Kinase family

We have previously calculated conformational free energy differences for a well-suited model system, the catalytic subunit of cAMP-dependent protein kinase (cAPK), which is the best characterized member of the protein kinase family. It has been crystallized in three different conformations and our main focus was on how ligand binding shifts the equilibrium among these ([Helms and McCammon 1997]). As an example using state-of-the-art computational techniques, we summarize the main conclusions of this study and discuss a variety of methods that may be used to extend this study into the dynamic regime of protein domain motion. 

IL-1 receptor associated kinase family-A with Toll-like receptor signalling. There are four members in this group to date IRAK-1,2,4 and M. They can phosphor-ylate among themselves, as well with other proteins involved in signalling such as TRAF-6. 

Fak (focal adhesion kinase) is expressed in most tissues and is evolutionary conserved across species. It is activated by integrin clustering and by stimulation of several G protein-coupled recqrtors and RTKs. Fak is associated with focal adhesions and regulates cell spreading and migration. The kinase is essential for embryonic development since the homozygote Fak knockout is embryonic lethal. Pyk2 (proline-rich tyrosine kinase 2), the second member of the Fak kinase family has a more restricted expression pattern (primarily neuronal and hematopoietic cells) and does not localize to focal adhesions. 

The abundance of structural information has led to a significant increase in the use of structure-based methods both to identify and to optimise inhibitors of protein kinases. The focus to date has centred upon small molecule ATP-competitive inhibitors and there are numerous examples of protein-ligand complexes available to guide design strategies. ATP binds in the cleft formed between the N- and C-terminal lobes of the protein kinase, forming several key interactions conserved across the protein kinase family. The adenine moiety lies in a hydrophobic region between the jS-sheet structure of subdomains I and II and residues from subdomains V and VIb. A... 

Hanks, S. K., Quinn, A. M., and Hunter, T. (1988). The protein kinase family conserved features and deduced phylogeny of the catalytic domains. Science 241 42-52. 

Dual Phosphorylation Sites in MAP Kinase Family Members... 

Each of these pathways involves a kinase cascade resulting in the phosphorylation and activation of the MAP kinase family member. Each contains a dual phosphorylation site (TEY, TPY, or TGY) and the central residue in the motif characteristic of the class, as shown in Table 8.1. It is evident that cells are endowed with parallel signal-transduction pathways and that they may operate individually or in combination to initiate specific patterns of gene expression. Additionally, crosstalk between the pathways undoubtedly occurs. None of these pathways has a unique function it is more likely that the combination of pathways that are activated (or silenced) together with the... 

FIGURE 8.6 Parallel pathways to transcription and the MAP kinase family. The MAP kinases can be classified into three groups, based on the identity of the intermediate residue in their dual phosphorylation motifs (TEY, TGY, or TPY). This classification also defines three distinct signal-transduction pathways indicated as the ERK, the JNK/SAPK, and the p38/HOG pathway, each having unique protein kinases acting upstream. 

Poteet-Smith, C. E., Smith, J. A., Lannigan, D. A., Freed, T. A., and Sturgill, T. W. (1999). Generation of constitutively active p90 ribosomal S6 kinase in vivo. Implications for the mitogen-activated protein kinase-activated protein kinase family. J. Biol. Chem. 274, 22135-22138. 

Which of the following is classified as belonging to the tyrosine kinase family of receptors ... 

AKT-1 kinase (also called protein kinase B or PKBa) is a serine/threonine kinase belonging to the AGC kinase family [1], AKT was identified from a viral oncogene, v-akt, found in tumor lines established from spontaneous thymomas found in AKR mice [2]. Subsequently, two more AKT isoforms, AKT-2 (or PKB(3) and AKT-3 (or PKBy) have been identified [3]. Reviews exist detailing the structural and cell biology of AKT and the reader is referred to these for further information [4,7,12]. 

PI3K p85B PI3-kinase family, p85-binding domain E(M) 0(0) 0(0) ... 

PI3Ka Phosphoinositide 3-kinase family, accessory domain (PIK domain) E(MFP) 2(2) 3(3) 1QMM... 

Phosphorylation has been thought to be correlated to the mitotic chromatin condensation and the transcriptional regulation in interphase (Nowak and Corces, 2004). The mitotic phosphorylation, which was first identified in 1978 (Gurley et al, 1978), occurs at Ser (Wei et al, 1998), Ser (Goto et al, 1999), and Thr (Preuss et al, 2003) in histone H3. The Ser phosphorylation is catalyzed by the aurora kinase family (de la Barre et al, 2000), and is required for the initiation of chromosome condensation but not for its maintenance (dephosphorylation of mitotic chromosomes does not induce chromosome decondensation) (Van Hooser et fl/.,1998). In meiosis, Ser phosphorylation is also required for the cohesion of sister chromatids rather than the condensation (Kaszas and Cande, 2000). 

Members of the phosphoinositide (PI)-3 kinase family appear to be involved in the phosphorylation of H2A.X. The SQ motif matches a common target site for these kinases and the formation of y-H2A.X in response to double stranded breaks is inhibited by wortmannin, an inhibitor of PI-3 kinases [63]. Examination of cell lines deficient in the PI-3 kinase ATM indicated that it has a major role in phosphorylating H2A.X in response to double strand breaks [64]. ATM can phosphorylate H2A.X in vitro suggesting that it may directly phosphorylate H2A.X in vivo [64]. Another PI-3 kinase ATR appears to be involved in phosphorylating H2A.X in response to replicational stress induced by treatment of dividing cells with hydroxyurea or by irradiating them with ultraviolet light [65]. It has been hypothesized that PI-3 kinases such as ATM are recruited to, or activated at, the site of the double stranded break and then phosphorylate H2A.X molecules around the break point [40,64,66]. 

Finally, we propose that APR becomes phosphorylated by the putative APR-kinase April and thereby inactivated, as a second resistance mechanism in addition to the 16S rRNA methylation by KamB, during biosynthesis or thereafter. Because AprZ is significantly similar to the StrK protein, a member of the protein family of extracellular alkaline phosphates and a STR-phosphate-specific dephosphorylase (see Section 2.2.1.2), this modification is urgently suggested by presence of the conserved aprZ gene in the biosynthetic cluster. April is a member of the large kinase family comprising all the antibiotic and protein kinases. As in the STR producers, the postulated APR-phosphate would exported via the ABC transport system AprV/AprW and set free by dephosphorylation outside the cells via the phospatase AprZ. 

Figure 3.5. Aminoglycoside kinases are members of the protein kinase family. Comparison of c-AMP-dependent protein kinase (cAPK) to APH(3 )-IIa and APH(3 )-IIIa. (A) cAPK (catalytic domain) from Mus musculus (pdb ID 2CPK). (B) APH(3 )-IIa from Klebsiella pneumoniae (pdb ID 1ND4). (C) APH(3 )-IIIa from Enterococcus faecalis (pdb ID 1L8T).

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