title: Signatures of the ATP-binding pocket as a basis for structural classification of the serine/threonine protein kinases of gram-positive bacteria.
abstract: Eukaryotic-like serine/threonine protein kinases (ESTPKs) are widely spread throughout the bacterial genomes. These enzymes can be potential targets of new antibacterial drugs useful for the treatment of socially important diseases such as tuberculosis. In this study, ESTPKs of pathogenic, probiotic, and antibiotic-producing Gram-positive bacteria were classified according to the physicochemical properties of amino acid residues in the ATP-binding site of the enzyme. Nine residues were identified that line the surface of the adenine-binding pocket, and ESTPKs were classified based on these signatures. Twenty groups were discovered, five of them containing >10 representatives. The two most abundant groups contained >150 protein kinases that belong to the various branches of the phylogenetic tree, whereas certain groups are genus- or even species-specific. Homology modeling of the typical representatives of each group revealed that the classification is reliable, and the differences between the protein kinase ATP-binding pockets predicted based on their signatures are apparent in their structure. The classification is expected to be useful for the selection of targets for new anti-infective drugs.
authors.affiliation: Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia. zakharevich@yandex.ru
authors.forename: Natalia V
authors.initials: NV
authors.lastname: Zakharevich
authors.forename: Dmitry I
authors.initials: DI
authors.lastname: Osolodkin
authors.forename: Irena I
authors.initials: II
authors.lastname: Artamonova
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Palyulin
authors.forename: Nikolay S
authors.initials: NS
authors.lastname: Zefirov
authors.forename: Valery N
authors.initials: VN
authors.lastname: Danilenko
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D006094:Gram-Positive Bacteria / Q000145:classification* / Q000201:enzymology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D000255:Adenosine Triphosphate; D017346:Protein Serine-Threonine Kinases