1MDV

KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Key role of phenylalanine 20 in cytochrome c3: structure, stability, and function studies.

Dolla, A.Arnoux, P.Protasevich, I.Lobachov, V.Brugna, M.Giudici-Orticoni, M.T.Haser, R.Czjzek, M.Makarov, A.Bruschi, M.

(1999) Biochemistry 38: 33-41

  • DOI: 10.1021/bi981593h

  • PubMed Abstract: 
  • Aromatic residues in c-type cytochromes might have an important function in the folding and/or electron transferring properties of the molecule. In the tetraheme cytochrome c3 (Mr 13 000) from Desulfovibrio vulgaris Hildenborough, Phe20, is located b ...

    Aromatic residues in c-type cytochromes might have an important function in the folding and/or electron transferring properties of the molecule. In the tetraheme cytochrome c3 (Mr 13 000) from Desulfovibrio vulgaris Hildenborough, Phe20, is located between heme 1 and heme 3 with its aromatic ring close and almost parallel to the ring plane of heme 1. We replaced this residue by a nonaromatic hydrophobe residue, leucine, and analyzed the effects in terms of functional, structural, and physicochemical properties. While the F20L replacement did not have any strong effects on the heme region stability, a decrease of the thermostability of the whole molecule was observed. In the same way, the four macroscopic redox potentials were affected by the mutation as well as the flexibility of the surface loop around heme 4. The F20L replacement itself and/or this structural modification might be responsible for the loss of the intermolecular cooperativity between F20L cytochrome c3 molecules.


    Related Citations: 
    • Effects of Amino Acid Substitution on Three-Dimensional Structure: An X-Ray Analysis of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 2 A Resolution
      Morimoto, Y.,Tani, T.,Okumura, H.,Higuchi, Y.,Yasuoka, N.
      (1991) J.Biochem.(Tokyo) 110: 532
    • Structure Analysis of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.9 A Resolution
      Matias, P.M.,Frazao, C.,Morais, J.,Coll, M.,Carrondo, M.A.
      (1993) J.Mol.Biol. 234: 680


    Organizational Affiliation

    Laboratoire de Bioénergétique et Ingénierie des protéines, UPR 9036 C.N.R.S., Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C3
A, B
107Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)N/A
Find proteins for P00131 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303))
Go to UniProtKB:  P00131
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.224 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 97.220α = 90.00
b = 97.220β = 90.00
c = 36.030γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance