4RYF

ClpP1/2 heterocomplex from Listeria monocytogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and mechanism of the caseinolytic protease ClpP1/2 heterocomplex from Listeria monocytogenes.

Dahmen, M.Vielberg, M.T.Groll, M.Sieber, S.A.

(2015) Angew Chem Int Ed Engl 54: 3598-3602

  • DOI: https://doi.org/10.1002/anie.201409325
  • Primary Citation of Related Structures:  
    4RYF

  • PubMed Abstract: 

    Listeria monocytogenes is a devastating bacterial pathogen. Its virulence and intracellular stress tolerance are supported by caseinolytic protease P (ClpP), an enzyme that is conserved among bacteria. L. monocytogenes expresses two ClpP isoforms that are only distantly related by sequence and differ in catalysis, oligomerization, active-site composition, and N-terminal interaction sites for associated AAA(+) chaperones. The crystal structure of the ClpP1/2 heterocomplex from L. monocytogenes was solved, and in combination with biochemical studies, it provides insights into the mode of action. The results demonstrate that structural interlocking of LmClpP1 with LmClpP2 leads to the formation of a tetradecamer, aligns all 14 active sites, and enhances proteolytic activity. Furthermore, the catalytic center was identified as being responsible for the transient stability of ClpPs.


  • Organizational Affiliation

    Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstr. 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
A, B, C, D, E
A, B, C, D, E, F, G
201Listeria monocytogenesMutation(s): 0 
Gene Names: clpP
EC: 3.4.21.92
UniProt
Find proteins for Q8Y7Y1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y7Y1 
Go to UniProtKB:  Q8Y7Y1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y7Y1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
H, I, J, K, L
H, I, J, K, L, M, N
204Listeria monocytogenesMutation(s): 0 
Gene Names: clpP
EC: 3.4.21.92
UniProt
Find proteins for Q9RQI6 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q9RQI6 
Go to UniProtKB:  Q9RQI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RQI6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
BA [auth K]
DA [auth L]
FA [auth M]
HA [auth N]
V [auth H]
BA [auth K],
DA [auth L],
FA [auth M],
HA [auth N],
V [auth H],
X [auth I],
Z [auth J]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth J]
CA [auth K]
EA [auth L]
GA [auth M]
IA [auth N]
AA [auth J],
CA [auth K],
EA [auth L],
GA [auth M],
IA [auth N],
O [auth A],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
T [auth F],
U [auth G],
W [auth H],
Y [auth I]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.23α = 90
b = 127.15β = 90
c = 265.5γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description