title: Is it possible for Fe2+ to approach protoporphyrin IX from the side of Tyr-13 in Bacillus subtilis ferrochelatase? An answer from QM/MM study.
abstract: We previously reported the insertion process of the ferrous ion into the protoporphyrin IX from the side of the residue His-183 (J. Inorg. Biochem. 103 (2009) 1680-1686). Sellers et al. suggested that the ferrous ion probably approaches the protoporphyrin IX via the opposite side in the human enzyme. In this paper, we simulated the insertion process of Fe(2+) into the protoporphyrin IX from the side of the residue Tyr-13 at the opposite site of His-183 by QM/MM method on Bacillus subtilis ferrochelatase. The model was built with Fe(2+) ion coordinated by Tyr-13, His-88 and two water molecules. Geometries were optimized at the BP86/6-31G* level and energies were calculated at the B3LYP/6-311+G(2d,2p) level. The overall process involves the displacement of the residues Tyr-13, His-88 and one water molecule and deprotonation of the porphyrin ring. All the local minimum structures and energy barriers were obtained and an optimal insertion pathway was suggested. The rate-determining step is the removing of the second proton from the porphyrin accompanied by the formation of the fourth Fe-N bond with an energy barrier of 138.00 kJ/mol.
authors.affiliation: School of Chemistry and Chemical Engineering, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China.
authors.forename: Yaxue
authors.initials: Y
authors.lastname: Wang
authors.forename: Yong
authors.initials: Y
authors.lastname: Shen
mesh_terms: D001412:Bacillus subtilis / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D002413:Cations, Divalent; D005294:Ferrochelatase / Q000737:chemistry*; D006639:Histidine / Q000737:chemistry; D006801:Humans; D007501:Iron / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011522:Protons; D011524:Protoporphyrins / Q000737:chemistry*; D011789:Quantum Theory; D013816:Thermodynamics; D014443:Tyrosine / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D002413:Cations, Divalent; D011522:Protons; D011524:Protoporphyrins; D014867:Water; D014443:Tyrosine; D006639:Histidine; C028025:protoporphyrin IX; D007501:Iron; D005294:Ferrochelatase