Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N-diacetylchitobiose deacetylase

Shouhei Mine, Mayumi Niiyama, Wakana Hashimoto, Takahisa Ikegami, Daisuke Koma, Takashi Ohmoto, Yohta Fukuda, Tsuyoshi Inoue, Yoshito Abe, Tadashi Ueda, Junji Morita, Koichi Uegaki, Tsutomu Nakamura

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

In order to develop a structure-based understanding of the chitinolytic pathway in hyperthermophilic Pyrococcus species, we performed crystallographic studies on N,N-diacetylchitobiose deacetylases (Dacs) from Pyrococcus horikoshii (Ph-Dac) and Pyrococcus furiosus (Pf-Dac). Neither Ph-Dac nor Pf-Dac was expressed in the soluble fraction of Escherichia coli harboring the expression plasmid. However, insertion of the target genes into the chromosome of E. coli yielded the soluble recombinant protein. The purified Pyrococcus Dacs were active and thermostable up to 85 C. The crystal structures of Ph-Dac and Pf-Dac were determined at resolutions of 2.0 Å and 1.54 Å, respectively. The Pyrococcus Dac forms a hexamer composed of two trimers. These Dacs are characterized by an intermolecular cleft, which is formed by two polypeptides in the trimeric assembly. In Ph-Dac, catalytic Zn situated at the end of the cleft is coordinated by three side chain ligands from His44, Asp47, and His155, and by a phosphate ion derived from the crystallization reservoir solution. We considered that the bound phosphate mimicked the tetrahedral oxyanion, which is an intermediate of hydrolysis of the N-acetyl group, and proposed an appropriate reaction mechanism. In the proposed mechanism, the Nε atom of His264 (from the adjacent polypeptide in the Ph-Dac sequence) is directly involved in the stabilization of the oxyanion intermediate. Mutation analysis also indicated that His264 was essential to the catalysis. These factors give the archaeal Dacs an unprecedented active site architecture a Zn-dependent deacetylases.

Original languageEnglish
Pages (from-to)2584-2596
Number of pages13
JournalFEBS Journal
Volume281
Issue number11
DOIs
Publication statusPublished - Jan 1 2014

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Chromosomes
Pyrococcus
Escherichia coli
Phosphates
Peptides
Crystallization
Recombinant Proteins
Catalysis
Hydrolysis
Plasmids
Stabilization
Genes
Crystal structure
Ions
Ligands
Pyrococcus horikoshii
Chromosomes, Human, 16-18
Atoms
Pyrococcus furiosus
Insertional Mutagenesis

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Mine, S., Niiyama, M., Hashimoto, W., Ikegami, T., Koma, D., Ohmoto, T., ... Nakamura, T. (2014). Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N-diacetylchitobiose deacetylase. FEBS Journal, 281(11), 2584-2596. https://doi.org/10.1111/febs.12805

Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N-diacetylchitobiose deacetylase. / Mine, Shouhei; Niiyama, Mayumi; Hashimoto, Wakana; Ikegami, Takahisa; Koma, Daisuke; Ohmoto, Takashi; Fukuda, Yohta; Inoue, Tsuyoshi; Abe, Yoshito; Ueda, Tadashi; Morita, Junji; Uegaki, Koichi; Nakamura, Tsutomu.

In: FEBS Journal, Vol. 281, No. 11, 01.01.2014, p. 2584-2596.

Research output: Contribution to journalArticle

Mine, S, Niiyama, M, Hashimoto, W, Ikegami, T, Koma, D, Ohmoto, T, Fukuda, Y, Inoue, T, Abe, Y, Ueda, T, Morita, J, Uegaki, K & Nakamura, T 2014, 'Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N-diacetylchitobiose deacetylase', FEBS Journal, vol. 281, no. 11, pp. 2584-2596. https://doi.org/10.1111/febs.12805
Mine, Shouhei ; Niiyama, Mayumi ; Hashimoto, Wakana ; Ikegami, Takahisa ; Koma, Daisuke ; Ohmoto, Takashi ; Fukuda, Yohta ; Inoue, Tsuyoshi ; Abe, Yoshito ; Ueda, Tadashi ; Morita, Junji ; Uegaki, Koichi ; Nakamura, Tsutomu. / Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N-diacetylchitobiose deacetylase. In: FEBS Journal. 2014 ; Vol. 281, No. 11. pp. 2584-2596.
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AU - Fukuda, Yohta

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