title: Cleavage mechanism of ATP-dependent Lon protease toward ribosomal S2 protein.
abstract: The Escherichia coli ATP-dependent protease Lon degrades ribosomal S2 protein in the presence of inorganic polyphosphate (polyP). In this study, the process of the degradation was investigated in detail. During the degradation, 68 peptides with various sizes (4-29 residues) were produced in a processive fashion. Cleavage occurred at 45 sites, whose P1 and P3 positions were dominantly occupied by hydrophobic residues. These cleavage sites were located preferentially at the regions with rigid secondary structures and the P1 residues of the major cleavage sites appeared to be concealed from the surface of the substrate molecule. Furthermore, polyP changed not only the substrate preference but also the oligomeric structure of the enzyme.
authors.affiliation: School of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. wnishii@ls.toyaku.ac.jp
authors.forename: Wataru
authors.initials: W
authors.lastname: Nishii
authors.forename: Taichiro
authors.initials: T
authors.lastname: Suzuki
authors.forename: Mayumi
authors.initials: M
authors.lastname: Nakada
authors.forename: Yong-Tae
authors.initials: YT
authors.lastname: Kim
authors.forename: Tomonari
authors.initials: T
authors.lastname: Muramatsu
authors.forename: Kenji
authors.initials: K
authors.lastname: Takahashi
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism*; D000595:Amino Acid Sequence; D002850:Chromatography, Gel; D002851:Chromatography, High Pressure Liquid; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D006868:Hydrolysis; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D013058:Mass Spectrometry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D008970:Molecular Weight; D010449:Peptide Mapping; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011122:Polyphosphates / Q000378:metabolism; D049070:Protease La / Q000737:chemistry / Q000378:metabolism*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity; D013997:Time Factors
chemical_list: D029968:Escherichia coli Proteins; D010455:Peptides; D011122:Polyphosphates; D011994:Recombinant Proteins; D012269:Ribosomal Proteins; C030004:ribosomal protein S2; C053139:sulA protein, E coli; D000255:Adenosine Triphosphate; D049070:Protease La