Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates

Naoki Shibata, Hiroko Tamagaki, Naoki Hieda, Keita Akita, Hirofumi Komori, Yasuhito Shomura, Shin Ichi Terawaki, Koichi Mori, Noritake Yasuoka, Yoshiki Higuchi, Tetsuo Toraya

Research output: Contribution to journalArticle

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Abstract

N-terminal truncation of the Escherichia coli ethanolamine ammonia-lyase β-subunit does not affect the catalytic properties of the enzyme (Akita, K., Hieda, N., Baba, N., Kawaguchi, S., Sakamoto, H., Nakanishi, Y., Yamanishi, M., Mori, K., and Toraya, T. (2010) J. Biochem. 147, 83-93). The binary complex of the truncated enzyme with cyanocobalamin and the ternary complex with cyanocobalamin or adeninylpentylcobalamin and substrates were crystallized, and their x-ray structures were analyzed. The enzyme exists as a trimer of the (αβ)2 dimer. The active site is in the (β/α)8 barrel of the α-subunit; the β-subunit covers the lower part of the cobalamin that is bound in the interface of the α- and β-subunits. The structure complexed with adeninylpentylcobalamin revealed the presence of an adenine ring-binding pocket in the enzyme that accommodates the adenine moiety through a hydrogen bond network. The substrate is bound by six hydrogen bonds with active-site residues. Argα160 contributes to substrate binding most likely by hydrogen bonding with the O1 atom. The modeling study implies that marked angular strains and tensile forces induced by tight enzyme-coenzyme interactions are responsible for breaking the coenzyme Co-C bond. The coenzyme adenosyl radical in the productive conformation was modeled by superimposing its adenine ring on the adenine ring-binding site followed by ribosyl rotation around the N-glycosidic bond. A major structural change upon substrate binding was not observed with this particular enzyme. Gluα287, one of the substrate-binding residues, has a direct contact with the ribose group of the modeled adenosylcobalamin, which may contribute to the substrate-induced additional labilization of the Co-C bond.

Original languageEnglish
Pages (from-to)26484-26493
Number of pages10
JournalJournal of Biological Chemistry
Volume285
Issue number34
DOIs
Publication statusPublished - Aug 20 2010

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Ethanolamine Ammonia-Lyase
Adenine
Crystal structure
Vitamin B 12
Substrates
Enzymes
Coenzymes
Hydrogen bonds
Hydrogen
Catalytic Domain
Enzymes and Coenzymes
Ribose
Hydrogen Bonding
Dimers
Escherichia coli
Binding Sites
X-Rays
Conformations
cobamamide
X rays

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Shibata, N., Tamagaki, H., Hieda, N., Akita, K., Komori, H., Shomura, Y., ... Toraya, T. (2010). Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates. Journal of Biological Chemistry, 285(34), 26484-26493. https://doi.org/10.1074/jbc.M110.125112

Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates. / Shibata, Naoki; Tamagaki, Hiroko; Hieda, Naoki; Akita, Keita; Komori, Hirofumi; Shomura, Yasuhito; Terawaki, Shin Ichi; Mori, Koichi; Yasuoka, Noritake; Higuchi, Yoshiki; Toraya, Tetsuo.

In: Journal of Biological Chemistry, Vol. 285, No. 34, 20.08.2010, p. 26484-26493.

Research output: Contribution to journalArticle

Shibata, N, Tamagaki, H, Hieda, N, Akita, K, Komori, H, Shomura, Y, Terawaki, SI, Mori, K, Yasuoka, N, Higuchi, Y & Toraya, T 2010, 'Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates', Journal of Biological Chemistry, vol. 285, no. 34, pp. 26484-26493. https://doi.org/10.1074/jbc.M110.125112
Shibata, Naoki ; Tamagaki, Hiroko ; Hieda, Naoki ; Akita, Keita ; Komori, Hirofumi ; Shomura, Yasuhito ; Terawaki, Shin Ichi ; Mori, Koichi ; Yasuoka, Noritake ; Higuchi, Yoshiki ; Toraya, Tetsuo. / Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates. In: Journal of Biological Chemistry. 2010 ; Vol. 285, No. 34. pp. 26484-26493.
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AU - Terawaki, Shin Ichi

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