Ferrochelatase

 

Ferrochelatase (protoheme ferrolyase) catalyses the terminal step in heme biosynthesis, the insertion of ferrous iron into protoporphyrin IX to form protoheme IX (heme). In eukaryotes, the enzyme is nuclear encoded, synthesised in the cytoplasm, and translocated to the mitochondrion where it is proteolytically processed to its mature size of 42 kDa. Within the mitochondria, ferrochelatase is associated with the inner mitochondrial membrane with the active site facing the mitochondrial matrix.

 

Reference Protein and Structure

Sequence
P22830 UniProt (4.99.1.1) IPR001015 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1hrk - CRYSTAL STRUCTURE OF HUMAN FERROCHELATASE (2.0 Å) PDBe PDBsum 1hrk
Catalytic CATH Domains
3.40.50.1400 CATHdb (see all for 1hrk)
Click To Show Structure

Enzyme Reaction (EC:4.99.1.1)

iron(2+)
CHEBI:29033ChEBI
+
protoporphyrin(2-)
CHEBI:57306ChEBI
→
ferroheme b(2-)
CHEBI:60344ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Ferro-protoporphyrin chelatase, Heme synthase, Heme synthetase, Iron chelatase, Protoheme ferro-lyase, Ferrochelatase,

Enzyme Mechanism

Introduction

Fe begins being coordinated to Glu343, His 263 and two water molecules. The bond between Fe and Glu343 is broken, Fe immediately forms a new bond with one of the unprotonated nitrogens of the porphyrin ring. Glu343 deprotonates one of the nitrogens of the porphyrin ring allowing the second Fe-N bond to be formed. One of the water molecules dissociates from Fe. The bond between His263 and Fe breaks allowing the third Fe-N bond to be formed. His263 deprotonates the final nitrogen of the porphyrin ring allowing the fourth Fe-N bond to be formed.The second water molecule dissociates from Fe. Leaving Fe bound to the porphyrin ring.

Catalytic Residues Roles

UniProt PDB* (1hrk)
Arg164, Tyr165 Arg164(100)A, Tyr165(101)A Associated with bringing the metal ion in. Mutagenesis has proved lower affinity for iron but not for the porphyrin substrate.
His263, Glu343 His263(199)A, Glu343(279)A Primarily a general base to deprotonate the pyrrole ring, the proton is then passed down a proton shuttle. metal ligand, proton acceptor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

decoordination from a metal ion, coordination, overall reactant used, rate-determining step, proton transfer, overall product formed

References

  1. Wang Y et al. (2009), J Inorg Biochem, 103, 1680-1686. QM/MM study of the insertion of metal ion into protoporphyrin IX by ferrochelatase. DOI:10.1016/j.jinorgbio.2009.09.013. PMID:19850353.
  2. Wu J et al. (2016), J Chem Inf Model, 56, 2421-2433. Human Ferrochelatase: Insights for the Mechanism of Ferrous Iron Approaching Protoporphyrin IX by QM/MM and QTCP Free Energy Studies. DOI:10.1021/acs.jcim.6b00216. PMID:27801584.
  3. Sellers VM et al. (2001), Biochemistry, 40, 9821-9827. Human Ferrochelatase:  Characterization of Substrate−Iron Binding and Proton-Abstracting Residues†. DOI:10.1021/bi010012c. PMID:11502175.
  4. Wu CK et al. (2001), Nat Struct Biol, 8, 156-160. The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis. DOI:10.1038/84152. PMID:11175906.

Step 1. The bond between Fe and Glu343 is broken, Fe immediately forms a new bond with one of the unprotonated nitrogens of the porphyrin ring.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His263(199)A metal ligand
Glu343(279)A metal ligand

Chemical Components

decoordination from a metal ion, coordination, overall reactant used, rate-determining step

Step 2. Glu343 deprotonates one of the nitrogens of the porphyrin ring allowing the second Fe-N bond to be formed. One of the water molecules dissociates from Fe.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His263(199)A metal ligand
Glu343(279)A proton acceptor

Chemical Components

proton transfer, coordination, decoordination from a metal ion

Step 3. The bond between His263 and Fe breaks allowing the third Fe-N bond to be formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His263(199)A metal ligand

Chemical Components

decoordination from a metal ion, coordination

Step 4. His263 deprotonates the final nitrogen of the porphyrin ring allowing the fourth Fe-N bond to be formed.The second water molecule dissociates from Fe.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His263(199)A proton acceptor

Chemical Components

coordination, proton transfer, overall product formed, decoordination from a metal ion
Download: Image, Marvin File

Step 1. The bond between Fe and Glu343 is broken, Fe immediately forms a new bond with one of the unprotonated nitrogens of the porphyrin ring.

Step 2. Glu343 deprotonates one of the nitrogens of the porphyrin ring allowing the second Fe-N bond to be formed. One of the water molecules dissociates from Fe.

Step 3. The bond between His263 and Fe breaks allowing the third Fe-N bond to be formed.

Step 4. His263 deprotonates the final nitrogen of the porphyrin ring allowing the fourth Fe-N bond to be formed.The second water molecule dissociates from Fe.

Products.

Contributors

Anna Waters, Craig Porter, Gemma L. Holliday, James Willey