A new variant of the Ntn hydrolase fold revealed by the crystal structure of l-aminopeptidase d-Ala-esterase/amidase from Ochrobactrum anthropi

Bompard-Gilles, C.; Villeret, Vincent; Davies, G.J.; Fanuel, Laurence; Joris, Bernard; Frère, Jean‐Marie; Beeumen, Jozef Van

doi:10.1016/s0969-2126(00)00091-5

Cited by 44 publications

(56 citation statements)

References 48 publications

(82 reference statements)

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“…The following four proteins (including one hypothetical protein) that exhibited high z-scores (z-score Ͼ14) were identified: L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi (DmpA; z-score ϭ 26.3; PDB ID code: 1B65) (18), hypothetical Daminopeptidase (z-score ϭ 25.9; PDB ID code, 2DRH), ␤-peptidyl aminopeptidase from Sphingosinicella xenopeptidilytica (BapA; z-score ϭ 25.2; PDB ID code: 3N33) (20), and ornithine acetyltransferase from Streptomyces clavuligerus (OAT; z-score ϭ 14.1; PDB ID code: 1VZ6) (21) (supplemental Table S3). In contrast, the DALI z-scores of the other proteins in the PDB were determined to be below 8.…”

Section: Subunit Structure and Function Relationship With Other N-tn mentioning

confidence: 99%

“…Additionally, the newly generated N-terminal Ser-250 of the ␤-subunit plays the roles of both the nucleophile (hydroxyl group) and the general base (␣-amino group) in catalytic reactions (18). In NylC, Thr-267 participates in a hydrogen-bonding network with Asn-219, Asp-306, and Gly-307 (backbone-N).…”

Section: Residues Responsible For Autoprocessing and Catalytic Functionmentioning

confidence: 99%

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Three-dimensional Structure of Nylon Hydrolase and Mechanism of Nylon-6 Hydrolysis

Negoro

Shibata

Tanaka

et al. 2012

Journal of Biological Chemistry

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Background: Biodegradation of polyamides is important from the industrial and environmental point of view. Results: We identified the catalytic residue of nylon hydrolase as Thr-267 and enhanced the protein thermostability by 36°C (T m ϭ 88°C) by introducing mutations at the subunit interfaces of tetramer structure. Conclusion:We revealed the mechanism of nylon-6 hydrolysis. Significance: We established an approach to biodegrade polymeric nylon-6.

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Section: Subunit Structure and Function Relationship With Other N-tn mentioning

confidence: 99%

Section: Residues Responsible For Autoprocessing and Catalytic Functionmentioning

confidence: 99%

Three-dimensional Structure of Nylon Hydrolase and Mechanism of Nylon-6 Hydrolysis

Negoro

Shibata

Tanaka

et al. 2012

Journal of Biological Chemistry

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“…After autocleavage, Ser250 becomes the first residue of the mature protein and the a-amino group of the newly generated N terminus of the protein functions as the general base in catalysis abstracting a proton from the Ser250 hydroxyl group. The protein fold of this protease is novel and characterized by a four-layered abba topology (Bompard-Gilles et al 2000) called the N-terminal nucleophile hydrolase fold (Brannigan et al 1995).…”

Section: Nucleoporinmentioning

confidence: 99%

Unconventional serine proteases: Variations on the catalytic Ser/His/Asp triad configuration

2008

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Serine proteases comprise nearly one-third of all known proteases identified to date and play crucial roles in a wide variety of cellular as well as extracellular functions, including the process of blood clotting, protein digestion, cell signaling, inflammation, and protein processing. Their hallmark is that they contain the so-called ''classical'' catalytic Ser/His/Asp triad. Although the classical serine proteases are the most widespread in nature, there exist a variety of ''nonclassical'' serine proteases where variations to the catalytic triad are observed. Such variations include the triads Ser/His/Glu, Ser/ His/His, and Ser/Glu/Asp, and include the dyads Ser/Lys and Ser/His. Other variations are seen with certain serine and threonine peptidases of the Ntn hydrolase superfamily that carry out catalysis with a single active site residue. This work discusses the structure and function of these novel serine proteases and threonine proteases and how their catalytic machinery differs from the prototypic serine protease class.

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“…The 10 N-terminal residues obtained by protein sequencing were identical to those deduced from the nucleotide sequence starting from Thr267, demonstrating that NylC A and NylC K were subjected to specific cleavage at Asn266/Thr267, which has previously been identified as a cleavage site in NylC p2 (4). The observed processing is a specific feature of the N-terminal nucleophile (Ntn) hydrolase family, in which cleavage is performed auto-catalytically to generate two subunits (1,2,3,8).…”

Section: Fig 2 Tlc Of Various Nylon Oligomers and Reaction Productsmentioning

confidence: 99%

6-Aminohexanoate Oligomer Hydrolases from the Alkalophilic Bacteria Agromyces sp. Strain KY5R and Kocuria sp. Strain KY2

Yasuhira

Tanaka

Shibata

et al. 2007

Appl Environ Microbiol

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Alkalophilic, nylon oligomer-degrading strains, Agromyces sp. and Kocuria sp., were isolated from the wastewater of a nylon-6 factory and from activated sludge from a sewage disposal plant. The 6-aminohexanoate oligomer hydrolases (NylC) from the alkalophilic strains had 95.8 to 98.6% similarity to the enzyme in neutrophilic Arthrobacter sp. but had superior thermostability, activity under alkaline conditions, and affinity for nylon-related substrates, which would be advantageous for biotechnological applications.The biodegradation of unnatural synthetic compounds which have been released into the natural environment with the development of the chemical industry provides a suitable system for investigating how microorganisms evolve the enzymes essential for the degradation of such xenobiotic compounds. We have studied the degradation of by-products of the manufacture of nylon-6, namely, 6-aminohexanoate (Ahx) oligomers (nylon oligomers), by Arthrobacter sp. strain KI72 (formerly called a Flavobacterium sp. [see Addendum]) as a model system (9, 10). We found that three enzymes, the Ahx cyclicdimer hydrolase (NylA) (6), the Ahx dimer hydrolase (NylB) (7,12,13), and the Ahx endo-type-oligomer hydrolase (NylC) (4, 11), are responsible for the degradation of the nylon oligomers ( Fig. 1).Nylon oligomers are discharged from nylon factories as an alkaline solution. However, the optimum pH for the growth of strain KI72 is approximately 7, and thus far, no alkalophilic, nylon oligomer-degrading strains have been isolated. Therefore, if such microorganisms could be isolated, they would be useful for the direct treatment of wastes from nylon-6 factories. In addition, comparative analyses for the responsible enzymes are expected to provide information on the evolutionary and functional divergence of these enzymes. In this paper, we report the isolation of alkalophilic, nylon oligomer-degrading bacteria, their genetic cloning, and the characterization of their nylon oligomer-degrading enzymes.Isolation of alkalophilic nylon oligomer-degrading bacteria. The nylon oligomer mixture (NOM) (Toyobo Co., Tsuruga, Japan) used is a mixture of Ahx cyclic and linear oligomers. To obtain the cyclic-oligomer-enriched fraction used for bacterial screening, the NOM was extensively washed with hot water on filter paper to remove water-soluble linear oligomers. After being dried, washed NOM (NOM-W) was obtained. Thin-layer chromatography (TLC) analysis revealed that no free amino groups were detected by ninhydrin in NOM-W, which indicates the absence of the linear oligomer, while several spots appeared in the original NOM (Fig. 2C).Microorganisms included in activated sludge from a sewage disposal plant (sample 1) and in wastewater from a nylon-6 factory (sample 2) were enriched in NOM10 medium (0.4% NOM-W, 0.2% Na 3 PO 4 ⅐ 12H 2 O, 0.1% K 2 HPO 4 , 0.26% Na 2 CO 3 , 0.2% NaHCO 3 , 0.02% MgSO 4 ⅐ 7H 2 O, 0.5% NaCl, 0.01% yeast extract, pH 10). The cultures were diluted with sterilized water and plated on LB-NOM10 plates (LB plates containing...

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A new variant of the Ntn hydrolase fold revealed by the crystal structure of l-aminopeptidase d-Ala-esterase/amidase from Ochrobactrum anthropi

Cited by 44 publications

References 48 publications

Three-dimensional Structure of Nylon Hydrolase and Mechanism of Nylon-6 Hydrolysis

Three-dimensional Structure of Nylon Hydrolase and Mechanism of Nylon-6 Hydrolysis

Unconventional serine proteases: Variations on the catalytic Ser/His/Asp triad configuration

6-Aminohexanoate Oligomer Hydrolases from the Alkalophilic Bacteria Agromyces sp. Strain KY5R and Kocuria sp. Strain KY2

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