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Literature summary for 3.5.1.107 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
Search for more literature for 3.5.1.107

Metals/Ions

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

Natural Substrates/ Products (Substrates)

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

Organism

Organism UniProt Comment Textmining
Bordetella bronchiseptica A0A0H3LKK8
-
-
Bordetella bronchiseptica ATCC BAA-588 A0A0H3LKK8
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
maleamate + H2O
-
 Bordetella bronchiseptica maleate + NH3
-
 ?
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
-
 ?
maleamate + H2O
-
 Bordetella bronchiseptica ATCC BAA-588 maleate + NH3
-
 ?
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

Synonyms Comment Organism
NicF
-
 Bordetella bronchiseptica

General Information

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