EXAFS and NRVS Reveal a Conformational Distortion of the FeMo-cofactor in the MoFe Nitrogenase Propargyl Alcohol Complex

Simon J. George; Brett M. Barney; Devrani Mitra; Robert Y. Igarashi; Yisong Guo; Dennis R. Dean; Stephen P. Cramer; Lance C. Seefeldt

doi:10.1016/j.jinorgbio.2012.02.004

EXAFS and NRVS Reveal a Conformational Distortion of the FeMo-cofactor in the MoFe Nitrogenase Propargyl Alcohol Complex

Simon J. George, Brett M. Barney, Devrani Mitra, Robert Y. Igarashi, Yisong Guo, Dennis R. Dean, Stephen P. Cramer, Lance C. Seefeldt

Bioproducts and Biosystems Engineering

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Abstract

We have used EXAFS and NRVS spectroscopies to examine the structural changes in the FeMo-cofactor active site of the α-70^Ala variant of Azotobacter vinelandii nitrogenase on binding and reduction of propargyl alcohol (PA). The Mo K-edge near-edge and EXAFS spectra are very similar in the presence and absence of PA, suggesting PA does not bind at Mo. By contrast, Fe EXAFS spectra show a clear and reproducible change in the long Fe-Fe interaction at ~ 3.7 Å on PA binding with the apparent appearance of a new Fe-Fe interaction at 3.99 Å. An analogous change in the long Mo-Fe 5.1 Å interaction is not seen. The NRVS spectra exclude the possibility of large-scale structural change of the FeMo-cofactor involving breaking the μ² Fe-S-Fe bonds of the Fe₆S₉X core. The simplest chemically consistent structural change is that the bound form of PA is coordinated at Fe atoms (Fe6 or Fe7) adjacent to the Mo terminus, with a concomitant movement of the Fe away from the central atom X and along the Fe-X bond by about 0.35 Å. This study comprises the first experimental evidence of the conformational changes of the FeMo-cofactor active site on binding a substrate or product.

Original language	English (US)
Pages (from-to)	85-92
Number of pages	8
Journal	Journal of Inorganic Biochemistry
Volume	112
DOIs	https://doi.org/10.1016/j.jinorgbio.2012.02.004
State	Published - Jul 2012

Bibliographical note

Funding Information:
This work was funded by NIH GM-65440 (SPC), GM-59087 (LCS and DRD) and NSF CHE-0745353 (SPC). ABEX is supported by the U.S. Department of Energy, Office of Biological and Environmental Research (DOE OBER). Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource (SSRL), a national user facility operated by Stanford University on behalf of the DOE Office of Basic Energy Sciences (OBES). The SSRL Structural Molecular Biology Program is supported by the DOE OBER, and the NIH, National Center for Research Resources, Biomedical Technology Program. Portions of this work were also carried out at SPring-8 with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) under Proposal # 4032LD3-NP. Use of the Advanced Photon Source was supported by the DOE OBES under Contract No. DE-AC02-06CH11357.

Keywords

Extended Absorption Fine Structure (EXAFS)
Metalloprotein
Nitrogen Fixation
Nitrogenase
Nuclear Resonant Vibrational Spectroscopy (NRVS)
X-ray Absorption Spectroscopy (XAS)

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@article{074228eeb06a466188386a6d16cf18b4,

title = "EXAFS and NRVS Reveal a Conformational Distortion of the FeMo-cofactor in the MoFe Nitrogenase Propargyl Alcohol Complex",

abstract = "We have used EXAFS and NRVS spectroscopies to examine the structural changes in the FeMo-cofactor active site of the α-70Ala variant of Azotobacter vinelandii nitrogenase on binding and reduction of propargyl alcohol (PA). The Mo K-edge near-edge and EXAFS spectra are very similar in the presence and absence of PA, suggesting PA does not bind at Mo. By contrast, Fe EXAFS spectra show a clear and reproducible change in the long Fe-Fe interaction at ~ 3.7 {\AA} on PA binding with the apparent appearance of a new Fe-Fe interaction at 3.99 {\AA}. An analogous change in the long Mo-Fe 5.1 {\AA} interaction is not seen. The NRVS spectra exclude the possibility of large-scale structural change of the FeMo-cofactor involving breaking the μ2 Fe-S-Fe bonds of the Fe6S9X core. The simplest chemically consistent structural change is that the bound form of PA is coordinated at Fe atoms (Fe6 or Fe7) adjacent to the Mo terminus, with a concomitant movement of the Fe away from the central atom X and along the Fe-X bond by about 0.35 {\AA}. This study comprises the first experimental evidence of the conformational changes of the FeMo-cofactor active site on binding a substrate or product.",

keywords = "Extended Absorption Fine Structure (EXAFS), Metalloprotein, Nitrogen Fixation, Nitrogenase, Nuclear Resonant Vibrational Spectroscopy (NRVS), X-ray Absorption Spectroscopy (XAS)",

author = "George, {Simon J.} and Barney, {Brett M.} and Devrani Mitra and Igarashi, {Robert Y.} and Yisong Guo and Dean, {Dennis R.} and Cramer, {Stephen P.} and Seefeldt, {Lance C.}",

note = "Funding Information: This work was funded by NIH GM-65440 (SPC), GM-59087 (LCS and DRD) and NSF CHE-0745353 (SPC). ABEX is supported by the U.S. Department of Energy, Office of Biological and Environmental Research (DOE OBER). Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource (SSRL), a national user facility operated by Stanford University on behalf of the DOE Office of Basic Energy Sciences (OBES). The SSRL Structural Molecular Biology Program is supported by the DOE OBER, and the NIH, National Center for Research Resources, Biomedical Technology Program. Portions of this work were also carried out at SPring-8 with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) under Proposal # 4032LD3-NP. Use of the Advanced Photon Source was supported by the DOE OBES under Contract No. DE-AC02-06CH11357. ",

year = "2012",

month = jul,

doi = "10.1016/j.jinorgbio.2012.02.004",

language = "English (US)",

volume = "112",

pages = "85--92",

journal = "Journal of Inorganic Biochemistry",

issn = "0162-0134",

publisher = "Elsevier Inc.",

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TY - JOUR

T1 - EXAFS and NRVS Reveal a Conformational Distortion of the FeMo-cofactor in the MoFe Nitrogenase Propargyl Alcohol Complex

AU - George, Simon J.

AU - Barney, Brett M.

AU - Mitra, Devrani

AU - Igarashi, Robert Y.

AU - Guo, Yisong

AU - Dean, Dennis R.

AU - Cramer, Stephen P.

AU - Seefeldt, Lance C.

N1 - Funding Information: This work was funded by NIH GM-65440 (SPC), GM-59087 (LCS and DRD) and NSF CHE-0745353 (SPC). ABEX is supported by the U.S. Department of Energy, Office of Biological and Environmental Research (DOE OBER). Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource (SSRL), a national user facility operated by Stanford University on behalf of the DOE Office of Basic Energy Sciences (OBES). The SSRL Structural Molecular Biology Program is supported by the DOE OBER, and the NIH, National Center for Research Resources, Biomedical Technology Program. Portions of this work were also carried out at SPring-8 with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) under Proposal # 4032LD3-NP. Use of the Advanced Photon Source was supported by the DOE OBES under Contract No. DE-AC02-06CH11357.

PY - 2012/7

Y1 - 2012/7

N2 - We have used EXAFS and NRVS spectroscopies to examine the structural changes in the FeMo-cofactor active site of the α-70Ala variant of Azotobacter vinelandii nitrogenase on binding and reduction of propargyl alcohol (PA). The Mo K-edge near-edge and EXAFS spectra are very similar in the presence and absence of PA, suggesting PA does not bind at Mo. By contrast, Fe EXAFS spectra show a clear and reproducible change in the long Fe-Fe interaction at ~ 3.7 Å on PA binding with the apparent appearance of a new Fe-Fe interaction at 3.99 Å. An analogous change in the long Mo-Fe 5.1 Å interaction is not seen. The NRVS spectra exclude the possibility of large-scale structural change of the FeMo-cofactor involving breaking the μ2 Fe-S-Fe bonds of the Fe6S9X core. The simplest chemically consistent structural change is that the bound form of PA is coordinated at Fe atoms (Fe6 or Fe7) adjacent to the Mo terminus, with a concomitant movement of the Fe away from the central atom X and along the Fe-X bond by about 0.35 Å. This study comprises the first experimental evidence of the conformational changes of the FeMo-cofactor active site on binding a substrate or product.

AB - We have used EXAFS and NRVS spectroscopies to examine the structural changes in the FeMo-cofactor active site of the α-70Ala variant of Azotobacter vinelandii nitrogenase on binding and reduction of propargyl alcohol (PA). The Mo K-edge near-edge and EXAFS spectra are very similar in the presence and absence of PA, suggesting PA does not bind at Mo. By contrast, Fe EXAFS spectra show a clear and reproducible change in the long Fe-Fe interaction at ~ 3.7 Å on PA binding with the apparent appearance of a new Fe-Fe interaction at 3.99 Å. An analogous change in the long Mo-Fe 5.1 Å interaction is not seen. The NRVS spectra exclude the possibility of large-scale structural change of the FeMo-cofactor involving breaking the μ2 Fe-S-Fe bonds of the Fe6S9X core. The simplest chemically consistent structural change is that the bound form of PA is coordinated at Fe atoms (Fe6 or Fe7) adjacent to the Mo terminus, with a concomitant movement of the Fe away from the central atom X and along the Fe-X bond by about 0.35 Å. This study comprises the first experimental evidence of the conformational changes of the FeMo-cofactor active site on binding a substrate or product.

KW - Extended Absorption Fine Structure (EXAFS)

KW - Metalloprotein

KW - Nitrogen Fixation

KW - Nitrogenase

KW - Nuclear Resonant Vibrational Spectroscopy (NRVS)

KW - X-ray Absorption Spectroscopy (XAS)

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U2 - 10.1016/j.jinorgbio.2012.02.004

DO - 10.1016/j.jinorgbio.2012.02.004

M3 - Article

C2 - 22564272

AN - SCOPUS:84860525282

SN - 0162-0134

VL - 112

SP - 85

EP - 92

JO - Journal of Inorganic Biochemistry

JF - Journal of Inorganic Biochemistry

ER -

EXAFS and NRVS Reveal a Conformational Distortion of the FeMo-cofactor in the MoFe Nitrogenase Propargyl Alcohol Complex

Abstract

Bibliographical note

Keywords

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