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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.jmb.2008.03.040
  • Primary Citation of Related Structures:  

  • 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 prese ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferrochelatase
A
309Bacillus subtilis (strain 168)Mutation(s): 1 
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
H02
Query on H02

Download SDF File 
Download CCD File 
A
N-METHYL PROTOPORPHYRIN IX 2,4-DISULFONIC ACID
3,3'-(7,12-DIETHYL-3,8,13,17,22-PENTAMETHYL-22,24-DIHYDROPORPHYRIN-2,18-DIYL)DIPROPANOIC ACID
C35 H42 N4 O4
VIEXPEPYGOTUBM-UQOLDQHFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.780α = 90.00
b = 58.570β = 90.00
c = 97.830γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNSphasing
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2018-03-07
    Type: Data collection