] Focus chain DB [auth b] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain MA [auth K] Focus chain NA [auth L] Focus chain OA [auth M] Focus chain PA [auth N] Focus chain QA [auth O] Focus chain RA [auth P] Focus chain SA [auth Q] Focus chain TA [auth R] Focus chain UA [auth S] Focus chain VA [auth T] Focus chain WA [auth U] Focus chain XA [auth V] Focus chain YA [auth W] Focus chain ZA [auth X] Interactions & Density Focus chain AB [auth Y] Focus chain BB [auth Z] Focus chain CA [auth A] Focus chain CB [auth a] Focus chain DA [auth B] Focus chain DB [auth b] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain GA [auth E] Focus chain HA [auth F] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain MA [auth K] Focus chain NA [auth L] Focus chain OA [auth M] Focus chain PA [auth N] Focus chain QA [auth O] Focus chain RA [auth P] Focus chain SA [auth Q] Focus chain TA [auth R] Focus chain UA [auth S] Focus chain VA [auth T] Focus chain WA [auth U] Focus chain XA [auth V] Focus chain YA [auth W] Focus chain ZA [auth X]