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Structure analysis of eEF2K

The human eEF2K protein is made up of 725 amino acids with an estimated molecular weight of 82kDA. It phosphorylates eEF2 at serine 56 which impedes it from binding to the ribosome, ultimately inhibiting the process of translation. EEF2K is therefore a protein kinase involved in the regulation of protein translation in the cell.

 

Currently, neither the protein structure nor the modular domains of eEF2K have been crystallised. However eEF2K shares homology to Dicytostelium myosin heavy chain kinase A (MHCK A) and also to the mouse transient receptor potential melastatin-like 7 (TRPM 7). These alpha kinases already have their structures crystallised and therefore serve as models for the research on eEF2K’s protein structure.

Figure 1: Domain analysis of eEF2K from ScanProsite.​

Based on ScanProsite (Figure 1), the domain analysis showed that an alpha kinase domain is present in eEF2K between the residues 116-326. Domain analysis was repeated using Interpro and the results supported the presence of the alpha kinase domain as well as the SEL 1-like repeats at the C-terminal region of the protein.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

However, the several databases did not detect the calmodulin-binding domain of eEF2K which should be present in the protein as its kinase activity is dependent on calcium and calmodulin. This could be due to the fact that eEF2K lacks homology to other calmodulin-dependent protein kinases. Experimental studies have mapped the calmodulin-binding domain to be adjacent to the catalytic domain, between the residues 51-96 (1). 

 

Hence, research has shown that eEF2K consists of 3 functional domains; calmodulin-binding domain, the alpha kinase domain and the SEL 1-like repeats.

 

The proposed structural layout is as shown in Figure 3.

Figure 2: Domain analysis of eEF2K (IPR017400) from Interpro.

Figure 3: The structural layout and domain structures of eEF2K. The calmodulin-binding domain isfound adjacent to the alpha kinase domain, which is the catalytic domain. Furthermore, the N-terminal domains are held together with the SEL1-containing region by the linker. Image adaptedfrom Pigott et al, 2012. (2)

Secondary structure

 

As shown in Figure 4, Phyre was used to predict the secondary structure of eEF2K. It does so by first scanning the protein sequence using PSI-Blast to detect sequence homologues. The secondary structure and disorder is then predicted using Psi-pred and Diso-pred.

 

The predicted structure contains 40% of alpha helices, 11% of beta strands while 40% of the proteinstructure is disordered (3).

 

Figure 4. Secondary structure prediction of eEF2K using Phyre (3).

References

 

1. Pavur KS, Petrov AN, Ryazanov AG. Mapping the functional domains of elongation factor-2 kinase. Biochemistry. 2000;39(40):12216-24. Available from:

http://www.ncbi.nlm.nih.gov/pubmed/11015200

 

2. Pigott CR, Mikolajek H, Moore CE, Finn SJ, Phippen CW, Werner JM, et al. Insights into the regulation of eukaryotic elongation factor 2 kinase and the interplay between its domains. Biochem J. 2012;442(1):105-18. Available from:

http://www.ncbi.nlm.nih.gov/pubmed/22115317

 

3. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protocols. 2015;10(6):845-58. Available from:

http://www.ncbi.nlm.nih.gov/pubmed/25950237

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