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Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase

Cao, Lili LU ; Caldararu, Octav LU ; Rosenzweig, Amy C. and Ryde, Ulf LU (2018) In Angewandte Chemie - International Edition 57(1). p.162-166
Abstract

Particulate methane monooxygenase (pMMO) is one of the few enzymes that can activate methane. The metal content of this enzyme has been highly controversial, with suggestions of a dinuclear Fe site or mono-, di-, or trinuclear Cu sites. Crystal structures have shown a mono- or dinuclear Cu site, but the resolution was low and the geometry of the dinuclear site unusual. We have employed quantum refinement (crystallographic refinement enhanced with quantum-mechanical calculations) to improve the structure of the active site. We compared a number of different mono- and dinuclear geometries, in some cases enhanced with more protein ligands or one or two water molecules, to determine which structure fits two sets of crystallographic raw data... (More)

Particulate methane monooxygenase (pMMO) is one of the few enzymes that can activate methane. The metal content of this enzyme has been highly controversial, with suggestions of a dinuclear Fe site or mono-, di-, or trinuclear Cu sites. Crystal structures have shown a mono- or dinuclear Cu site, but the resolution was low and the geometry of the dinuclear site unusual. We have employed quantum refinement (crystallographic refinement enhanced with quantum-mechanical calculations) to improve the structure of the active site. We compared a number of different mono- and dinuclear geometries, in some cases enhanced with more protein ligands or one or two water molecules, to determine which structure fits two sets of crystallographic raw data best. In all cases, the best results were obtained with mononuclear Cu sites, occasionally with an extra water molecule. Thus, we conclude that there is no crystallographic support for a dinuclear Cu site in pMMO.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
copper, density functional theory, particulate methane monooxygenase, quantum refinement
in
Angewandte Chemie - International Edition
volume
57
issue
1
pages
5 pages
publisher
John Wiley & Sons
external identifiers
  • scopus:85039050887
ISSN
1433-7851
DOI
10.1002/anie.201708977
language
English
LU publication?
yes
id
dbd56fa0-8972-4cc4-8d12-4575729eb36b
date added to LUP
2018-01-05 10:09:46
date last changed
2018-01-06 03:00:02
@article{dbd56fa0-8972-4cc4-8d12-4575729eb36b,
  abstract     = {<p>Particulate methane monooxygenase (pMMO) is one of the few enzymes that can activate methane. The metal content of this enzyme has been highly controversial, with suggestions of a dinuclear Fe site or mono-, di-, or trinuclear Cu sites. Crystal structures have shown a mono- or dinuclear Cu site, but the resolution was low and the geometry of the dinuclear site unusual. We have employed quantum refinement (crystallographic refinement enhanced with quantum-mechanical calculations) to improve the structure of the active site. We compared a number of different mono- and dinuclear geometries, in some cases enhanced with more protein ligands or one or two water molecules, to determine which structure fits two sets of crystallographic raw data best. In all cases, the best results were obtained with mononuclear Cu sites, occasionally with an extra water molecule. Thus, we conclude that there is no crystallographic support for a dinuclear Cu site in pMMO.</p>},
  author       = {Cao, Lili and Caldararu, Octav and Rosenzweig, Amy C. and Ryde, Ulf},
  issn         = {1433-7851},
  keyword      = {copper,density functional theory,particulate methane monooxygenase,quantum refinement},
  language     = {eng},
  month        = {01},
  number       = {1},
  pages        = {162--166},
  publisher    = {John Wiley & Sons},
  series       = {Angewandte Chemie - International Edition},
  title        = {Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase},
  url          = {http://dx.doi.org/10.1002/anie.201708977},
  volume       = {57},
  year         = {2018},
}