5T69

The HhoA protease from Synechocystis sp. PCC 6803, active site mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The HhoA protease from Synechocystis sp. PCC 6803 - Novel insights into structure and activity regulation.

Hall, M.Wagner, R.Lam, X.T.Funk, C.Persson, K.

(2017) J Struct Biol 198: 147-153

  • DOI: https://doi.org/10.1016/j.jsb.2016.12.004
  • Primary Citation of Related Structures:  
    5T63, 5T69

  • PubMed Abstract: 

    Proteases play a vital role in the removal of proteins, which become damaged due to temperature or oxidative stress. Important to this process in the cyanobacterium Synechocystis sp. PCC6803 is the family of Deg/HtrA proteases; HhoA (sll1679), HhoB (sll1427) and HtrA (slr1204). While previous studies have elucidated the structures of Deg/HtrA proteases from Escherichia coli and from the chloroplast of the higher plant Arabidopsis thaliana, no structural data have been available for any Deg/HtrA protease from cyanobacteria, the evolutionary ancestor of the chloroplast. To gain a deeper insight into the molecular mechanisms and regulation of these proteins we have solved the structure of the Synechocystis HhoA protease in complex with a co-purified peptide by X-ray crystallography. HhoA assembles into stable trimers, mediated by its protease domain and further into a cage-like hexamer by a novel interaction between the PDZ domains of opposing trimers. Each PDZ domain contains two loops for PDZ-PDZ formation: interaction clamp one and two (IC1, IC2). IC1 interacts with IC2 on the opposing PDZ domain and vice versa. Our structure shows a peptide bound to a conserved groove on the PDZ domain and the properties of this pocket suggest that it binds substrate proteins as well as the neo C-termini of cleaved substrates. In agreement with previous studies showing the proteolytic activity of HhoA to be activated by Ca 2+ or Mg 2+ , binding of divalent metal ions to the central channel of the trimer by the L1 activation loop was observed.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative serine protease HhoA367Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 1 
Gene Names: hhoAsll1679
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
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.276α = 90
b = 134.276β = 90
c = 115.29γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Energy AgencySweden2012-005889
formasSweden2013-2014-1504
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description