1LBQ

The crystal structure of Saccharomyces cerevisiae ferrochelatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Metal binding to Saccharomyces cerevisiae ferrochelatase

Karlberg, T.Lecerof, D.Gora, M.Silvegren, G.Labbe-Bois, R.Hansson, M.Al-Karadaghi, S.

(2002) Biochemistry 41: 13499-13506

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ferrochelatase is the terminal enzyme in the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into protoporphyrin IX to produce protoheme IX. The crystal structures of ferrochelatase from Saccharomyces cerevisiae in free form, in ...

    Ferrochelatase is the terminal enzyme in the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into protoporphyrin IX to produce protoheme IX. The crystal structures of ferrochelatase from Saccharomyces cerevisiae in free form, in complex with Co(II), a substrate metal ion, and in complex with two inhibitors, Cd(II) and Hg(I), are presented in this work. The enzyme is a homodimer, with clear asymmetry between the monomers with regard to the porphyrin binding cleft and the mode of metal binding. The Co(II) and Cd(II) complexes reveal the metal binding site which consists of the invariant amino acids H235, E314, and S275 and solvent molecules. The shortest distance to the metal reveals that amino acid H235 is the primary metal binding residue. A second site with bound Cd(II) was found close to the surface of the molecule, approximately 14 A from H235, with E97, H317, and E326 participating in metal coordination. It is suggested that this site corresponds to the magnesium binding site in Bacillus subtilis ferrochelatase. The latter site is also located at the surface of the molecule and thought to be involved in initial metal binding and regulation.


    Organizational Affiliation

    Department of Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferrochelatase
A, B
362Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: HEM15
EC: 4.99.1.1
Find proteins for P16622 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16622
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.610α = 90.00
b = 97.169β = 90.00
c = 121.574γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CNSphasing
CNSrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-20
    Type: Initial release
  • Version 1.1: 2008-05-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Data collection, Refinement description