6H23

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.215 

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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

  • DOI: https://doi.org/10.1002/anie.201808189
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
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
229Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16740
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FJT
Query on FJT

Download Ideal Coordinates CCD File 
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
FA [auth N],
P [auth A],
U [auth E],
W [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.504α = 90
b = 97.153β = 93.53
c = 127.249γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyClpP SI1096/8-1
German Research FoundationGermanySCHN1273/6-1
German Research FoundationGermanySFB1035
German Research FoundationGermanyCIPSM

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references