2HRE

Structure of human ferrochelatase variant E343K with protoporphyrin IX bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate interactions with human ferrochelatase

Medlock, A.Swartz, L.Dailey, T.A.Dailey, H.A.Lanzilotta, W.N.

(2007) Proc.Natl.Acad.Sci.Usa 104: 1789-1793

  • DOI: 10.1073/pnas.0606144104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme IX. Human ferrochelatase is a homodimeric, inner mitochondrial membrane-associated enzyme that possesses an ess ...

    Ferrochelatase, the terminal enzyme in heme biosynthesis, catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme IX. Human ferrochelatase is a homodimeric, inner mitochondrial membrane-associated enzyme that possesses an essential [2Fe-2S] cluster. In this work, we report the crystal structure of human ferrochelatase with the substrate protoporphyrin IX bound as well as a higher resolution structure of the R115L variant without bound substrate. The data presented reveal that the porphyrin substrate is bound deep within an enclosed pocket. When compared with the location of N-methylmesoporphyrin in the Bacillus subtilis ferrochelatase, the porphyrin is rotated by approximately 100 degrees and is buried an additional 4.5 A deeper within the active site. The propionate groups of the substrate do not protrude into solvent and are bound in a manner similar to what has been observed in uroporphyrinogen decarboxylase. Furthermore, in the substrate-bound form, the jaws of the active site mouth are closed so that the porphyrin substrate is completely engulfed in the pocket. These data provide insights that will aid in the determination of the mechanism for ferrochelatase.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferrochelatase
A, B, C, D
359Homo sapiensMutation(s): 1 
Gene Names: FECH
EC: 4.99.1.1
Find proteins for P22830 (Homo sapiens)
Go to Gene View: FECH
Go to UniProtKB:  P22830
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CHD
Query on CHD

Download SDF File 
Download CCD File 
B, D
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A, B, C, D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
PP9
Query on PP9

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX
C34 H34 N4 O4
FEDYMSUPMFCVOD-UJJXFSCMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.952α = 102.41
b = 88.388β = 109.34
c = 93.253γ = 105.58
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance