6P41

Yeast cytochrome c peroxidase (W191Y:L232E) in complex with iso-1 cytochrome c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping.

Yee, E.F.Dzikovski, B.Crane, B.R.

(2019) J Am Chem Soc 141: 17571-17587

  • DOI: https://doi.org/10.1021/jacs.9b05715
  • Primary Citation of Related Structures:  
    6P41, 6P42, 6P43

  • PubMed Abstract: 

    Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase, and many other proteins. However, Tyr and Trp are not functionally interchangeable, and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191 •+ radical to oxidize reduced cytochrome c ( Cc ). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc . Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191 (via Leu232His or Glu) substantially alters activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191 by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191 formal potential of ∼200 mV in the presence of E232. Hence, Y191 inactivity results from a potential drop owing to Y191 •+ deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr potential into a range where it can effectively oxidize Cc . These findings have implications for the Y Z /Y D radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c peroxidase, mitochondrial
A, C
294Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: CCP1CCPCPOYKR066C
EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00431
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c iso-1
B, D
103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CYC1YJR048WJ1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00044 
Go to UniProtKB:  P00044
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00044
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.803α = 90
b = 112.07β = 104.64
c = 88.327γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description