Y48H mutant of human cytochrome c

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

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Heightened Dynamics of the Oxidized Y48H Variant of Human Cytochrome c Increases Its Peroxidatic Activity.

Deacon, O.M.Karsisiotis, A.I.Moreno-Chicano, T.Hough, M.A.Macdonald, C.Blumenschein, T.M.A.Wilson, M.T.Moore, G.R.Worrall, J.A.R.

(2017) Biochemistry 56: 6111-6124

  • DOI: https://doi.org/10.1021/acs.biochem.7b00890
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Proteins performing multiple biochemical functions are called "moonlighting proteins" or extreme multifunctional (EMF) proteins. Mitochondrial cytochrome c is an EMF protein that binds multiple partner proteins to act as a signaling molecule, transfers electrons in the respiratory chain, and acts as a peroxidase in apoptosis. Mutations in the cytochrome c gene lead to the disease thrombocytopenia, which is accompanied by enhanced apoptotic activity. The Y48H variant arises from one such mutation and is found in the 40-57 Ω-loop, the lowest-unfolding free energy substructure of the cytochrome c fold. A 1.36 Å resolution X-ray structure of the Y48H variant reveals minimal structural changes compared to the wild-type structure, with the axial Met80 ligand coordinated to the heme iron. Despite this, the intrinsic peroxidase activity is enhanced, implying that a pentacoordinate heme state is more prevalent in the Y48H variant, corroborated through determination of a Met80 "off rate" of >125 s -1 compared to a rate of ∼6 s -1 for the wild-type protein. Heteronuclear nuclear magnetic resonance measurements with the oxidized Y48H variant reveal heightened dynamics in the 40-57 Ω-loop and the Met80-containing 71-85 Ω-loop relative to the wild-type protein, illustrating communication between these substructures. Placed into context with the G41S cytochrome c variant, also implicated in thrombocytopenia, a dynamic picture associated with this disease relative to cytochrome c is emerging whereby increasing dynamics in substructures of the cytochrome c fold serve to facilitate an increased population of the peroxidatic pentacoordinate heme state in the following order: wild type < G41S < Y48H.

  • Organizational Affiliation

    School of Biological Sciences, University of Essex , Wivenhoe Park, Colchester CO4 3SQ, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c
A, B
104Homo sapiensMutation(s): 1 
Gene Names: CYCSCYC
UniProt & NIH Common Fund Data Resources
Find proteins for P99999 (Homo sapiens)
Explore P99999 
Go to UniProtKB:  P99999
PHAROS:  P99999
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP99999
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.36 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.937α = 90
b = 36.498β = 116.65
c = 60.7γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Leverhulme TrustUnited KingdomRPG-2013-164

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release