Computational characterization of Set domain group proteins (SDG) present in Arabidopsis thaliana, Zea mays and Oryza sativa japonica

Mutyala, Satish (2016) Computational characterization of Set domain group proteins (SDG) present in Arabidopsis thaliana, Zea mays and Oryza sativa japonica. Masters thesis, Indian Institute of Technology Hyderabad.

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Abstract

Most Histone lysine methyltransferases of H3K4, H3K9 and H3K27 have (Su(var), E(z), and Trithorax) SET domain for methylation on substrate lysine present on N-terminal histone3 (H3) tail. The catalytic activity of these proteins depends on substrate recognizing residues, SAM binding pocket functionality and residues surrounding catalytic site. ATX2, 4 and 5 proteins of Oryza sativa japonica, ATX1, 2, 3,4 and 5 of Arabidopsis thaliana, and ZmSET16, ZmSET32 and ZmSETUK of Zea mays may exhibit high specificity towards H3K4 peptide, and SAM binding as well product specificity similar to MLL3. Except ZmSETUK, remaining proteins may have fully functional Post-SET domain therefore, ZmSETUK may be catalytically dead. All SUVH proteins except SUVH10 of Arabidopsis thaliana may recognize H3K9 peptide. Product specificity of these proteins depends on presence of number of tyrosine and non-tyrosine residues around the catalytic site. Highly conserved SAM binding site and Post-SET domain are present in all these proteins except SUVH2, SUVH9, ZmSET11, ZmSET31, SDG713, SDG715 and SDG726 proteins. E(Z) proteins present in afore mentioned plants can tri-methylate substrate similar to EZH2 of human because they have properly formed H3K27 peptide binding and catalytic sites, and SAM binding pocket.

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