3HCP

Human ferrochelatase with Mn and deuteroporphyrin bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Product release rather than chelation determines metal specificity for ferrochelatase.

Medlock, A.E.Carter, M.Dailey, T.A.Dailey, H.A.Lanzilotta, W.N.

(2009) J Mol Biol 393: 308-319

  • DOI: 10.1016/j.jmb.2009.08.042
  • Primary Citation of Related Structures:  
    3HCN, 3HCO, 3HCP, 3HCR

  • PubMed Abstract: 
  • Ferrochelatase (protoheme ferrolyase, E.C. 4.99.1.1) is the terminal enzyme in heme biosynthesis and catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme IX (heme). Within the past two years, X-ray crystallographic data obtained with human ferrochelatase have clearly shown that significant structural changes occur during catalysis that are predicted to facilitate metal insertion and product release ...

    Ferrochelatase (protoheme ferrolyase, E.C. 4.99.1.1) is the terminal enzyme in heme biosynthesis and catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme IX (heme). Within the past two years, X-ray crystallographic data obtained with human ferrochelatase have clearly shown that significant structural changes occur during catalysis that are predicted to facilitate metal insertion and product release. One unanswered question about ferrochelatase involves defining the mechanism whereby some metals, such as divalent Fe, Co, Ni, and Zn, can be used by the enzyme in vitro to produce the corresponding metalloporphyrins, while other metals, such as divalent Mn, Hg, Cd, or Pb, are inhibitors of the enzyme. Through the use of high-resolution X-ray crystallography along with characterization of metal species via their anomalous diffraction, the identity and position of Hg, Cd, Ni, or Mn in the center of enzyme-bound porphyrin macrocycle were determined. When Pb, Hg, Cd, or Ni was present in the macrocycle, the conserved pi helix was in the extended, partially unwound "product release" state. Interestingly, in the structure of ferrochelatase with Mn-porphyrin bound, the pi helix is not extended or unwound and is in the "substrate-bound" conformation. These findings show that at least in the cases of Mn, Pb, Cd, and Hg, metal "inhibition" of ferrochelatase is not due to the inability of the enzyme to insert the metal into the macrocycle or by binding to a second metal binding site as has been previously proposed. Rather, inhibition occurs after metal insertion and results from poor or diminished product release. Possible explanations for the lack of product release are proposed herein.


    Organizational Affiliation

    Biomedical and Health Sciences Institute, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, 30602, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferrochelatase, mitochondrialA, B359Homo sapiensMutation(s): 1 
Gene Names: FECH
EC: 4.99.1.1
Find proteins for P22830 (Homo sapiens)
Explore P22830 
Go to UniProtKB:  P22830
NIH Common Fund Data Resources
PHAROS:  P22830
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDE
Query on FDE

Download Ideal Coordinates CCD File 
H [auth A], M [auth B]FE(III) DEUTEROPORPHYRIN IX
C30 H28 Fe N4 O4
QQYZTXBVPVYDJC-ZECKXRTNDU
 Ligand Interaction
CHD
Query on CHD

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], J [auth B], K [auth B]CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
C [auth A], I [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
G [auth A], L [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.574α = 90
b = 93.687β = 90
c = 109.483γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description