2QD5

Structure of wild type human ferrochelatase in complex with a lead-porphyrin compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A pi-Helix Switch Selective for Porphyrin Deprotonation and Product Release in Human Ferrochelatase.

Medlock, A.E.Dailey, T.A.Ross, T.A.Dailey, H.A.Lanzilotta, W.N.

(2007) J Mol Biol 373: 1006-1016

  • DOI: 10.1016/j.jmb.2007.08.040
  • Primary Citation of Related Structures:  
    2QD5, 2QD4, 2QD3, 2QD2, 2QD1

  • PubMed Abstract: 
  • Ferrochelatase (protoheme ferrolyase, EC 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). Due to the many critical roles of heme, synthesis of heme is required by the vast majority of organisms ...

    Ferrochelatase (protoheme ferrolyase, EC 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). Due to the many critical roles of heme, synthesis of heme is required by the vast majority of organisms. Despite significant investigation of both the microbial and eukaryotic enzyme, details of metal chelation remain unidentified. Here we present the first structure of the wild-type human enzyme, a lead-inhibited intermediate of the wild-type enzyme with bound metallated porphyrin macrocycle, the product bound form of the enzyme, and a higher resolution model for the substrate-bound form of the E343K variant. These data paint a picture of an enzyme that undergoes significant changes in secondary structure during the catalytic cycle. The role that these structural alterations play in overall catalysis and potential protein-protein interactions with other proteins, as well as the possible molecular basis for these changes, is discussed. The atomic details and structural rearrangements presented herein significantly advance our understanding of the substrate binding mode of ferrochelatase and reveal new conformational changes in a structurally conserved pi-helix that is predicted to have a central role in product release.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferrochelatase AB359Homo sapiensMutation(s): 0 
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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PP9
Query on PP9

Download Ideal Coordinates CCD File 
A, B
PROTOPORPHYRIN IX
C34 H34 N4 O4
FEDYMSUPMFCVOD-UJJXFSCMSA-N
 Ligand Interaction
CHD
Query on CHD

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A, B
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
PB
Query on PB

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A, B
LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
OXY
Query on OXY

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B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.218α = 90
b = 92.811β = 90
c = 109.808γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance