7VGE

Structure of the PDZ deleted variant of HtrA2 protease (S306A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.269 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inter-subunit crosstalk via PDZ synergistically governs allosteric activation of proapoptotic HtrA2.

Parui, A.L.Mishra, V.Dutta, S.Bhaumik, P.Bose, K.

(2022) Structure 30: 1307-1320.e5

  • DOI: https://doi.org/10.1016/j.str.2022.06.001
  • Primary Citation of Related Structures:  
    7VGE

  • PubMed Abstract: 

    The mitochondrial serine protease High-temperature requirement A2 (HtrA2) is associated with various diseases including neurodegenerative disorders and cancer. Despite availability of structural details, the reports on HtrA2's mechanistic regulation that varies with the type of activation signals still remain non-concordant. To expound the role of regulatory PDZ (Postsynaptic density-95/Discs large/Zonula occludens-1) domains in multimodal activation of HtrA2, we generated heterotrimeric HtrA2 variants comprising different numbers of PDZs and/or active-site mutations. Sequential deletion of PDZs from the trimeric ensemble significantly affected its residual activity in a way that proffered a hypothesis advocating inter-molecular allosteric crosstalk via PDZs in HtrA2. Furthermore, structural and computational snapshots affirmed the role of PDZs in secondary structural element formation around the regulatory loops and coordinated reorganization of the N-terminal region. Therefore, apart from providing cues for devising structure-guided therapeutic strategies, this study establishes a physiologically relevant working model of complex allosteric regulation through a trans-mediated cooperatively shared energy landscape.


  • Organizational Affiliation

    Integrated Biophysics and Structural Biology Lab, ACTREC - Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai 400094, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease HTRA2, mitochondrial
A, B, C
203Homo sapiensMutation(s): 1 
Gene Names: HTRA2OMIPRSS25
EC: 3.4.21.108
UniProt & NIH Common Fund Data Resources
Find proteins for O43464 (Homo sapiens)
Explore O43464 
Go to UniProtKB:  O43464
PHAROS:  O43464
GTEx:  ENSG00000115317 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43464
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease HTRA2, mitochondrial
D, F
202Homo sapiensMutation(s): 1 
Gene Names: HTRA2OMIPRSS25
EC: 3.4.21.108
UniProt & NIH Common Fund Data Resources
Find proteins for O43464 (Homo sapiens)
Explore O43464 
Go to UniProtKB:  O43464
PHAROS:  O43464
GTEx:  ENSG00000115317 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43464
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease HTRA2, mitochondrial201Homo sapiensMutation(s): 1 
Gene Names: HTRA2OMIPRSS25
EC: 3.4.21.108
UniProt & NIH Common Fund Data Resources
Find proteins for O43464 (Homo sapiens)
Explore O43464 
Go to UniProtKB:  O43464
PHAROS:  O43464
GTEx:  ENSG00000115317 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43464
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.269 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.88α = 90
b = 82.88β = 90
c = 395.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/HRD/NWBA/37/01/2015

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2022-09-14
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description