1L8X

Crystal Structure of Ferrochelatase from the Yeast, Saccharomyces cerevisiae, with Cobalt(II) as the Substrate Ion

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

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

  • DOI: 10.1021/bi0260785
  • Primary Citation of Related Structures:  
    1L8X, 1LBQ

  • 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 complex with Co(II), a substrate metal ion, and in complex with two inhibitors, Cd(II) and Hg(I), are presented in this work ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FerrochelataseA, B362Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HEMZ
EC: 4.99.1.1
UniProt
Find proteins for P16622 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P16622 
Go to UniProtKB:  P16622
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16622
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.38α = 90
b = 96.66β = 90
c = 120.7γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection, Refinement description