5ILB

Crystal structure of protease domain of Deg2 linked with the PDZ domain of Deg9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of Deg9 reveals a novel octameric-type HtrA protease

Ouyang, M.Li, X.Zhao, S.Pu, H.Shen, J.Adam, Z.Clausen, T.Zhang, L.

(2017) Nat Plants 3: 973-982

  • DOI: 10.1038/s41477-017-0060-2
  • Primary Citation of Related Structures:  
    5IL9, 5ILA, 5ILB, 5JYK

  • PubMed Abstract: 
  • The high temperature requirement A (HtrA) proteases (also termed Deg proteases) play important roles in diverse organisms by regulating protein quality and quantity. One of the 16 Arabidopsis homologs, Deg9, is located in the nucleus where it modulates cytokinin- and light-mediated signalling via degrading the ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4) ...

    The high temperature requirement A (HtrA) proteases (also termed Deg proteases) play important roles in diverse organisms by regulating protein quality and quantity. One of the 16 Arabidopsis homologs, Deg9, is located in the nucleus where it modulates cytokinin- and light-mediated signalling via degrading the ARABIDOPSIS RESPONSE REGULATOR 4 (ARR4). To uncover the structural features underlying the proteolytic activity of Deg9, we determined its crystal structure. Unlike the well-established trimeric building block of HtrAs, Deg9 displays a novel octameric structure consisting of two tetrameric rings that have distinct conformations. Based on the structural architecture, we generated several mutant variants of Deg9, determined their structure and tested their proteolytic activity towards ARR4. The results of the structural and biochemical analyses allowed us to propose a model for a novel mechanism of substrate recognition and activity regulation of Deg9. In this model, protease activation of one tetramer is mediated by en-bloc reorientation of the protease domains to open an entrance for the substrate in the opposite (inactive) tetramer. This study provides the structural basis for understanding how the levels of nuclear signal components are regulated by a plant protease.


    Organizational Affiliation

    College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China. Zhanglixin@ibcas.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protease Do-like 2, chloroplastic,Protease Do-like 9A, B474Arabidopsis thalianaMutation(s): 0 
Gene Names: DEGP2At2g47940F17A22.33T9J23.7DEGP9At5g40200MSN9.10MSN9.100
EC: 3.4.21
UniProt
Find proteins for Q9FL12 (Arabidopsis thaliana)
Explore Q9FL12 
Go to UniProtKB:  Q9FL12
Find proteins for O82261 (Arabidopsis thaliana)
Explore O82261 
Go to UniProtKB:  O82261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO82261Q9FL12
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.093α = 90
b = 106.093β = 90
c = 255.956γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2017-12-20
    Changes: Database references