1HRK

CRYSTAL STRUCTURE OF HUMAN FERROCHELATASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.

Wu, C.K.Dailey, H.A.Rose, J.P.Burden, A.Sellers, V.M.Wang, B.C.

(2001) Nat Struct Biol 8: 156-160

  • DOI: https://doi.org/10.1038/84152
  • Primary Citation of Related Structures:  
    1HRK

  • PubMed Abstract: 

    Human ferrochelatase (E.C. 4.99.1.1) is a homodimeric (86 kDa) mitochondrial membrane-associated enzyme that catalyzes the insertion of ferrous iron into protoporphyrin to form heme. We have determined the 2.0 A structure from the single wavelength iron anomalous scattering signal. The enzyme contains two NO-sensitive and uniquely coordinated [2Fe-2S] clusters. Its membrane association is mediated in part by a 12-residue hydrophobic lip that also forms the entrance to the active site pocket. The positioning of highly conserved residues in the active site in conjunction with previous biochemical studies support a catalytic model that may have significance in explaining the enzymatic defects that lead to the human inherited disease erythropoietic protoporphyria.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FERROCHELATASE
A, B
359Homo sapiensMutation(s): 2 
EC: 4.99.1.1 (PDB Primary Data), 4.98.1.1 (UniProt)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P22830 (Homo sapiens)
Explore P22830 
Go to UniProtKB:  P22830
PHAROS:  P22830
GTEx:  ENSG00000066926 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22830
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHD
Query on CHD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.433α = 90
b = 87.569β = 90
c = 109.699γ = 90
Software Package:
Software NamePurpose
ISASmodel building
CNSrefinement
CrystalCleardata reduction
DENZOdata reduction
SCALEPACKdata scaling
ISASphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-07
    Changes: Data collection