title: The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix.
abstract: 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 degrees C for 10 min. The enzyme has a molecular mass of approximately 93 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 alpha/beta-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.
authors.affiliation: Department of Biological Science and Technology, Faculty of Engineering, University of Tokushima, Japan.
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Sakuraba
authors.forename: Hideaki
authors.initials: H
authors.lastname: Tsuge
authors.forename: Ikuko
authors.initials: I
authors.lastname: Shimoya
authors.forename: Ryushi
authors.initials: R
authors.lastname: Kawakami
authors.forename: Shuichiro
authors.initials: S
authors.lastname: Goda
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Kawarabayasi
authors.forename: Nobuhiko
authors.initials: N
authors.lastname: Katunuma
authors.forename: Hideo
authors.initials: H
authors.lastname: Ago
authors.forename: Masashi
authors.initials: M
authors.lastname: Miyano
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Ohshima
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000201:enzymology*; D019843:Archaeal Proteins / Q000737:chemistry*; D004795:Enzyme Stability; D004926:Escherichia coli / Q000201:enzymology; D005634:Fructose-Bisphosphate Aldolase / Q000737:chemistry* / Q000235:genetics; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D021122:Protein Subunits; D011994:Recombinant Proteins / Q000737:chemistry; D012267:Ribosemonophosphates / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D021122:Protein Subunits; D011994:Recombinant Proteins; D012267:Ribosemonophosphates; C058245:2-deoxyribose 5-phosphate; D005634:Fructose-Bisphosphate Aldolase