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Geometric and electronic structures of the Ni(I) and methyl-Ni(III) intermediates of methyl-coenzyme M reductase.

Sarangi R, Dey M, Ragsdale SW - Biochemistry (2009)

Bottom Line: Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH).The formation and stability of this species support mechanism I, and the Ni-C bond length suggests a homolytic cleavage of the Ni(III)-methyl bond in the subsequent catalytic step.The XAS data provide insight into the role of the unique F(430) cofactor in tuning the stability of the different redox states of MCR.

View Article: PubMed Central - PubMed

Affiliation: Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA. ritis@slac.stanford.edu

ABSTRACT
Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni-F(430) cofactor, which can exist in different oxidation states. The catalytic mechanism of methane formation has remained elusive despite intense spectroscopic and theoretical investigations. On the basis of spectroscopic and crystallographic data, the first step of the mechanism is proposed to involve a nucleophilic attack of the Ni(I) active state (MCR(red1)) on Me-SCoM to form a Ni(III)-methyl intermediate, while computational studies indicate that the first step involves the attack of Ni(I) on the sulfur of Me-SCoM, forming a CH(3)(*) radical and a Ni(II)-thiolate species. In this study, a combination of Ni K-edge X-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations have been performed on the Ni(I) (MCR(red1)), Ni(II) (MCR(red1-silent)), and Ni(III)-methyl (MCR(Me)) states of MCR to elucidate the geometric and electronic structures of the different redox states. Ni K-edge EXAFS data are used to reveal a five-coordinate active site with an open upper axial coordination site in MCR(red1). Ni K-pre-edge and EXAFS data and time-dependent DFT calculations unambiguously demonstrate the presence of a long Ni-C bond ( approximately 2.04 A) in the Ni(III)-methyl state of MCR. The formation and stability of this species support mechanism I, and the Ni-C bond length suggests a homolytic cleavage of the Ni(III)-methyl bond in the subsequent catalytic step. The XAS data provide insight into the role of the unique F(430) cofactor in tuning the stability of the different redox states of MCR.

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(A) Comparison of the Ni K-pre-edge XAS data (—) with the TD-DFT calculated spectra (---): MCRred1−silent (red), MCRred1 (green), MCRMe (blue), and MCRMe−NA (gray).
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fig5: (A) Comparison of the Ni K-pre-edge XAS data (—) with the TD-DFT calculated spectra (---): MCRred1−silent (red), MCRred1 (green), MCRMe (blue), and MCRMe−NA (gray).

Mentions: To support the Ni K-pre-edge analysis, TD-DFT calculations were performed on starting active site structures of MCRred1−silent, MCRred1, and MCRMe, which were generated by considering the crystal structure of MCRred1−silent and the EXAFS data presented herein. Selected DFT parameters are listed in Table 3. The calculated spectra on the geometry-optimized structures are presented in Figure 5. The calculated pre-edge energies are 8118.8, 8119.2, and 8119.6 eV for MCRred1, MCRred1−silent, and MCRMe. The trend in energy position is in reasonable agreement with the experimental data (see Table 1).


Geometric and electronic structures of the Ni(I) and methyl-Ni(III) intermediates of methyl-coenzyme M reductase.

Sarangi R, Dey M, Ragsdale SW - Biochemistry (2009)

(A) Comparison of the Ni K-pre-edge XAS data (—) with the TD-DFT calculated spectra (---): MCRred1−silent (red), MCRred1 (green), MCRMe (blue), and MCRMe−NA (gray).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667316&req=5

fig5: (A) Comparison of the Ni K-pre-edge XAS data (—) with the TD-DFT calculated spectra (---): MCRred1−silent (red), MCRred1 (green), MCRMe (blue), and MCRMe−NA (gray).
Mentions: To support the Ni K-pre-edge analysis, TD-DFT calculations were performed on starting active site structures of MCRred1−silent, MCRred1, and MCRMe, which were generated by considering the crystal structure of MCRred1−silent and the EXAFS data presented herein. Selected DFT parameters are listed in Table 3. The calculated spectra on the geometry-optimized structures are presented in Figure 5. The calculated pre-edge energies are 8118.8, 8119.2, and 8119.6 eV for MCRred1, MCRred1−silent, and MCRMe. The trend in energy position is in reasonable agreement with the experimental data (see Table 1).

Bottom Line: Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH).The formation and stability of this species support mechanism I, and the Ni-C bond length suggests a homolytic cleavage of the Ni(III)-methyl bond in the subsequent catalytic step.The XAS data provide insight into the role of the unique F(430) cofactor in tuning the stability of the different redox states of MCR.

View Article: PubMed Central - PubMed

Affiliation: Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA. ritis@slac.stanford.edu

ABSTRACT
Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni-F(430) cofactor, which can exist in different oxidation states. The catalytic mechanism of methane formation has remained elusive despite intense spectroscopic and theoretical investigations. On the basis of spectroscopic and crystallographic data, the first step of the mechanism is proposed to involve a nucleophilic attack of the Ni(I) active state (MCR(red1)) on Me-SCoM to form a Ni(III)-methyl intermediate, while computational studies indicate that the first step involves the attack of Ni(I) on the sulfur of Me-SCoM, forming a CH(3)(*) radical and a Ni(II)-thiolate species. In this study, a combination of Ni K-edge X-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations have been performed on the Ni(I) (MCR(red1)), Ni(II) (MCR(red1-silent)), and Ni(III)-methyl (MCR(Me)) states of MCR to elucidate the geometric and electronic structures of the different redox states. Ni K-edge EXAFS data are used to reveal a five-coordinate active site with an open upper axial coordination site in MCR(red1). Ni K-pre-edge and EXAFS data and time-dependent DFT calculations unambiguously demonstrate the presence of a long Ni-C bond ( approximately 2.04 A) in the Ni(III)-methyl state of MCR. The formation and stability of this species support mechanism I, and the Ni-C bond length suggests a homolytic cleavage of the Ni(III)-methyl bond in the subsequent catalytic step. The XAS data provide insight into the role of the unique F(430) cofactor in tuning the stability of the different redox states of MCR.

Show MeSH