Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
A Mechanism from Quantum Chemical Studies for Methane Formation in Methanogenesis
Stockholm University, Faculty of Science, Department of Physics.
Stockholm University, Faculty of Science, Department of Physics.
Stockholm University, Faculty of Science, Department of Physics.
2002 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 124, no 15, 4039-4049 p.Article in journal (Refereed) Published
Abstract [en]

The mechanism for methane formation in methyl-coenzyme M reductase (MCR) has been investigated using the B3LYP hybrid density functional method and chemical models consisting of 107 atoms. The experimental X-ray crystal structure of the enzyme in the inactive MCRox1-silent state was used to set up the initial model structure. The calculations suggest a mechanism not previously proposed, in which the most remarkable feature is the formation of an essentially free methyl radical at the transition state. The reaction cycle suggested starts from a Michaelis complex with CoB and methyl-CoM coenzymes bound and with a squareplanar coordination of the Ni(I) center in the tetrapyrrole F430 prosthetic group. In the rate-limiting step the methyl radical is released from methyl-CoM, induced by the attack of Ni(I) on the methyl-CoM thioether sulfur. In this step, the metal center is oxidized from Ni(I) to Ni(II). The resulting methyl radical is rapidly quenched by hydrogen-atom transfer from the CoB thiol group, yielding the methane molecule and the CoB radical. The estimated activation energy is around 20 kcal/mol, which includes a significant contribution from entropy due to the formation of the free methyl. The mechanism implies an inversion of configuration at the reactive carbon. The size of the inversion barrier is used to explain the fact that CF3−S−CoM is an inactive substrate. Heterodisulfide CoB−S−S−CoM formation is proposed in the final step in which nickel is reduced back to Ni(I). The suggested mechanism agrees well with experimental observations.

Place, publisher, year, edition, pages
American Chemical Society , 2002. Vol. 124, no 15, 4039-4049 p.
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:su:diva-23842DOI: 10.1021/ja011664rOAI: oai:DiVA.org:su-23842DiVA: diva2:194868
Note
Part of urn:nbn:se:su:diva-513Available from: 2005-05-05 Created: 2005-05-05 Last updated: 2017-12-13Bibliographically approved
In thesis
1. Theoretical Modeling of Enzyme Catalysis with Focus on Radical Chemistry
Open this publication in new window or tab >>Theoretical Modeling of Enzyme Catalysis with Focus on Radical Chemistry
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Hybrid density functional theory (DFT) B3LYP method is applied to study the four diverse enzyme systems: zinc-containing peptidases (thermolysin and stromelysin), methyl-coenzyme M reductase, ribonucleotide reductases (classes I and III), and superoxide dismutases (Cu,Zn- and Ni-dependent enzymes). Powerfull tools of modern quantum chemistry are used to address the questions of biological pathways at their molecular level, proposing a novel mechanism for methane production by methyl-coenzyme M reductase and providing additional insights into hydrolysis by zinc peptidases, substrate conversion by ribonucleotide reductases, and biological superoxide dismutation. Catalysis by these enzymes, with the exception of zinc peptidases, involves radical chemistry.

Place, publisher, year, edition, pages
Stockholm: Fysikum, 2005. 104 p.
Keyword
density functional theory, enzyme catalysis, radical chemistry, zinc-containing peptidase, methyl-coenzyme M reductase, ribonucleotide reductase, superoxide dismutase
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:su:diva-513 (URN)91-7155-018-6 (ISBN)
Public defence
2005-05-26, sal FA32, AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 10:00
Opponent
Supervisors
Available from: 2005-05-05 Created: 2005-05-05Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Blomberg, Margareta R ASiegbahn, Per E M
By organisation
Department of Physics
In the same journal
Journal of the American Chemical Society
Physical Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 43 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf