Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.12 kDa 
• Atom Count: 5675 
• Residue Count: 709 
• Unique protein chains: 1

1L8X

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

• DOI: 10.2210/pdb1L8X/pdb

• Classification: LYASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-03-22 Released: 2002-11-20 
• Deposition Author(s): Karlberg, T., Lecerof, D., Gora, M., Silvegren, G., Labbe-Bois, R., Hansson, M., Al-Karadaghi, S.

---

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 

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

• PubMed: 12427010 
• DOI: 10.1021/bi0260785
• Structures With Same Primary Citation


• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ferrochelatase	A, B	362	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: HEMZ EC: 4.99.1.1
Find proteins for P16622 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P16622

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	A, B	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

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 = 84.38	α = 90
b = 96.66	β = 90
c = 120.7	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
XDS	data reduction
CNS	refinement
XDS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-22 
• Released Date: 2002-11-20 
Deposition Author(s): Karlberg, T., Lecerof, D., Gora, M., Silvegren, G., Labbe-Bois, R., Hansson, M., Al-Karadaghi, S.

Revision History 

• 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