2HK6

Crystal Structure of B. subtilis ferrochelatase with Iron bound at the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Amino Acid Residues His183 and Glu264 in Bacillus subtilis Ferrochelatase Direct and Facilitate the Insertion of Metal Ion into Protoporphyrin IX

Hansson, M.D.Karlberg, T.Rahardja, M.A.Al-Karadaghi, S.Hansson, M.

(2007) Biochemistry 46: 87-94

  • DOI: 10.1021/bi061760a
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ferrochelatase catalyzes the terminal step in the heme biosynthetic pathway, i.e., the incorporation of Fe(II) into protoporphyrin IX. Various biochemical and biophysical methods have been used to probe the enzyme for metal binding residues and the l ...

    Ferrochelatase catalyzes the terminal step in the heme biosynthetic pathway, i.e., the incorporation of Fe(II) into protoporphyrin IX. Various biochemical and biophysical methods have been used to probe the enzyme for metal binding residues and the location of the active site. However, the location of the metal binding site and the path of the metal into the porphyrin are still disputed. Using site-directed mutagenesis on Bacillus subtilis ferrochelatase we demonstrate that exchange of the conserved residues His183 and Glu264 affects the metal affinity of the enzyme. We also present the first X-ray crystal structure of ferrochelatase with iron. Only a single iron was found in the active site, coordinated in a square pyramidal fashion by two amino acid residues, His183 and Glu264, and three water molecules. This iron was not present in the structure of a His183Ala modified ferrochelatase. The results strongly suggest that the insertion of a metal ion into protoporphyrin IX by ferrochelatase occurs from a metal binding site represented by His183 and Glu264.


    Organizational Affiliation

    Department of Biochemistry and Department of Molecular Biophysics, Lund University, Box 124, 221 00 Lund, Sweden. matthias.hansson@biochemistry.lu.se



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FerrochelataseA310Bacillus subtilisMutation(s): 0 
Gene Names: hemHhemF
EC: 4.99.1.1 (PDB Primary Data), 4.99.1.9 (UniProt)
Find proteins for P32396 (Bacillus subtilis (strain 168))
Explore P32396 
Go to UniProtKB:  P32396
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.65α = 90
b = 49.98β = 90
c = 118.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection