Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

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Unveiling a Hidden Folding Intermediate in c-Type Cytochromes by Protein Engineering

Borgia, A.Bonivento, D.Travaglini-Allocatelli, C.Di Matteo, A.Brunori, M.

(2006) J Biol Chem 281: 9331-9336

  • DOI: https://doi.org/10.1074/jbc.M512127200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Several investigators have highlighted a correlation between the basic features of the folding process of a protein and its topology, which dictates the folding pathway. Within this conceptual framework we proposed that different members of the cytochrome c (cyt c) family share the same folding mechanism, involving a consensus partially structured state. Pseudomonas aeruginosa cyt c(551) (Pa cyt c(551)) folds via an apparent two-state mechanism through a high energy intermediate. Here we present kinetic evidence demonstrating that it is possible to switch its folding mechanism from two to three state, stabilizing the high energy intermediate by rational mutagenesis. Characterization of the folding kinetics of one single-site mutant of the Pa cyt c(551) (Phe(7) to Ala) indeed reveals an additional refolding phase and a fast unfolding process which are explained by the accumulation of a partially folded species. Further kinetic analysis highlights the presence of two parallel processes both leading to the native state, suggesting that the above mentioned species is a non obligatory on-pathway intermediate. Determination of the crystallographic structure of F7A shows the presence of an extended internal cavity, which hosts three "bound" water molecules and a H-bond in the N-terminal helix, which is shorter than in the wild type protein. These two features allow us to propose a detailed structural interpretation for the stabilization of the native and especially the intermediate states induced by a single crucial mutation. These results show how protein engineering, x-ray crystallography and state-of-the-art kinetics concur to unveil a folding intermediate and the structural determinants of its stability.

  • Organizational Affiliation

    Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche, Università di Roma "La Sapienza," P.le A. Moro 5, 00185 Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-551A,
B [auth C]
82Pseudomonas aeruginosaMutation(s): 1 
Gene Names: nirM
Find proteins for P00099 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P00099 
Go to UniProtKB:  P00099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00099
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.766α = 90
b = 66.766β = 90
c = 62.462γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations