title: Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis.
abstract: The crystal structure of the aminopeptidase APDkam589 from the thermophilic crenarchaeon Desulfurococcus kamchatkensis was determined at a resolution of 3.0 Å. In the crystal, the monomer of APDkam589 and its symmetry-related monomers are densely packed to form a 12-subunit complex. Single-particle electron-microscopy analysis confirms that APDkam589 is present as a compact dodecamer in solution. The APDkam589 molecule is built similarly to the molecules of the PhTET peptidases, which have the highest sequence identity to APDkam589 among known structures and were isolated from the more thermostable archaeon Pyrococcus horikoshii. A comparison of the interactions of the subunits in APDkam589 with those in PhTET1, PhTET2 and PhTET3 reveals that APDkam589 has a much lower total number of salt bridges, which correlates with the lower thermostability of APDkam589. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. A superposition of the structure of APDkam589 with those having a high sequence similarity to APDkam589 reveals that, although the positions of Trp45, Trp252 and Trp358 are not conserved in the sequences, the spatial locations of the Trp residues in these models are similar.
authors.affiliation: A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation.
authors.forename: T E
authors.initials: TE
authors.lastname: Petrova
authors.affiliation: A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation.
authors.forename: E S
authors.initials: ES
authors.lastname: Slutskaya
authors.affiliation: A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation.
authors.forename: K M
authors.initials: KM
authors.lastname: Boyko
authors.affiliation: Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/73, Moscow 119991, Russian Federation.
authors.forename: O S
authors.initials: OS
authors.lastname: Sokolova
authors.affiliation: NRC `Kurchatov Institute', Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation.
authors.forename: T V
authors.initials: TV
authors.lastname: Rakitina
authors.affiliation: NRC `Kurchatov Institute', Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation.
authors.forename: D A
authors.initials: DA
authors.lastname: Korzhenevskiy
authors.affiliation: NRC `Kurchatov Institute', Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation.
authors.forename: M A
authors.initials: MA
authors.lastname: Gorbacheva
authors.affiliation: A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation.
authors.forename: E Y
authors.initials: EY
authors.lastname: Bezsudnova
authors.affiliation: A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation.
authors.forename: V O
authors.initials: VO
authors.lastname: Popov
mesh_terms: D000595:Amino Acid Sequence; D000626:Aminopeptidases / Q000737:chemistry*; D019843:Archaeal Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D017124:Conserved Sequence; D019620:Desulfurococcaceae / Q000201:enzymology*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary
chemical_list: D019843:Archaeal Proteins; D000626:Aminopeptidases
keywords: APDkam598; Desulfurococcus kamchatkensis; aminopeptidase; thermostability