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Literature summary for 1.4.9.1 extracted from

  • Zelleke, T.; Marx, D.
    Free-energy landscape and proton transfer pathways in oxidative deamination by methylamine dehydrogenase (2017), Chemphyschem, 18, 208-222 .
    View publication on PubMed
Search for more literature for 1.4.9.1

Activating Compound

Activating Compound Comment Organism Structure
amicyanin
-
 Paracoccus denitrificans

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
methylamine + H2O + 2 amicyanin Paracoccus denitrificans
-
 formaldehyde + NH3 + 2 reduced amicyanin
-
 ?

Organism

Organism UniProt Comment Textmining
Paracoccus denitrificans P22619 AND P29894 alpha and beta subunits
-

Reaction

Reaction Comment Organism Reaction ID
methylamine + H2O + 2 amicyanin = formaldehyde + NH3 + 2 reduced amicyanin the rate-determining step in the reductive half-reaction of the bacterial enzyme methylamine dehydrogenase is the proton abstraction from the native substrate methylamine, ab initio QM/MM molecular dynamics simulations, average flow of electronic charge within the QM subsystem during proton transfer to OD1 computed from randomly selected subsets of the reactant, model comparisons, detailed overview Paracoccus denitrificans
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
methylamine + H2O + 2 amicyanin
-
 Paracoccus denitrificans formaldehyde + NH3 + 2 reduced amicyanin
-
 ?

Subunits

Subunits Comment Organism
heterotetramer
-
 Paracoccus denitrificans

Synonyms

Synonyms Comment Organism
MADH
-
 Paracoccus denitrificans
methylamine dehydrogenase
-
 Paracoccus denitrificans

Cofactor

Cofactor Comment Organism Structure
tryptophan tryptophylquinone TTQ Paracoccus denitrificans

General Information

General Information Comment Organism
additional information QM/MM molecular dynamics simulations at room temperature generate a multidimensional thermal free-energy landscape without restriction of the degrees of freedom beyond a multidimensional reaction subspace mapping two rather similar pathways for the underlying proton transfer to one of two aspartate carboxyl oxygen atoms, termed OD1 and OD2, which hydrogen bond with Thr122 and Trp108, respectively. Despite significant large-amplitude motion perpendicular to the one-dimensional proton transfer coordinate, due to fluctuations of the donor-acceptor distance of about 3 a, it is found that the one-dimensional proton transfer free-energy profiles are essentially identical to the minimum free-energy pathways on the multidimensional free-energy landscapes for both proton transfer channels. Proton transfer to one of the acceptor oxygen atoms (the OD2 site) is slightly favored in methylamine dehydrogenase both kinetically and thermodynamically. Modeling is based on the crysta structure of the substrate-free enzyme MADH from Paracoccus denitrificans resolved at 1.75 A, PDB ID 2BBK Paracoccus denitrificans