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Literature summary extracted from

  • Baba, T.; Boero, M.; Kamiya, K.; Ando, H.; Negoro, S.; Nakano, M.; Shigeta, Y.
    Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes (2015), Phys. Chem. Chem. Phys., 17, 4492-4504.
    View publication on PubMed

Protein Variants

EC Number Protein Variants Comment Organism
3.5.1.117 D15G site-directed mutagenesis Arthrobacter sp.
3.5.1.117 D181G site-directed mutagenesis Arthrobacter sp.
3.5.1.117 G181D/H266N site-directed mutagenesis Arthrobacter sp.
3.5.1.117 G181D/H266N/D370Y site-directed mutagenesis Arthrobacter sp.
3.5.1.117 P4R site-directed mutagenesis Arthrobacter sp.
3.5.1.117 S8Q site-directed mutagenesis Arthrobacter sp.
3.5.1.117 T3A site-directed mutagenesis Arthrobacter sp.
3.5.1.117 T5S site-directed mutagenesis Arthrobacter sp.
3.5.1.117 Y170F site-directed mutagenesis, the Tyr170 is replaced by phenylalanine, which is unable to form a hydrogen bond with the amide bond, thus, resulting in an increase in the activation barrier of more than 10 kcal/mol, but despite the lack of hydrogen bonding between the Y170F and the substrate, the highest free energy barrier for the induced-fit is similar to that of wild-type suggesting that in the induced-fit process, kinetics is little affected by the mutation, hybrid quantum mechanics/molecular mechanics (QM/MM) dynamical simulations Arthrobacter sp.

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.117 [N-(6-aminohexanoyl)]n + H2O Arthrobacter sp.
-
 [N-(6-aminohexanoyl)]n-x + [N-(6-aminohexanoyl)]x
-
 ?
3.5.1.117 [N-(6-aminohexanoyl)]n + H2O Arthrobacter sp. KI72
-
 [N-(6-aminohexanoyl)]n-x + [N-(6-aminohexanoyl)]x
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.117 Arthrobacter sp.
-
-
-
3.5.1.117 Arthrobacter sp. KI72
-
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
3.5.1.117 [N-(6-aminohexanoyl)]n + H2O = [N-(6-aminohexanoyl)]n-x + [N-(6-aminohexanoyl)]x the Tyr170 residue points the NH group towards the proton-acceptor site of an artificial amide bond, reaction mechanism, overview Arthrobacter sp.
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.117 nylon-6 polymer + H2O
-
 Arthrobacter sp. ?
-
 ?
3.5.1.117 nylon-6 polymer + H2O
-
 Arthrobacter sp. KI72 ?
-
 ?
3.5.1.117 [N-(6-aminohexanoyl)]n + H2O
-
 Arthrobacter sp. [N-(6-aminohexanoyl)]n-x + [N-(6-aminohexanoyl)]x
-
 ?
3.5.1.117 [N-(6-aminohexanoyl)]n + H2O
-
 Arthrobacter sp. KI72 [N-(6-aminohexanoyl)]n-x + [N-(6-aminohexanoyl)]x
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.5.1.117 NylB
-
 Arthrobacter sp.
3.5.1.117 nylon oligomer hydrolase
-
 Arthrobacter sp.

General Information

EC Number General Information Comment Organism
3.5.1.117 evolution NylB belongs to the class C of the beta-lactamase family, which is characterized by the presence of a catalytic triad, namely, Ser, Tyr, and Lys, having the ability to promote the hydrolysis of amide and/or ester bonds. Natural selection is responsible for the development of the peculiar hydrolytic activity of Arthrobacter sp. KI72 Arthrobacter sp.
3.5.1.117 additional information the enzyme can adopt two different conformations: a substrate-free form (open form) and a substrate-bound form (closed from), hybrid quantum mechanics/molecular mechanics (QM/MM) dynamical simulations complemented with free energy sampling methods, allow to determine the reaction mechanismin NylB and address one of the possible roles of Tyr170 during the acylation process, enzyme structure and induced-fit process, detailed overview Arthrobacter sp.