PDBsum entry 2dcf

Hydrolase

PDB id: 2dcf

Contents

Protein chain

384 a.a. *

Ligands

SO4 ×2

ACA-ACA

MES

GOL ×4

Waters ×479

* Residue conservation analysis

PDB id:

2dcf

Name:

Hydrolase

Title:

Crystal structure of 6-aminohexanoate-dimer hydrolase s112a/g181d/h266n mutant with substrate

Structure:

6-aminohexanoate-dimer hydrolase. Chain: a. Engineered: yes. Mutation: yes

Source:

Flavobacterium sp.. Organism_taxid: 239. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.183 R-free: 0.195

Authors:

T.Ohki,N.Shibata,Y.Higuchi,M.Takeo,S.Negoro

Key ref:

S.Negoro et al. (2007). Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase. J Mol Biol, 370, 142-156. PubMed id: 17512009 DOI: 10.1016/j.jmb.2007.04.043

Date:

06-Jan-06 Release date: 09-Jan-07

Protein chain

P07062  (NYLB2_PAEUR) -  6-aminohexanoate-dimer hydrolase from Paenarthrobacter ureafaciens

Seq: 392 a.a.

Struc: 384 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.1.46 - 6-aminohexanoate-oligomer exohydrolase.
• Reaction:
  1. [N-(6-aminohexanoyl)](n) + H2O = [N-(6-aminohexanoyl)](n-1) + 6-aminohexanoate
  2. N-(6-aminohexanoyl)-6-aminohexanoate + H2O = 2 6-aminohexanoate

[N-(6-aminohexanoyl)](n) + H2O = [N-(6-aminohexanoyl)](n-1) (Bound ligand (Het Group name = ACA) matches with 88.89% similarity) + 6-aminohexanoate

N-(6-aminohexanoyl)-6-aminohexanoate + H2O = 2 × 6-aminohexanoate (Bound ligand (Het Group name = ACA) matches with 88.89% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2007.04.043

J Mol Biol 370:142-156 (2007)

PubMed id: 17512009

Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase.

S.Negoro, T.Ohki, N.Shibata, K.Sasa, H.Hayashi, H.Nakano, K.Yasuhira, D.Kato, M.Takeo, Y.Higuchi.

ABSTRACT

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.

Selected figure(s)

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.).

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 142-156) copyright 2007.

Figures were selected by the author.