7MRI

Crystal structure of N63T yeast iso-1-cytochrome c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Literature

Effect on intrinsic peroxidase activity of substituting coevolved residues from Omega-loop C of human cytochrome c into yeast iso-1-cytochrome c.

Frederick, A.K.Thompson, S.L.Vakharia, Z.M.Cherney, M.M.Lei, H.Evenson, G.Bowler, B.E.

(2022) J Inorg Biochem 232: 111819-111819

  • DOI: 10.1016/j.jinorgbio.2022.111819
  • Primary Citation of Related Structures:  
    7MRI

  • PubMed Abstract: 
  • Naturally-occurring variants of human cytochrome c (Cytc) that induce thrombocytopenia IV occur within Ω-loop C (residues 40-57). These variants enhance the peroxidase activity of human Cytc apparently by facilitating access to the heme by destabilizing Ω-loops C and D (residues 70-85) ...

    Naturally-occurring variants of human cytochrome c (Cytc) that induce thrombocytopenia IV occur within Ω-loop C (residues 40-57). These variants enhance the peroxidase activity of human Cytc apparently by facilitating access to the heme by destabilizing Ω-loops C and D (residues 70-85). Given the importance of peroxidase activity in the early stages of apoptosis, we identified three sites with the EVmutation algorithm in or near Ω-loop C that coevolve and differ between yeast iso-1-Cytc and human Cytc. We prepared iso-1-Cytc variants with all possible combinations of the S40T, V57I and N63T substitutions to determine if these residues decrease the peroxidase activity of iso-1-Cytc to that of human Cytc producing an effective off state for a peroxidase signaling switch. At pH 6 and above, all variants significantly decreased peroxidase activity. However, the correlation of peroxidase activity with local and global stability, expected if cooperative unfolding of Ω-loops C and D is required for peroxidase activity, was generally poor. The m-values derived from the guanidine hydrochloride dependence of the kinetics of imidazole binding to horse Cytc, which is well-characterized by native-state hydrogen exchange methods, and K72A/K73A/K79A iso-1-Cytc show that local structural fluctuations and not subglobal cooperative unfolding of Ω-loops C and D are sufficient to permit binding of a small molecule like peroxide to the heme. A 2.46 Å structure of N63T iso-1-Cytc identifies a change to a hydrogen bond network linking Ω-loops C and D that could modulate the local fluctuations needed for the intrinsic peroxidase activity of Cytc.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States. Electronic address: bruce.bowler@umontana.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c isoform 1A,
B [auth C],
C [auth E]
107Saccharomyces 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
D [auth A],
E [auth C],
F [auth E]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.25α = 90
b = 59.25β = 90
c = 92.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1904895
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM103546

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release