scholarly journals Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates

2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Boris Sobolev ◽  
Dmitry Filimonov ◽  
Alexey Lagunin ◽  
Alexey Zakharov ◽  
Olga Koborova ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Amino Acid Sequences ◽  
Functional Classification ◽  
Kinase Substrates

scholarly journals The substrate specificity of adenosine 3′:5′-cyclic monophosphate-dependent protein kinase of rabbit skeletal muscle

1977 ◽  
Vol 162 (2) ◽  
pp. 411-421 ◽  
Author(s):  
S J Yeaman ◽  
P Cohen ◽  
D C Watson ◽  
G H Dixon
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Kinase ◽  
Phosphorylation Site ◽  
Amino Acid Sequences ◽  
Beta Subunit ◽  
Alpha Subunit ◽  
Phosphorylase Kinase ◽  
Dependent Protein Kinase ◽  
Dependent Protein

The known amino acid sequences at the two sites on phosphorylase kinase that are phosphorylated by cyclic AMP-dependent protein kinase were extended. The sequences of 42 amino acids around the phosphorylation site on the alpha-subunit and of 14 amino acids around the phosphorylation site on the beta-subunit were shown to be: alpha-subunit Phe-Arg-Arg-Leu-Ser(P)-Ile-Ser-Thr-Glu-Ser-Glx-Pro-Asx-Gly-Gly-His-Ser-Leu-Gly-Ala-Asp-Leu-Met-Ser-Pro-Ser-Phe-Leu-Ser-Pro-Gly-Thr-Ser-Val-Phe(Ser,Pro,Gly)His-Thr-Ser-Lys; beta-subunit, Ala-Arg-Thr-Lys-Arg-Ser-Gly-Ser(P)-VALIle-Tyr-Glu-Pro-Leu-Lys. The sites on histone H2B which are phosphorylated by cyclic AMP-dependent protein kinase in vitro were identified as serine-36 and serine-32. The amino acid sequence in this region is: Lys-Lys-Arg-Lys-Arg-Ser32(P)-Arg-Lys-Glu-Ser36(P)-Tyr-Ser-Val-Tyr-Val- [Iwai, K., Ishikawa, K. & Hayashi, H. (1970) Nature (London) 226, 1056-1058]. Serine-36 was phosphorylated at 50% of the rate at which the beta-subunit of phosphorylase kinase was phosphorylated, and it was phosphorylated 6-7-fold more rapidly than was serine-32. The amino acid sequences when compared with those at the phosphorylation sites of other physiological substrates suggest that the presence of two adjacent basic amino acids on the N-terminal side of the susceptible serine residue may be critical for specific substrate recognition in vivo.

Functional Classification of Protein Kinase Binding Sites Using Cavbase

ChemMedChem ◽  
2007 ◽  
Vol 2 (10) ◽  
pp. 1432-1447 ◽  
Author(s):  
Daniel Kuhn ◽  
Nils Weskamp ◽  
Eyke Hüllermeier ◽  
Gerhard Klebe
Keyword(s):  
Protein Kinase ◽  
Binding Sites ◽  
Functional Classification

Aza-β3-amino acid containing peptidomimetics as cAMP-dependent protein kinase substrates

2010 ◽  
Vol 38 (5) ◽  
pp. 229-233 ◽  
Author(s):  
Ksenija Kisseljova ◽  
Aleksei Kuznetsov ◽  
Michèle Baudy-Floc’h ◽  
Jaak Järv
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Dependent Protein Kinase ◽  
Camp Dependent Protein Kinase ◽  
Dependent Protein ◽  
Kinase Substrates

Old versus new characters for systematics: Cautionary tales from virology

1990 ◽  
Vol 3 (1) ◽  
pp. 159
Author(s):  
A Gibbs ◽  
A Ding ◽  
J Howe ◽  
P Keese ◽  
A MacKenzie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Recombination ◽  
Large Subunit ◽  
Molecular Taxonomy ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Molecular Sequence ◽  
Taxonomic Methods ◽  
Cautionary Tales

Molecular sequence information about viruses has mostly confirmed the groupings devised by traditional taxonomic methods, but shown in addition that the genes of related species may differ in number, arrangement, orientation and in sequence homology. It has also revealed that true genetic recombination between viruses has been common, even among those with RNA genomes, indeed most virus groups seem to have arisen y recombination. Thus, there is an unexpected wealth of genetic chaos hidden behind the fatade of the phenotype, and it is possible that the difficulties that plant taxonomists have had in identifying the relationships of the major groupings of plants could have similar causes. Nonetheless, molecular taxonomy does give sensible results and this is illustrated by a classification of the large subunit Rubisco proteins of 21 plant species based on their amino acid sequences.

Two amino acid sequences direct Aspergillus nidulans protein kinase C (PkcA) localization to hyphal apices and septation sites

Mycologia ◽  
2015 ◽  
Vol 107 (3) ◽  
pp. 452-459 ◽  
Author(s):  
Loretta Jackson-Hayes ◽  
Terry W. Hill ◽  
Darlene M. Loprete ◽  
Claire E. DelBove ◽  
Justin A. Shapiro ◽  
...  
Keyword(s):  
Protein Kinase C ◽  
Amino Acid ◽  
Protein Kinase ◽  
Aspergillus Nidulans ◽  
Amino Acid Sequences ◽  
Kinase C

scholarly journals Bacterial lipolytic enzymes: classification and properties

1999 ◽  
Vol 343 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Jean Louis ARPIGNY ◽  
Karl-Erich JAEGER
Keyword(s):  
Amino Acid ◽  
Structural Features ◽  
Biological Properties ◽  
Amino Acid Sequences ◽  
Important Class ◽  
Lipolytic Enzymes ◽  
Disulphide Bonds ◽  
Enzyme Families

Knowledge of bacterial lipolytic enzymes is increasing at a rapid and exciting rate. To obtain an overview of this industrially very important class of enzymes and their characteristics, we have collected and classified the information available from protein and nucleotide databases. Here we propose an updated and extensive classification of bacterial esterases and lipases based mainly on a comparison of their amino acid sequences and some fundamental biological properties. These new insights result in the identification of eight different families with the largest being further divided into six subfamilies. Moreover, the classification enables us to predict (1) important structural features such as residues forming the catalytic site or the presence of disulphide bonds, (2) types of secretion mechanism and requirement for lipase-specific foldases, and (3) the potential relationship to other enzyme families. This work will therefore contribute to a faster identification and to an easier characterization of novel bacterial lipolytic enzymes.

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