The protein kinase resource

Smith, Christopher M.; Shindyalov, Ilya N.; Veretnik, Stella; Gribskov, Michael; Taylor, Susan S.; Eyck, Lynn F. Ten; Bourne, Philip E.

doi:10.1016/s0968-0004(97)01131-6

Cited by 96 publications

(50 citation statements)

References 10 publications

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“…The insert is present in all of the protein kinases in this subgroup, though the functional significance of the insert is largely unknown except for animal Ndr, where the insert is used as a nuclear localization signal. A similar insert is found in some other protein kinases (e.g., plant PVPK-1 and yeast DBF2) belonging to a different subgroup of AGC protein kinases (Smith et al 1997). The insert has not been found in any of the authentic AGC protein kinases.…”

Section: Discussionsupporting

confidence: 54%

“…The AGC group of protein kinases was first defined by Hanks and Hunter (1995), and is represented by PKA, PKG, PKC and ribosomal S6 kinase. Later, the group was divided into nine subgroups based on sequence similarities (Smith et al 1997). To clarify the relationship of RsNdrs to the protein kinases in the AGC group, molecular phylogenetic analysis was carried out.…”

Section: Discussionmentioning

confidence: 99%

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Cloning and characterization of a novel radish protein kinase which is homologous to fungal cot-I like and animal Ndr protein kinases

et al. 2004

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According to the similarity of the amino acid sequences in their catalytic domains, eukaryotic protein kinases have been classified into the five main groups: 'AGC', 'CaMK', 'CMGC', 'PTK' and 'other'. The AGC group, represented by the cyclic nucleotide-dependent kinases (PKA and PKG), the calcium-phospholipid-dependent kinases (PKC) and the ribosomal S6 protein kinases, are poorly characterized in plants except for a few cases. In this study, in order to gain a better understanding of plant protein kinases in the AGC group, three cDNAs encoding novel protein kinases, RsNdr1 and RsNdr2a/b, were cloned from radish and characterized by molecular and biochemical methods.The deduced amino acid sequences of RsNdr1 and RsNdr2a/b contained all 12 conserved catalytic subdomains which are characteristic of the eukaryotic Ser/Thr protein kinases. A cell lysate from E. coli overexpressing RsNdr1 fusion protein had protein kinase activity toward a conventional protein substrate (myelin basic protein), whereas that from E. coli harboring a fusion plasmid encoding kinasedead RsNdr1 or RsNdr2 did not show any protein kinase activity. A phylogenetic tree for 17 protein kinases from various organisms showed that the RsNdrs are more closely related to the protein kinases in a particular subgroup of the 'AGC' (fungal cot1 -like and animal Ndr kinases) than to the authentic 'AGC' protein kinases, such as PKA, PKC or ribosomal S6 kinase.

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Section: Discussionsupporting

confidence: 54%

Section: Discussionmentioning

confidence: 99%

Cloning and characterization of a novel radish protein kinase which is homologous to fungal cot-I like and animal Ndr protein kinases

et al. 2004

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“…To determine the conservation of the residues in the mutated region in the kinase domain the four human paralogs were aligned using CLUSTALW (15). We also assessed the statistical significance of the observed mutations and evaluated residue distribution in the kinases related to FGFR1 by using the Protein Kinase Resource (PKR) (16). The PKR hierarchical classification system includes classes (e.g., tyrosine kinases), groups (smaller subclasses with higher internal sequence similarity, such as FGFR or insulin receptor kinases), and families (the lowest level of closely related kinases).…”

Section: Mapping Of Mutations To the Three-dimensional Structure Of Fmentioning

confidence: 99%

Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas

Rand

Huang

Stockwell

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

137

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It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey mutational changes in cancer in a high-throughput and comprehensive manner. Here we report on the sequence analysis of members of the receptor tyrosine kinase (RTK) gene family in the genomes of glioblastoma brain tumors. Previous studies have identified a number of molecular alterations in glioblastoma, including amplification of the RTK epidermal growth factor receptor. We have identified mutations in two other RTKs: (i) fibroblast growth receptor 1, including the first mutations in the kinase domain in this gene observed in any cancer, and (ii) a frameshift mutation in the platelet-derived growth factor receptor-␣ gene. Fibroblast growth receptor 1, platelet-derived growth factor receptor-␣, and epidermal growth factor receptor are all potential entry points to the phosphatidylinositol 3-kinase and mitogenactivated protein kinase intracellular signaling pathways already known to be important for neoplasia. Our results demonstrate the utility of applying DNA sequencing technology to systematically assess the coding sequence of genes within cancer genomes.cancer ͉ genome ͉ fibroblast growth factor receptor 1 ͉ platelet-derived growth factor receptor-␣

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“…Hanks classification of kinases was used as standard. Four representative sets of proteins were chosen corresponding to the four kinase classes described by Hanks [11,24]. Only protein with associated three-dimensional structural information were considered.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Classification of proteins based on similarity of two-dimensional protein maps

Albrecht

Grant

Sisu

et al. 2008

Biophysical Chemistry

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Data reduction techniques are now a vital part of numerical analysis and principal component analysis is often used to identify important molecular features from a set of descriptors. We now take a different approach and apply data reduction techniques directly to protein structure. With this we can reduce the three-dimensional structural data into two-dimensions while preserving the correct relationships. With two-dimensional representations, structural comparisons between proteins are accelerated significantly. This means that protein-protein similarity comparisons are now feasible on a large scale. We show how the approach can help to predict the function of kinase structures according to the Hanks' classification based on their structural similarity to different kinase classes.

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The protein kinase resource

Cited by 96 publications

References 10 publications

Cloning and characterization of a novel radish protein kinase which is homologous to fungal cot-I like and animal Ndr protein kinases

Cloning and characterization of a novel radish protein kinase which is homologous to fungal cot-I like and animal Ndr protein kinases

Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas

Classification of proteins based on similarity of two-dimensional protein maps

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