PDBsum entry 2ac4

Lyase

PDB id: 2ac4

Contents

Protein chain

309 a.a. *

Waters ×73

* Residue conservation analysis

PDB id:

2ac4

Name:

Lyase

Title:

Crystal structure of the his183cys mutant variant of bacillus subtilis ferrochelatase

Structure:

Ferrochelatase. Chain: a. Synonym: protoheme ferro-lyase, heme synthetase. Engineered: yes. Mutation: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: hemh, hemf. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.214 R-free: 0.276

Authors:

S.Shipovskov,T.Karlberg,M.Fodje,M.D.Hansson,G.C.Ferreira,M.Hansson, C.T.Reimann,S.Al-Karadaghi

Key ref:

S.Shipovskov et al. (2005). Metallation of the transition-state inhibitor N-methyl mesoporphyrin by ferrochelatase: implications for the catalytic reaction mechanism. J Mol Biol, 352, 1081-1090. PubMed id: 16140324 DOI: 10.1016/j.jmb.2005.08.002

Date:

18-Jul-05 Release date: 20-Sep-05

Protein chain

P32396  (HEMH_BACSU) -  Coproporphyrin III ferrochelatase from Bacillus subtilis (strain 168)

Seq: 310 a.a.

Struc: 309 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.99.1.9 - coproporphyrin ferrochelatase.
• Reaction: Fe-coproporphyrin III + 2 H⁺ = coproporphyrin III + Fe²⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1016/j.jmb.2005.08.002

J Mol Biol 352:1081-1090 (2005)

PubMed id: 16140324

Metallation of the transition-state inhibitor N-methyl mesoporphyrin by ferrochelatase: implications for the catalytic reaction mechanism.

S.Shipovskov, T.Karlberg, M.Fodje, M.D.Hansson, G.C.Ferreira, M.Hansson, C.T.Reimann, S.Al-Karadaghi.

ABSTRACT

Insertion of metals into various tetrapyrroles is catalysed by a group of enzymes called chelatases, e.g. nickel, cobalt, magnesium and ferro-chelatase. It has been proposed that catalytic metallation includes distorting the porphyrin substrate by the enzyme towards a transition state-like geometry in which at least one of the pyrrole rings will be available for metal chelation. Here, we present a study of metal insertion into the transition-state inhibitor of protoporphyrin IX ferrochelatase, N-methyl mesoporphyrin (N-MeMP), by time-resolved crystallography and mass spectrometry with and without the presence of ferrochelatase. The results show that metallation of N-MeMP has a very limited effect on the conformation of the residues that participate in porphyrin and metal binding. These findings support theoretical data, which indicate that product release is controlled largely by the strain created by metal insertion into the distorted porphyrin. The results suggest that, similar to non-catalytic metallation of N-MeMP, the ferrochelatase-assisted metallation depends on the ligand exchange rate for the respective metal. Moreover, ferrochelatase catalyses insertion of Cu(II) and Zn(II) into N-MeMP with a rate that is about 20 times faster than non-enzymatic metallation in solution, suggesting that the catalytic strategy of ferrochelatase includes a stage of acceleration of the rate of ligand exchange for the metal substrate. The greater efficiency of N-MeMP metallation by Cu(II), as compared to Zn(II), contrasts with the K(m) values for Zn(II) (17 microM) and Cu(II) (170 microM) obtained for metallation of protoporphyrin IX. We suggest that this difference in metal specificity depends on the type of distortion imposed by the enzyme on protoporphyrin IX, which is different from the intrinsic non-planar distortion of N-MeMP. A mechanism of control of metal specificity by porphyrin distortion may be general for different chelatases, and may have common features with the mechanism of metal specificity in crown ethers.

Selected figure(s)

Figure 3.
Figure 3. Isotopic patterns of N-MeMP and its metallated forms. Theoretical (top row) and experimentally observed (bottom row) isotopic patterns for (a) N-MeMP, (b) N-MeMP:Cu(II) and (c) MP:Cu(II).

Figure 5.
Figure 5. (a) Metal insertion into N-MeMP in the presence and in the absence of enzyme. The relative intensity of mass spectral signals showing Cu(II) insertion into N-MeMP in solution in the absence (circles) and in the presence (squares) of B. subtilis ferrochelatase is shown. Zn(II) insertion in the presence of ferrochelatase is shown as triangles. (b) Cu(II) insertion into N-MeMP in the presence of B. subtilis ferrochelatase mutants H183C (diamonds) and Y13F (triangles), compared to metallation by the wild-type enzyme (squares).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 1081-1090) copyright 2005.

Figures were selected by an automated process.