5B6L

Structure of Deg protease HhoA from Synechocystis sp. PCC 6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the zinc-bound HhoA protease from Synechocystis sp. PCC 6803

Dong, W.Wang, J.Niu, G.Zhao, S.Liu, L.

(2016) FEBS Lett 590: 3435-3442

  • DOI: https://doi.org/10.1002/1873-3468.12416
  • Primary Citation of Related Structures:  
    5B6L, 5GND

  • PubMed Abstract: 

    The high temperature requirement A (HtrA) proteases are oligomeric serine proteases essential for protein quality control. HtrA homolog A (HhoA) from the photosynthetic cyanobacterium Synechocystis sp. PCC 6803 assembles into a proteolytically active hexamer. Herein, we present the crystal structure of the hexameric HhoA in complex with the copurified peptide. Our data indicate the presence of three methionines in close proximity to the peptide-binding site of the PDZ domain. Unexpectedly, we observed that a zinc ion is accommodated within the central channel formed by a HhoA trimer. However, neither calcium nor magnesium showed affinity for HhoA. The role of the zinc ion in HhoA was tested in an in vitro proteolytic assay against the nonspecific substrate β-casein and was found to be inhibitory. Our findings provide insights into the regulation of HhoA by a redox-related mechanism involving methionine residues and by zinc ion-binding within the central channel.


  • Organizational Affiliation

    Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative serine protease HhoA348Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: hhoA
UniProt
Find proteins for P72780 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P72780 
Go to UniProtKB:  P72780
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72780
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-UNK-UNK-UNK-TRPB [auth U]5Escherichia coli BL21(DE3)Mutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.359α = 90
b = 135.359β = 90
c = 114.386γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description