2Q3J

Crystal structure of the His183Ala variant of Bacillus subtilis ferrochelatase in complex with N-Methyl Mesoporphyrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Porphyrin binding and distortion and substrate specificity in the ferrochelatase reaction: the role of active site residues

Karlberg, T.Hansson, M.D.Yengo, R.K.Johansson, R.Thorvaldsen, O.H.Ferreira, G.C.Hansson, M.Al-Karadaghi, S.

(2008) J Mol Biol 378: 1074-1083

  • DOI: https://doi.org/10.1016/j.jmb.2008.03.040
  • Primary Citation of Related Structures:  
    2Q2N, 2Q2O, 2Q3J

  • PubMed Abstract: 

    The specific insertion of a divalent metal ion into tetrapyrrole macrocycles is catalyzed by a group of enzymes called chelatases. Distortion of the tetrapyrrole has been proposed to be an important component of the mechanism of metallation. We present the structures of two different inhibitor complexes: (1) N-methylmesoporphyrin (N-MeMP) with the His183Ala variant of Bacillus subtilis ferrochelatase; (2) the wild-type form of the same enzyme with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride (dSDP). Analysis of the structures showed that only one N-MeMP isomer out of the eight possible was bound to the protein and it was different from the isomer that was earlier found to bind to the wild-type enzyme. A comparison of the distortion of this porphyrin with other porphyrin complexes of ferrochelatase and a catalytic antibody with ferrochelatase activity using normal-coordinate structural decomposition reveals that certain types of distortion are predominant in all these complexes. On the other hand, dSDP, which binds closer to the protein surface compared to N-MeMP, does not undergo any distortion upon binding to the protein, underscoring that the position of the porphyrin within the active site pocket is crucial for generating the distortion required for metal insertion. In addition, in contrast to the wild-type enzyme, Cu(2+)-soaking of the His183Ala variant complex did not show any traces of porphyrin metallation. Collectively, these results provide new insights into the role of the active site residues of ferrochelatase in controlling stereospecificity, distortion and metallation.


  • Organizational Affiliation

    Department of Molecular Biophysics, Centre for Molecular Protein Science, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferrochelatase309Bacillus subtilisMutation(s): 1 
Gene Names: hemHhemF
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32396
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.78α = 90
b = 58.57β = 90
c = 97.83γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description