EC Number |
Substrates |
Organism |
Products |
Reversibility |
---|
3.5.1.107 | maleamate + H2O |
- |
Pseudomonas putida |
maleate + NH3 |
- |
? |
3.5.1.107 | maleamate + H2O |
- |
Bordetella bronchiseptica |
maleate + NH3 |
- |
? |
3.5.1.107 | maleamate + H2O |
aerobic catabolism of nicotinic acid |
Pseudomonas putida |
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 |
- |
? |
3.5.1.107 | maleamate + H2O |
- |
Bordetella bronchiseptica RB50 |
maleate + NH3 |
- |
? |