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Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets

Shuishu Wang1, Cameron Mura, Michael R Sawaya

  • 1UCLA-DOE Laboratory of Structure Biology, 611 Charles E. Young Drive East, 201 Boyer Hall, Los Angeles, CA 90095-1570, USA.

Acta Crystallographica. Section D, Biological Crystallography
|March 27, 2002
PubMed

Insights

Nudix hydrolases are key proteins that eliminate toxic compounds. This study reveals the thermostable structure of a Nudix hydrolase from Pyrobaculum aerophilum, highlighting its dimer interface and conserved Nudix motif.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Archaea Biology

Background:

  • Nudix proteins, also known as MutT homolog proteins, form a large family crucial for cellular detoxification.
  • They function as hydrolases, breaking down nucleoside diphosphate compounds linked to various moieties (X).
  • Understanding the structure of Nudix hydrolases is vital for elucidating their enzymatic mechanisms and stability.

Purpose of the Study:

  • To determine the crystal structure of a Nudix hydrolase from the hyperthermophilic archaeon Pyrobaculum aerophilum.
  • To investigate the structural basis for the thermostability of this archaeal Nudix protein.
  • To identify the location and characteristics of the conserved Nudix box motif within the determined structure.

Main Methods:

  • X-ray crystallography was employed to determine the protein structure.
  • Single-wavelength anomalous scattering (SAS) method was utilized.
  • Data collection was performed on an iridium-derivatized crystal at its peak anomalous wavelength.

Main Results:

  • The crystal structure revealed an extensive dimer interface, with significant inter-subunit beta-sheet interactions.
  • Each monomer consists of a mixed, highly twisted, and curved 11-stranded beta-sheet flanked by two alpha-helices, forming an alpha-beta-alpha sandwich.
  • The conserved Nudix box motif, containing essential catalytic residues, was localized to the N-terminal alpha-helix and adjacent beta-strand/loop regions.

Conclusions:

  • The dimeric structure and unusually short connections between secondary structural elements likely contribute to the high thermostability of the Pyrobaculum aerophilum Nudix protein.
  • The structural insights provide a foundation for understanding the catalytic mechanism and evolutionary adaptations of Nudix hydrolases in hyperthermophilic archaea.
  • This work expands the structural repertoire of Nudix hydrolases, offering potential for biotechnological applications requiring thermostable enzymes.

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