1C9E

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

• PDB DOI: https://doi.org/10.2210/pdb1C9E/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis
• Expression System: Bacteria
• Mutation(s): No 


• Deposited: 1999-08-02 Released: 2000-03-22 
• Deposition Author(s): Lecerof, D., Fodje, M.N., Hansson, A., Hansson, M., Al-Karadaghi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

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

• PubMed: 10704318 
• DOI: https://doi.org/10.1006/jmbi.2000.3569
• Primary Citation of Related Structures:  
  1C1H, 1C9E, 1DOZ


• 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 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.

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Organizational Affiliation: 

Department of Molecular Biophysics, Lund University, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.55 kDa 
• Atom Count: 2,758 
• Modelled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTOHEME FERROLYASE	A	306	Bacillus subtilis	Mutation(s): 0  EC: 4.99.1.1 (PDB Primary Data), 4.99.1.9 (UniProt)
UniProt
Find proteins for P32396 (Bacillus subtilis (strain 168)) Explore P32396  Go to UniProtKB:  P32396

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MP1	C [auth A]	N-METHYLMESOPORPHYRIN CONTAINING COPPER C35 H39 Cu N4 O4 CTVHSHALRXJQNK-ZHZUXMKXSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.84	α = 90
b = 58.56	β = 90
c = 98.02	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-22 
Deposition Author(s): Lecerof, D., Fodje, M.N., Hansson, A., Hansson, M., Al-Karadaghi, S.

Revision History  

• Version 1.0: 2000-03-22
  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: 2018-03-07
  Changes: Data collection
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations