Structural and functional studies on human PHD finger protein 2

Thesis

Histone lysine methylation is an important post-translational modification (PTM) that can regulate gene expression in eukaryotic genomes. Histone methylation states are dynamically altered by the activity of methyl-transferases and demethylases, including the Jumonji C-domain-containing histone demethylases (JHDMs). The JHDM enzymes are members of the Fe(II) and 2-oxoglutarate (2OG) dependent dioxygenases superfamily, which utilise Fe(II) as a cofactor, and 2OG and oxygen as co-substrates to catalyse oxidative demethylation.

This thesis presents structural and functional studies on an unusual JHDM, PHF2, which has an interesting metal binding site. The proposed substrate for PHF2 is histone H3K4me3K9me2 although no definitive in vitro demethylation activity for PHF2 has yet been demonstrated. Due to the unusual composition of the catalytic site of PHF2, it is questionable whether PHF2 is able to productively bind metal ions and catalyse demethylation reactions, as do other JHDMs. In this thesis, work investigating the cofactor/co-substrate binding ability of PHF2 and its substrate peptide recognition mechanism is described. The studies used a combination of biochemical/biophysical assays and structural methods including X-ray crystallography. The results confirmed that PHF2 is able to bind to a transition metal ion and 2OG/NOG. Further investigations revealed that substrate peptide binding is mostly determined by the PHD finger; and biochemical assays suggested that the JmjC domain is not involved in peptide binding, which offers a possible explanation for the difference between the results of in vitro and cell-based demethylation activity assays.

Inhibitor screening was also carried out for PHF2, and a list of initial hits was generated. Although the results of this work are preliminary, the initial hits will serve as templates for future development of PHF2 specific inhibitors, which could be used for both drug development and as probes to investigate the biological function of PHF2.

Authors: Xian, D

• Publication date: 2014
• Type of award: MSc by Research
• Level of award: Masters
• Awarding institution: University of Oxford
• Language: English
• Keywords: structures; human; kinetics; PHF2
• Subjects: Chemical biology