1C1H

CRYSTAL STRUCTURE OF BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX WITH N-METHYL MESOPORPHYRIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 1.4 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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERROCHELATASEA310Bacillus subtilisMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MMP (Subject of Investigation/LOI)
Query on MMP

Download Ideal Coordinates CCD File 
C [auth A]N-METHYLMESOPORPHYRIN
C35 H40 N4 O4
YNWHQWMCLCANDI-YIYRCNGCSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.97α = 90
b = 58.68β = 90
c = 98.05γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-17
    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: Data collection, Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation