6H23 | pdb_00006h23

Crystal structure of the hClpP Y118A mutant with an activating small molecule

PDB DOI: https://doi.org/10.2210/pdb6H23/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-07-13 Released: 2018-08-29
Deposition Author(s): Kick, L.M., Sieber, S.A., Schneider, S.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free:
0.261 (Depositor), 0.263 (DCC)
R-Value Work:
0.215 (Depositor), 0.218 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Selective Activation of Human Caseinolytic Protease P (ClpP).

Stahl, M., Korotkov, V.S., Balogh, D., Kick, L.M., Gersch, M., Pahl, A., Kielkowski, P., Richter, K., Schneider, S., Sieber, S.A.

(2018) Angew Chem Int Ed Engl 57: 14602-14607

PubMed: 30129683 Search on PubMed
DOI: https://doi.org/10.1002/anie.201808189
Primary Citation Related Structures:
6H23

PubMed Abstract:
Caseinolytic protease P (ClpP) is the proteolytic component of the ClpXP protein degradation complex. Eukaryotic ClpP was recently found to act within the mitochondria-specific unfolded protein response (UPR ^mt ). However, its detailed function and dedicated regulation remain largely unexplored. A small molecule (D9) acts as a potent and species-selective activator of human ClpP (hClpP) by mimicking the natural chaperone ClpX. Structure-activity relationship studies highlight the importance of a halogenated benzyl motif within D9 that interacts with a unique aromatic amino acid network in hClpP. Mutational and structural studies suggest that this YYW motif tightly controls hClpP activity and regulates substrate turnover by interaction with cognate ligands. This signature motif is unique to ClpP from higher organisms and does not exist in tested bacterial homologues, allowing a species-selective analysis. Thus, D9 is a versatile tool to analyze mechanistic features of hClpP.

Organizational Affiliation

Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany.

Macromolecule Content

Total Structure Weight: 357.66 kDa
Atom Count: 18,505
Modeled Residue Count: 2,328
Deposited Residue Count: 3,206
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, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	229	Homo sapiens	Mutation(s): 1 Gene Names: CLPP EC: 3.4.21.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q16740 (Homo sapiens) Explore Q16740 Go to UniProtKB: Q16740
PHAROS: Q16740 GTEx: ENSG00000125656
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16740
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FJT Query on FJT Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain Y [auth H] SDF format, chain X [auth G] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth B] SDF format, chain O [auth A] SDF format, chain EA [auth M] SDF format, chain DA [auth M] SDF format, chain CA [auth L] SDF format, chain BA [auth K] SDF format, chain AA [auth J] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth G] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth A] MOL2 format, chain EA [auth M] MOL2 format, chain DA [auth M] MOL2 format, chain CA [auth L] MOL2 format, chain BA [auth K] MOL2 format, chain AA [auth J] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth G] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth A] mmCIF format, chain EA [auth M] mmCIF format, chain DA [auth M] mmCIF format, chain CA [auth L] mmCIF format, chain BA [auth K] mmCIF format, chain AA [auth J]	AA [auth J] BA [auth K] CA [auth L] DA [auth M] EA [auth M] AA [auth J], BA [auth K], CA [auth L], DA [auth M], EA [auth M], O [auth A], Q [auth B], R [auth D], S [auth D], T [auth E], V [auth F], X [auth G], Y [auth H], Z [auth H]	~{N}-(1,3-benzodioxol-5-ylmethyl)-5-[(2-chloranyl-4-fluoranyl-phenyl)methyl]-1,3,4-oxadiazole-2-carboxamide C₁₈ H₁₃ Cl F N₃ O₄ DDGOMXRMDQDHAN-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth M] Focus chain EA [auth M] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth M] Focus chain EA [auth M] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain P [auth A] SDF format, chain FA [auth N] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain P [auth A] MOL2 format, chain FA [auth N] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain P [auth A] mmCIF format, chain FA [auth N]	FA [auth N], P [auth A], U [auth E], W [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth N] Focus chain P [auth A] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain FA [auth N] Focus chain P [auth A] Focus chain U [auth E] Focus chain W [auth F]

Binding Affinity Annotations
ID	Source	Binding Affinity
FJT	BindingDB: 6H23	EC50: 1.10e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.261 (Depositor), 0.263 (DCC)
R-Value Work: 0.215 (Depositor), 0.218 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.504	α = 90
b = 97.153	β = 93.53
c = 127.249	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
XDS	data scaling
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-29

Deposition Author(s):

Kick, L.M.

Sieber, S.A.

Schneider, S.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	ClpP SI1096/8-1
German Research Foundation	Germany	SCHN1273/6-1
German Research Foundation	Germany	SFB1035
German Research Foundation	Germany	CIPSM