5B3I

Homo-dimeric structure of cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Structural and functional insights into thermally stable cytochrome c' from a thermophile

Fujii, S.Oki, H.Kawahara, K.Yamane, D.Yamanaka, M.Maruno, T.Kobayashi, Y.Masanari, M.Wakai, S.Nishihara, H.Ohkubo, T.Sambongi, Y.

(2017) Protein Sci 26: 737-748

  • DOI: https://doi.org/10.1002/pro.3120
  • Primary Citation of Related Structures:  
    5B3I

  • PubMed Abstract: 

    Thermophilic Hydrogenophilus thermoluteolus cytochrome c' (PHCP) exhibits higher thermal stability than a mesophilic counterpart, Allochromatium vinosum cytochrome c' (AVCP), which has a homo-dimeric structure and ligand-binding ability. To understand the thermal stability mechanism and ligand-binding ability of the thermally stable PHCP protein, the crystal structure of PHCP was first determined. It formed a homo-dimeric structure, the main chain root mean square deviation (rmsd) value between PHCP and AVCP being 0.65 Å. In the PHCP structure, six specific residues appeared to strengthen the heme-related and subunit-subunit interactions, which were not conserved in the AVCP structure. PHCP variants having altered subunit-subunit interactions were more severely destabilized than ones having altered heme-related interactions. The PHCP structure further revealed a ligand-binding channel and a penta-coordinated heme, as observed in the AVCP protein. A spectroscopic study clearly showed that some ligands were bound to the PHCP protein. It is concluded that the dimeric PHCP from the thermophile is effectively stabilized through heme-related and subunit-subunit interactions with conservation of the ligand-binding ability. We report the X-ray crystal structure of cytochrome c' (PHCP) from thermophilic Hydrogenophilus thermoluteolus. The high thermal stability of PHCP was attributed to heme-related and subunit-subunit interactions, which were confirmed by a mutagenesis study. The ligand-binding ability of PHCP was examined by spectrophotometry. PHCP acquired the thermal stability with conservation of the ligand-binding ability. This study furthers the understanding of the stability and function of cytochromes c.


  • Organizational Affiliation

    Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c prime
A, B, C, D
135Hydrogenophilus thermoluteolusMutation(s): 0 
UniProt
Find proteins for F7J213 (Hydrogenophilus thermoluteolus)
Explore F7J213 
Go to UniProtKB:  F7J213
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7J213
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.243α = 90
b = 72.923β = 90
c = 132.365γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 2.0: 2019-10-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-10-16
    Changes: Structure summary