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PDBsum entry 2dcf
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References listed in PDB file
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Key reference
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Title
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Nylon-Oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-Aminohexanoate-Dimer hydrolase.
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Authors
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S.Negoro,
T.Ohki,
N.Shibata,
K.Sasa,
H.Hayashi,
H.Nakano,
K.Yasuhira,
D.Kato,
M.Takeo,
Y.Higuchi.
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Ref.
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J Mol Biol, 2007,
370,
142-156.
[DOI no: ]
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PubMed id
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Abstract
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We performed X-ray crystallographic analyses of 6-aminohexanoate-dimer hydrolase
(Hyb-24DN), an enzyme responsible for the degradation of nylon-6, an industry
by-product, and of a complex between Hyb-24DN-A(112) (S112A-mutant of Hyb-24DN)
and 6-aminohexanoate-linear dimer (Ald) at 1.58 A and 1.4 A resolution,
respectively. In Hyb-24DN, Asp181-O(delta) forms hydrogen bonds with
Tyr170-O(eta), -two of the catalytic and binding amino acids, and a loop between
Asn167 and Val177. This state is the so-called open form, allowing its substrate
to bind in the space between the loop and catalytic residues. Upon substrate
binding (in Hyb-24DN-A(112)/Ald complex), the loop is shifted 4.3 A at
Tyr170-C(alpha), and the side-chain of Tyr170 is rotated. By the combined
effect, Tyr170-O(eta) moves a total of 10.5 A, resulting in the formation of
hydrogen bonds with the nitrogen of amide linkage in Ald (closed form). In
addition, electrostatic interaction between Asp181-O(delta) and the amino group
in Ald stabilizes the substrate binding. We propose here that the enzyme
catalysis proceeds according to the following steps: (i) Ald-induced transition
from open to closed form, (ii) nucleophilic attack of Ser112 to Ald and
formation of a tetrahedral intermediate, (iii) formation of acyl enzyme and
transition to open form, (iv) deacylation. Amino acid substitutions reducing the
enzyme/Ald interaction at positions 181 or 170 drastically decreased the
Ald-hydrolytic activity, but had very little effect on esterolytic activity,
suggesting that esterolytic reaction proceeds regardless of conversion. Present
models illustrate why new activity against the nylon oligomer has evolved in an
esterase with beta-lactamase folds, while retaining the original esterolytic
functions.
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Figure 5.
Figure 5. Surface structure of entrance of catalytic
cleft of Hyb-24DN, DD-peptidase and class C β-lactamase.
(a) Hyb-24DN including Ald at spatially equivalent position
(open form). (b) Hyb-24DN-A^112/Ald complex (closed form). (c)
DD-Peptidase/substrate
(glycyl-L-α-amino-ε-pimelyl-D-alanyl-D-alanine) complex. (d)
Extended spectrum class C
β-lactamase/cefotaxime-analogue(m-nitrophenyl-2-(2-aminothiazol-4-yl)-2-[(Z)-methoxyimino]acetylaminomethyl
phosphonate) complex (PDB ID code: 1RGY). Substrates are shown
as stick model. Figures were generated with program MolFeat
(version 2.2, FiatLux Co.). Figure 5. Surface structure of
entrance of catalytic cleft of Hyb-24DN, DD-peptidase
and class C β-lactamase. (a) Hyb-24DN including Ald at
spatially equivalent position (open form). (b)
Hyb-24DN-A^112/Ald complex (closed form). (c)
DD-Peptidase/substrate
(glycyl-L-α-amino-ε-pimelyl-D-alanyl-D-alanine) complex. (d)
Extended spectrum class C
β-lactamase/cefotaxime-analogue(m-nitrophenyl-2-(2-aminothiazol-4-yl)-2-[(Z)-methoxyimino]acetylaminomethyl
phosphonate) complex (PDB ID code: 1RGY). Substrates are shown
as stick model. Figures were generated with program MolFeat
(version 2.2, FiatLux Co.).
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Figure 8.
Figure 8. Proposed catalytic mechanism of
6-aminohexanoate-dimer hydrolase. In this model, enzyme
catalysis proceeds according to the following steps: (i)
Ald-induced transition from open to closed form, (ii)
nucleophilic attack of Ser112 to Ald and formation of
tetrahedral intermediate, (iii) formation of acyl enzyme and
transition to open form, (iv) deacylation (formation of
tetrahedral intermediate and regeneration of free enzyme). (a)
Free enzyme, (d) acyl enzyme, and (e) tetrahedral intermediate
are present as open forms, and (b) enzyme + substrate and (c)
tetrahedral intermediate are present as closed forms. Figure
8. Proposed catalytic mechanism of 6-aminohexanoate-dimer
hydrolase. In this model, enzyme catalysis proceeds according to
the following steps: (i) Ald-induced transition from open to
closed form, (ii) nucleophilic attack of Ser112 to Ald and
formation of tetrahedral intermediate, (iii) formation of
acyl enzyme and transition to open form, (iv) deacylation
(formation of tetrahedral intermediate and regeneration of free
enzyme). (a) Free enzyme, (d) acyl enzyme, and (e) tetrahedral
intermediate are present as open forms, and (b) enzyme +
substrate and (c) tetrahedral intermediate are present as closed
forms.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
370,
142-156)
copyright 2007.
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