3QO6

Crystal structure analysis of the plant protease Deg1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural adaptation of the plant protease Deg1 to repair photosystem II during light exposure.

Kley, J.Schmidt, B.Boyanov, B.Stolt-Bergner, P.C.Kirk, R.Ehrmann, M.Knopf, R.R.Naveh, L.Adam, Z.Clausen, T.

(2011) Nat.Struct.Mol.Biol. 18: 728-731

  • DOI: 10.1038/nsmb.2055

  • PubMed Abstract: 
  • Deg1 is a chloroplastic protease involved in maintaining the photosynthetic machinery. Structural and biochemical analyses reveal that the inactive Deg1 monomer is transformed into the proteolytically active hexamer at acidic pH. The change in pH is ...

    Deg1 is a chloroplastic protease involved in maintaining the photosynthetic machinery. Structural and biochemical analyses reveal that the inactive Deg1 monomer is transformed into the proteolytically active hexamer at acidic pH. The change in pH is sensed by His244, which upon protonation, repositions a specific helix to trigger oligomerization. This system ensures selective activation of Deg1 during daylight, when acidification of the thylakoid lumen occurs and photosynthetic proteins are damaged.


    Organizational Affiliation

    Research Institute of Molecular Pathology (IMP), Vienna, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease Do-like 1, chloroplastic
A, B, C
348Arabidopsis thalianaGene Names: DEGP1 (DEG1, DEGP)
EC: 3.4.21.-
Find proteins for O22609 (Arabidopsis thaliana)
Go to UniProtKB:  O22609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide
D
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
peptide
E, H, I
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
peptide
F
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
peptide
G
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
D, E, F, G, H, I
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.215 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 126.135α = 90.00
b = 126.135β = 90.00
c = 328.303γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
ADSCdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-02-09 
  • Released Date: 2011-05-04 
  • Deposition Author(s): Clausen, T.

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-09-05
    Type: Derived calculations