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Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase

Bergmann, Justin LU ; Oksanen, Esko LU and Ryde, Ulf LU (2021) In Journal of Inorganic Biochemistry 219.
Abstract

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard... (More)

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard crystallographic refinement) and comparing different interpretations of the structure with normal crystallographic and quantum mechanical quality measures. We have performed such quantum-refinement calculations to address two important issues for nitrogenase. First, we show that the bidentate ligand of the active-site FeV cluster in V‑nitrogenase is carbonate, rather than bicarbonate or nitrate. Second, we study the CO-inhibited structure of Mo‑nitrogenase. CO binds to a reduced and protonated state of the enzyme by replacing one of the sulfide ions (S2B) in the active-site FeMo cluster. We examined if it is possible to deduce from the crystal structure the location of the protons. Our results indicates that the crystal structure is best modelled as fully deprotonated.

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type
Contribution to journal
publication status
published
subject
keywords
Carbonate, Nitrogenase, Protonation, Quantum refinement
in
Journal of Inorganic Biochemistry
volume
219
article number
111426
publisher
Elsevier
external identifiers
  • scopus:85102818877
  • pmid:33756394
ISSN
0162-0134
DOI
10.1016/j.jinorgbio.2021.111426
language
English
LU publication?
yes
id
b815c9e9-9854-4260-9e48-7b3fd002d76b
date added to LUP
2021-03-30 11:22:46
date last changed
2021-05-11 04:44:28
@article{b815c9e9-9854-4260-9e48-7b3fd002d76b,
  abstract     = {<p>Nitrogenase is the only enzyme that can cleave the triple bond in N<sub>2</sub>, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard crystallographic refinement) and comparing different interpretations of the structure with normal crystallographic and quantum mechanical quality measures. We have performed such quantum-refinement calculations to address two important issues for nitrogenase. First, we show that the bidentate ligand of the active-site FeV cluster in V‑nitrogenase is carbonate, rather than bicarbonate or nitrate. Second, we study the CO-inhibited structure of Mo‑nitrogenase. CO binds to a reduced and protonated state of the enzyme by replacing one of the sulfide ions (S2B) in the active-site FeMo cluster. We examined if it is possible to deduce from the crystal structure the location of the protons. Our results indicates that the crystal structure is best modelled as fully deprotonated.</p>},
  author       = {Bergmann, Justin and Oksanen, Esko and Ryde, Ulf},
  issn         = {0162-0134},
  language     = {eng},
  publisher    = {Elsevier},
  series       = {Journal of Inorganic Biochemistry},
  title        = {Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase},
  url          = {http://dx.doi.org/10.1016/j.jinorgbio.2021.111426},
  doi          = {10.1016/j.jinorgbio.2021.111426},
  volume       = {219},
  year         = {2021},
}