Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 116.42 kDa 
• Atom Count: 7728 
• Residue Count: 1014 
• Unique protein chains: 1

4IC6

Crystal structure of Deg8

• DOI: 10.2210/pdb4IC6/pdb

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


• Deposited: 2012-12-10 Released: 2013-05-01 
• Deposition Author(s): Gong, W., Sun, W., Fan, H., Gao, F., Liu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

The structures of Arabidopsis Deg5 and Deg8 reveal new insights into HtrA proteases

Sun, W., Gao, F., Fan, H., Shan, X., Sun, R., Liu, L., Gong, W.

(2013) Acta Crystallogr D Biol Crystallogr 69: 830-837

• PubMed: 23633592 
• DOI: 10.1107/S0907444913002023
• Primary Citation of Related Structures:  
  4IC6, 4IC5


• PubMed Abstract: 
  

Plant Deg5 and Deg8 are two members of the HtrA proteases, a family of oligomeric serine endopeptidases that are involved in a variety of protein quality-control processes. These two HtrA proteases are located in the thylakoid lumen and participate in high-light stress responses by collaborating with other chloroplast proteins. Deg5 and Deg8 degrade photodamaged D1 protein of the photosystem II reaction centre, allowing its in situ replacement. Here, the crystal structures of Arabidopsis thaliana Deg5 (S266A) and Deg8 (S292A) are reported at 2.6 and 2.0 Å resolution, respectively. The Deg5 trimer contains two calcium ions in a central channel, suggesting a link between photodamage control and calcium ions in chloroplasts. Previous structures of HtrA proteases have indicated that their regulation usually requires C-terminal PDZ domain(s). Deg5 is unique in that it contains no PDZ domain and the trimeric structure of Deg5 (S266A) reveals a novel catalytic triad conformation. A similar triad conformation is observed in the hexameric structure of the single PDZ-domain-containing Deg8 (S292A). These findings suggest a novel activation mechanism for plant HtrA proteases and provide structural clues to their function in light-stress response.

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Organizational Affiliation: 

Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease Do-like 8, chloroplastic	A, B, C	368	Arabidopsis thaliana	Mutation(s): 1  Gene Names: DEGP8, At5g39830, K13H13.1 EC: 3.4.21
Find proteins for Q9LU10 (Arabidopsis thaliana) Explore Q9LU10  Go to UniProtKB:  Q9LU10

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.475	α = 90
b = 124.175	β = 132.41
c = 93.274	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-10 
• Released Date: 2013-05-01 
Deposition Author(s): Gong, W., Sun, W., Fan, H., Gao, F., Liu, L.

Revision History 

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references