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.

Human Ferrochelatase: Insights for the Mechanism of Ferrous Iron Approaching Protoporphyrin IX by QM/MM and QTCP Free Energy Studies

“…The starting position of Fe 2+ greatly affects the pathway of its insertion into protoporphyrin. Similar with our previous study on B. subtilis ferrochelatase, , there are two possible sites sitting at the two sides of the protoporphyrin IX respectively for the binding of Fe 2+ . Besides, the coordinating states of Fe 2+ should be considered as well.…”

“…Another point of view is introduced to answer this issue. The study on the reaction path in B. subtilis ferrochelatase suggests that the bending of the H–N bond and the long H–N His183 distance (4 Å) lead to a high barrier energy of deprotonation . Similarly, in human ferrochelatase when Fe 2+ was in the binding site A, the porphyrin deprotonation by His263 required more than 40 kcal/mol energy.…”

Insight into the function of active site residues in the catalytic mechanism of human ferrochelatase

“…Crystal structures for three distinct conformational states of the human ferrochelatase enzyme have provided snap shots that support a putative enzyme mechanism for porphyrin macrocycle metallation. Additional support of this model comes from molecular dynamics (MD) 39,40 , high level quantum mechanical/molecular mechanics (QM/MM) and quantum mechanical thermodynamic cycle perturbation (QTCP) calculations 41 . These structure-based theoretical simulations elucidate molecular motions and structural interactions that occur for human ferrochelatase in going from the open, to closed, and finally release conformations.…”

Ferrochelatase: Mapping the Intersection of Iron and Porphyrin Metabolism in the Mitochondria

“…All variants of H263 studied to date are inactive, including H263C as well as H263A in the presence of imidazole ( Sellers et al, 2001 ; Dailey et al, 2007 ). Although H263 has been proposed to function both in metal binding ( Kohno et al, 1994 ) and proton abstraction ( Sellers et al, 2001 ), studies with catalytic antibodies ( Cochran and Schultz, 1990 ) and nucleic acids ( Conn et al, 1996 ; Li and Sen, 1996 ; 1997 ) as well as amide hydrogen/deuterium mass spectrometry ( Asuru and Busenlehner, 2011 ) and computational studies ( Sigfridsson and Ryde, 2003 ; Wang et al, 2013 ; Wang and Shen, 2013 ; Wu et al, 2016 ) are consistent with proton abstraction and metal insertion occurring on opposite face of the tetrapyrrole. In addition to H263 being conserved among all ferrochelatases, it is also the only basic residue in the vicinity of the pyrroles to be deprotonated.…”

“…However, both structural studies ( Medlock et al, 2012 ; Medlock et al, 2021 ). as well as molecular dynamics ( Wang et al, 2013 ; Wang and Shen, 2013 ) and high-level quantum mechanical/molecular mechanics and quantum mechanical thermodynamic cycle perturbation ( Wu et al, 2016 ) have provided significant insight. In the proposed model ferrous iron first undergoes desolvation either upon binding or during transit to the active site.…”