1KY9 | pdb_00001ky9

Crystal Structure of DegP (HtrA)

• PDB DOI: https://doi.org/10.2210/pdb1KY9/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-02-04 Released: 2002-04-03 
• Deposition Author(s): Krojer, T., Garrido-Franco, M., Huber, R., Ehrmann, M., Clausen, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.275 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine.

Krojer, T., Garrido-Franco, M., Huber, R., Ehrmann, M., Clausen, T.

(2002) Nature 416: 455-459

• PubMed: 11919638 
• DOI: https://doi.org/10.1038/416455a
• Primary Citation Related Structures: 
  1KY9


• PubMed Abstract: 
  

  Molecular chaperones and proteases monitor the folded state of other proteins. In addition to recognizing non-native conformations, these quality control factors distinguish substrates that can be refolded from those that need to be degraded. To investigate the molecular basis of this process, we have solved the crystal structure of DegP (also known as HtrA), a widely conserved heat shock protein that combines refolding and proteolytic activities. The DegP hexamer is formed by staggered association of trimeric rings. The proteolytic sites are located in a central cavity that is only accessible laterally. The mobile side-walls are constructed by twelve PDZ domains, which mediate the opening and closing of the particle and probably the initial binding of substrate. The inner cavity is lined by several hydrophobic patches that may act as docking sites for unfolded polypeptides. In the chaperone conformation, the protease domain of DegP exists in an inactive state, in which substrate binding in addition to catalysis is abolished.

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Organizational Affiliation: 
• Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18A, 82152 Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 95.02 kDa 
• Atom Count: 5,366 
• Modeled Residue Count: 707 
• Deposited Residue Count: 896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE DO	A, B	448	Escherichia coli	Mutation(s): 15  Gene Names: degP EC: 3.4.21 (PDB Primary Data), 3.4.21.107 (UniProt)
UniProt
Find proteins for P0C0V0 (Escherichia coli (strain K12)) Explore P0C0V0  Go to UniProtKB:  P0C0V0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.275 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.374	α = 90
b = 121.374	β = 90
c = 233.667	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-03 
Deposition Author(s): Krojer, T., Garrido-Franco, M., Huber, R., Ehrmann, M., Clausen, T.

Revision History  

• Version 1.0: 2002-04-03
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary