Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization

Yuichi Nishitani, Riku Aono, Akira Nakamura, Takaaki Sato, Haruyuki Atomi, Tadayuki Imanaka, Kunio Miki

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

AMP phosphorylase (AMPpase) catalyzes the initial reaction in a novel AMP metabolic pathway recently found in archaea, converting AMP and phosphate into adenine and ribose 1,5-bisphosphate. Gel-filtration chromatography revealed that AMPpase from Thermococcus kodakarensis (Tk-AMPpase) forms an exceptionally large macromolecular structure (> 40-mers) in solution. To investigate its unique multimerization feature, we determined the first crystal structures of Tk-AMPpase, in the apo-form and in complex with substrates. Structures of two truncated forms of Tk-AMPpase (Tk-AMPpaseΔN84 and Tk-AMPpaseΔC10) clarified that this multimerization is achieved by two dimer interfaces within a single molecule: one by the central domain and the other by the C-terminal domain, which consists of an unexpected domain-swapping interaction. The N-terminal domain, characteristic of archaeal enzymes, is essential for enzymatic activity, participating in multimerization as well as domain closure of the active site upon substrate binding. Moreover, biochemical analysis demonstrated that the macromolecular assembly of Tk-AMPpase contributes to its high thermostability, essential for an enzyme from a hyperthermophile. Our findings unveil a unique archaeal nucleotide phosphorylase that is distinct in both function and structure from previously known members of the nucleoside phosphorylase II family.

Original languageEnglish
Pages (from-to)2709-2721
Number of pages13
JournalJournal of Molecular Biology
Volume425
Issue number15
DOIs
Publication statusPublished - 2013 Aug 9
Externally publishedYes

Fingerprint

Phosphorylases
Dimerization
Adenosine Monophosphate
Thermococcus
Archaea
Adenine
Enzymes
Metabolic Networks and Pathways
Gel Chromatography
Catalytic Domain
Nucleotides
Phosphates

Keywords

  • archaea crystal
  • assembly nucleotide
  • metabolism phosphorylase
  • structure multimeric

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Nishitani, Y., Aono, R., Nakamura, A., Sato, T., Atomi, H., Imanaka, T., & Miki, K. (2013). Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. Journal of Molecular Biology, 425(15), 2709-2721. https://doi.org/10.1016/j.jmb.2013.04.026

Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. / Nishitani, Yuichi; Aono, Riku; Nakamura, Akira; Sato, Takaaki; Atomi, Haruyuki; Imanaka, Tadayuki; Miki, Kunio.

In: Journal of Molecular Biology, Vol. 425, No. 15, 09.08.2013, p. 2709-2721.

Research output: Contribution to journalArticle

Nishitani, Y, Aono, R, Nakamura, A, Sato, T, Atomi, H, Imanaka, T & Miki, K 2013, 'Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization', Journal of Molecular Biology, vol. 425, no. 15, pp. 2709-2721. https://doi.org/10.1016/j.jmb.2013.04.026
Nishitani, Yuichi ; Aono, Riku ; Nakamura, Akira ; Sato, Takaaki ; Atomi, Haruyuki ; Imanaka, Tadayuki ; Miki, Kunio. / Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. In: Journal of Molecular Biology. 2013 ; Vol. 425, No. 15. pp. 2709-2721.
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