A gene encoding a 2-deoxy-D-ribose-5-phosphate aldolase (DERA) homolog was identified in the hyperthermophilic Archaea Aeropyrum pernix. The gene was overexpressed in Escherichia coli, and the produced enzyme was purified and characterized. The enzyme is an extremely thermostable DERA; its activity was not lost after incubation at 100°C for 10 min. The enzyme has a molecular mass of ϳ93 kDa and consists of four subunits with an identical molecular mass of 24 kDa. This is the first report of the presence of tetrameric DERA. The three-dimensional structure of the enzyme was determined by x-ray analysis. The subunit folds into an ␣/␤-barrel. The asymmetric unit consists of two homologous subunits, and a crystallographic 2-fold axis generates the functional tetramer. The main chain coordinate of the monomer of the A. pernix enzyme is quite similar to that of the E. coli enzyme. There was no significant difference in hydrophobic interactions and the number of ion pairs between the monomeric structures of the two enzymes. However, a significant difference in the quaternary structure was observed. The area of the subunit-subunit interface in the dimer of the A. pernix enzyme is much larger compared with the E. coli enzyme. In addition, the A. pernix enzyme is 10 amino acids longer than the E. coli enzyme in the N-terminal region and has an additional N-terminal helix. The N-terminal helix produces a unique dimer-dimer interface. This promotes the formation of a functional tetramer of the A. pernix enzyme and strengthens the hydrophobic intersubunit interactions. These structural features are considered to be responsible for the extremely high stability of the A. pernix enzyme. This is the first description of the structure of hyperthermophilic DERA and of aldolase from the Archaea domain.Aldolases catalyze carbon-carbon bond formation and cleavage and are attractive as synthetic catalysts due to their ability to produce stereospecific carbohydrates (1). They are divided into two major classes based on the mode of stabilization of reaction intermediates. Class I and II aldolases employ a Schiff base mechanism (2, 3) and a divalent metal ion for intermediate stabilization (4), respectively. 2-Deoxy-D-ribose-5-phosphate aldolase (DERA 1 ; EC 4.1.2.4) belongs to the class I aldolases and catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. DERA is unique in catalyzing the aldol reaction between two aldehydes as both the aldol donor and acceptor components. Its broad substrate specificity is an attractive characteristic for the production of a variety of stereospecific materials (5). The enzyme has high potential utility as an environmentally benign alternative to chiral transition metal catalysis of the asymmetric aldol reaction (6). However, the practical application of DERA is still not successful because of its low stability.Since DERA was first described by Racker (7), who reported the presence of DERA in mammalian tissue as well as in Esc...

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