6A9U

Crystal strcture of Icp55 from Saccharomyces cerevisiae bound to apstatin inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function.

Singh, R.Goyal, V.D.Kumar, A.Sabharwal, N.S.Makde, R.D.

(2019) FEBS Lett 593: 443-454

  • DOI: https://doi.org/10.1002/1873-3468.13321
  • Primary Citation of Related Structures:  
    6A9T, 6A9U, 6A9V

  • PubMed Abstract: 

    Intermediate cleavage peptidase (Icp55) processes a subset of mitochondrial matrix proteins by removing a bulky residue at their N termini, leaving behind smaller N-terminal residues (icp activity). This contributes towards the stability of the mitochondrial proteome. We report crystal structures of yeast Icp55 including one bound to the apstatin inhibitor. Apart from icp activity, the enzyme was found to exhibit Xaa-Pro aminopeptidase activity in vitro. Structural and biochemical data suggest that the enzyme exists in a rapid equilibrium between monomer and dimer. Furthermore, the dimer, and not the monomer, was found to be the active species with loop dynamics at the dimer interface playing an important role in activity. Based on the new evidence, we propose a model for binding and processing of cellular targets by Icp55. DATABASE: The atomic coordinates and structure factors for the structures of Icp55 (code 6A9T, 6A9U, 6A9V) have been deposited in the Protein Data Bank (PDB) (http://www.pdb.org/).


  • Organizational Affiliation

    High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intermediate cleaving peptidase 55455Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: ICP55YER078C
EC: 3.4.11.26
UniProt
Find proteins for P40051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40051 
Go to UniProtKB:  P40051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40051
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
apstatin5PolypodiopsidaMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.089α = 90
b = 148.089β = 90
c = 124.989γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-11-22
    Changes: Refinement description