1C9E

STRUCTURE OF FERROCHELATASE WITH COPPER(II) N-METHYLMESOPORPHYRIN COMPLEX BOUND AT THE ACTIVE SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and mechanistic basis of porphyrin metallation by ferrochelatase.

Lecerof, D.Fodje, M.Hansson, A.Hansson, M.Al-Karadaghi, S.

(2000) J.Mol.Biol. 297: 221-232

  • DOI: 10.1006/jmbi.2000.3569
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ferrochelatase, the enzyme catalyzing metallation of protoporphyrin IX at the terminal step of heme biosynthesis, was co-crystallized with an isomer mixture of the potent inhibitor N-methylmesoporphyrin (N-MeMP). The X-ray structure revealed the acti ...

    Ferrochelatase, the enzyme catalyzing metallation of protoporphyrin IX at the terminal step of heme biosynthesis, was co-crystallized with an isomer mixture of the potent inhibitor N-methylmesoporphyrin (N-MeMP). The X-ray structure revealed the active site of the enzyme, to which only one of the isomers was bound, and for the first time allowed characterization of the mode of porphyrin macrocycle distortion by ferrochelatase. Crystallization of ferrochelatase and N-MeMP in the presence of Cu(2+) leads to metallation and demethylation of N-MeMP. A mechanism of porphyrin distortion is proposed, which assumes that the enzyme holds pyrrole rings B, C and D in a vice-like grip and forces a 36 degrees tilt on ring A.


    Organizational Affiliation

    Department of Molecular Biophysics, Lund University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTOHEME FERROLYASE
A
306Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: hemH (hemF)
EC: 4.99.1.1
Find proteins for P32396 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P32396
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MP1
Query on MP1

Download SDF File 
Download CCD File 
A
N-METHYLMESOPORPHYRIN CONTAINING COPPER
C35 H39 Cu N4 O4
CTVHSHALRXJQNK-GADMLGSJDS
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.840α = 90.00
b = 58.560β = 90.00
c = 98.020γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection