1LD3

Crystal Structure of B. subilis ferrochelatase with Zn(2+) bound at the active site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites

Lecerof, D.Fodje, M.N.Leon, R.A.Olsson, U.Hansson, A.Sigfridsson, E.Ryde, U.Hansson, M.Al-Karadaghi, S.

(2003) J.Biol.Inorg.Chem. 8: 452-458

  • DOI: 10.1007/s00775-002-0436-1
  • Primary Citation of Related Structures:  1N0I

  • PubMed Abstract: 
  • Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyses metal insertion into protoporphyrin IX. The location of the metal binding site with respect to the bound porphyrin substrate and the mode of metal binding are of central importance f ...

    Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyses metal insertion into protoporphyrin IX. The location of the metal binding site with respect to the bound porphyrin substrate and the mode of metal binding are of central importance for understanding the mechanism of porphyrin metallation. In this work we demonstrate that Zn(2+), which is commonly used as substrate in assays of the ferrochelatase reaction, and Cd(2+), an inhibitor of the enzyme, bind to the invariant amino acids His183 and Glu264 and water molecules, all located within the porphyrin binding cleft. On the other hand, Mg(2+), which has been shown to bind close to the surface at 7 A from His183, was largely absent from its site. Activity measurements demonstrate that Mg(2+) has a stimulatory effect on the enzyme, lowering K(M) for Zn(2+) from 55 to 24 micro M. Changing one of the Mg(2+) binding residues, Glu272, to serine abolishes the effect of Mg(2+). It is proposed that prior to metal insertion the metal may form a sitting-atop (SAT) complex with the invariant His-Glu couple and the porphyrin. Metal binding to the Mg(2+) site may stimulate metal release from the protein ligands and its insertion into the porphyrin.


    Organizational Affiliation

    Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, PO Box 124, 221 00 Lund, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferrochelatase
A
310Bacillus subtilis (strain 168)Gene Names: hemH (hemF)
EC: 4.99.1.1
Find proteins for P32396 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P32396
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.636α = 90.00
b = 49.876β = 90.00
c = 118.532γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CNSphasing
MAR345data collection
CNSrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    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