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Literature summary extracted from

  • Ion, B.F.; Meister, P.J.; Gauld, J.W.
    Multiscale computational study on the catalytic mechanism of the nonmetallo amidase maleamate amidohydrolase (NicF) (2019), J. Phys. Chem. A, 123, 7710-7719 .
    View publication on PubMed

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.107 additional information metal-dependent enzyme Bordetella bronchiseptica

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.107 maleamate + H2O Bordetella bronchiseptica
-
maleate + NH3
-
?
3.5.1.107 maleamate + H2O Bordetella bronchiseptica ATCC BAA-588
-
maleate + NH3
-
?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.107 Bordetella bronchiseptica A0A0H3LKK8
-
-
3.5.1.107 Bordetella bronchiseptica ATCC BAA-588 A0A0H3LKK8
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.107 maleamate + H2O
-
Bordetella bronchiseptica maleate + NH3
-
?
3.5.1.107 maleamate + H2O multiscale computational enzymology is used to investigate the catalytic mechanism, substrate binding, oxyanion hole, and roles of key active site residues of the enzyme. Molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) and QTAIM methods are applied. The mechanism of the NicF-catalyzed reaction proceeds by a nucleophilic addition-elimination sequence involving the formation of a thioester enzyme intermediate (IC2 in stage 1) followed by hydrolysis of the thioester bond to form the products (stage 2). Consequently, the formation of IC2 in stage 1 is the rate-limiting step with a barrier of 88.8 kJ/mol relative to the reactant complex, RC. Along with -NH- donor groups of the oxyanion hole (i.e., HN-Thr146, HN-Cys150), the active site beta-hydroxyl of threonine (HO-betaThr146) is concluded to play a role in stabilizing the carbonyl oxygen of maleamate during the mechanism Bordetella bronchiseptica maleate + NH3
-
?
3.5.1.107 maleamate + H2O
-
Bordetella bronchiseptica ATCC BAA-588 maleate + NH3
-
?
3.5.1.107 maleamate + H2O multiscale computational enzymology is used to investigate the catalytic mechanism, substrate binding, oxyanion hole, and roles of key active site residues of the enzyme. Molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) and QTAIM methods are applied. The mechanism of the NicF-catalyzed reaction proceeds by a nucleophilic addition-elimination sequence involving the formation of a thioester enzyme intermediate (IC2 in stage 1) followed by hydrolysis of the thioester bond to form the products (stage 2). Consequently, the formation of IC2 in stage 1 is the rate-limiting step with a barrier of 88.8 kJ/mol relative to the reactant complex, RC. Along with -NH- donor groups of the oxyanion hole (i.e., HN-Thr146, HN-Cys150), the active site beta-hydroxyl of threonine (HO-betaThr146) is concluded to play a role in stabilizing the carbonyl oxygen of maleamate during the mechanism Bordetella bronchiseptica ATCC BAA-588 maleate + NH3
-
?

Synonyms

EC Number Synonyms Comment Organism
3.5.1.107 NicF
-
Bordetella bronchiseptica

General Information

EC Number General Information Comment Organism
3.5.1.107 metabolism key enzyme in vitamin B3 metabolism Bordetella bronchiseptica