3AXG

Structure of 6-aminohexanoate-oligomer hydrolase

Summary for 3AXG

• Entry DOI: 10.2210/pdb3axg/pdb
• Descriptor: Endotype 6-aminohexanoat-oligomer hydrolase, SODIUM ION (3 entities in total)
• Functional Keywords: hydrolase, nylon oligomer
• Biological source: Agromyces
• Total number of polymer chains: 15
• Total formula weight: 554031.51

Authors

Negoro, S.,Shibata, N.,Tanaka, Y.,Yasuhira, K.,Shibata, H.,Hashimoto, H.,Lee, Y.H.,Ohshima, S.,Santa, R.,Mochiji, K.,Goto, Y.,Ikegami, T.,Nagai, K.,Kato, D.,Takeo, M.,Higuchi, Y. (deposition date: 2011-04-04, release date: 2011-12-21, Last modification date: 2024-03-13)

Primary citation

Negoro, S.,Shibata, N.,Tanaka, Y.,Yasuhira, K.,Shibata, H.,Hashimoto, H.,Lee, Y.H.,Oshima, S.,Santa, R.,Mochiji, K.,Goto, Y.,Ikegami, T.,Nagai, K.,Kato, D.,Takeo, M.,Higuchi, Y.
Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis
J.Biol.Chem., 287:5079-5090, 2012

PubMed Abstract: We performed x-ray crystallographic analyses of the 6-aminohexanoate oligomer hydrolase (NylC) from Agromyces sp. at 2.0 Å-resolution. This enzyme is a member of the N-terminal nucleophile hydrolase superfamily that is responsible for the degradation of the nylon-6 industry byproduct. We observed four identical heterodimers (27 kDa + 9 kDa), which resulted from the autoprocessing of the precursor protein (36 kDa) and which constitute the doughnut-shaped quaternary structure. The catalytic residue of NylC was identified as the N-terminal Thr-267 of the 9-kDa subunit. Furthermore, each heterodimer is folded into a single domain, generating a stacked αββα core structure. Amino acid mutations at subunit interfaces of the tetramer were observed to drastically alter the thermostability of the protein. In particular, four mutations (D122G/H130Y/D36A/E263Q) of wild-type NylC from Arthrobacter sp. (plasmid pOAD2-encoding enzyme), with a heat denaturation temperature of T(m) = 52 °C, enhanced the protein thermostability by 36 °C (T(m) = 88 °C), whereas a single mutation (G111S or L137A) decreased the stability by ∼10 °C. We examined the enzymatic hydrolysis of nylon-6 by the thermostable NylC mutant. Argon cluster secondary ion mass spectrometry analyses of the reaction products revealed that the major peak of nylon-6 (m/z 10,000-25,000) shifted to a smaller range, producing a new peak corresponding to m/z 1500-3000 after the enzyme treatment at 60 °C. In addition, smaller fragments in the soluble fraction were successively hydrolyzed to dimers and monomers. Based on these data, we propose that NylC should be designated as nylon hydrolase (or nylonase). Three potential uses of NylC for industrial and environmental applications are also discussed.

PubMed: 22187439
DOI: 10.1074/jbc.M111.321992

Experimental method

X-RAY DIFFRACTION (2 Å)