2PO5

Crystal structure of human ferrochelatase mutant with His 263 replaced by Cys


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Altered orientation of active site residues in variants of human ferrochelatase. Evidence for a hydrogen bond network involved in catalysis

Dailey, H.A.Wu, C.-K.Horanyi, P.Medlock, A.E.Najahi-Missaoui, W.Burden, A.E.Dailey, T.A.Rose, J.P.

(2007) Biochemistry 46: 7973-7979

  • DOI: 10.1021/bi700151f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ferrochelatase catalyzes the terminal step in heme biosynthesis, the insertion of ferrous iron into protoporphyrin to form protoheme IX. The crystal structures of human ferrochelatase both with and without the protoporphyrin substrate bound have been ...

    Ferrochelatase catalyzes the terminal step in heme biosynthesis, the insertion of ferrous iron into protoporphyrin to form protoheme IX. The crystal structures of human ferrochelatase both with and without the protoporphyrin substrate bound have been determined previously. The substrate-free enzyme has an open active site pocket, while in the substrate-bound enzyme, the active site pocket is closed around the porphyrin macrocycle and a number of active site residues have reoriented side chains. To understand how and why these structural changes occur, we have substituted three amino acid residues (H263, H341, and F337) whose side chains occupy different spatial positions in the substrate-free versus substrate-bound ferrochelatases. The catalytic and structural properties of ferrochelatases containing the amino acid substitutions H263C, H341C, and F337A were examined. It was found that in the H263C and H341C variants, but not the F337A variant enzymes, the side chains of N75, M76, R164, H263, F337, H341, and E343 are oriented in a fashion similar to what is found in ferrochelatase with the bound porphyrin substrate. However, all of the variant forms possess open active site pockets which are found in the structure of porphyrin-free ferrochelatase. Thus, while the interior walls of the active site pocket are remodeled in these variants, the exterior lips remain unaltered in position. One possible explanation for this collective reorganization of active site side chains is the presence of a hydrogen bond network among H263, H341, and E343. This network is disrupted in the variants by alteration of H263C or H341C. In the substrate-bound enzyme, the formation of a hydrogen bond between H263 and a pyrrole nitrogen results in disruption of the network. The possible role of this network in catalysis is discussed.


    Related Citations: 
    • 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.Mol.Biol. 8: 156
    • Human Ferrochelatase: Crystallization, Characterization of the [2Fe-2S] Cluster and Determination that the Enzyme is a Homodimer
      Burden, A.E.,Wu, C.-K.,Dailey, T.A.,Busch, J.L.H.,Dhawan, I.K.,Rose, J.P.,Wang, B.C.,Dailey, H.A.
      (1999) Biochim.Biophys.Acta 1435: 191


    Organizational Affiliation

    Biomedical and Health Sciences Institute, Department of Microbiology, Paul D. Coverdell Center, University of Georgia, Athens, Georgia 30602, USA. hdailey@uga.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferrochelatase, mitochondrial
A, B
359Homo sapiensMutation(s): 2 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CHD
Query on CHD

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

Download SDF File 
Download CCD File 
A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.420α = 90.00
b = 87.730β = 90.00
c = 109.580γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CrystalCleardata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2016-02-24
    Type: Data collection
  • Version 1.3: 2017-10-18
    Type: Refinement description