3QO6

Crystal structure analysis of the plant protease Deg1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.228 

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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease Do-like 1, chloroplasticA, B, C348Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g27925DEG1DEGPDEGP1K16N12.18
EC: 3.4.21
Find proteins for O22609 (Arabidopsis thaliana)
Explore O22609 
Go to UniProtKB:  O22609
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptideD7unidentifiedMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
peptideE, H, I4unidentifiedMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
peptideF5unidentifiedMutation(s): 0 
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
peptideG3unidentifiedMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.228 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.135α = 90
b = 126.135β = 90
c = 328.303γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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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
    Changes: Version format compliance
  • Version 1.2: 2012-09-05
    Changes: Derived calculations