Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain

Eerappa, Rajakumara and Nakarakanti, N K and Nivya, M Angel and M, Satish (2016) Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain. Scientific Reports, 6 (20161). pp. 1-11. ISSN 2045-2322

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Abstract

5-Methylcytosine (5 mC) is associated with epigenetic gene silencing in mammals and plants. 5 mC is consecutively oxidized to 5-hydroxymethylcytosine (5 hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) by ten-eleven translocation enzymes. We performed binding and structural studies to investigate the molecular basis of the recognition of the 5 mC oxidation derivatives in the context of a CG sequence by the SET- and RING-associated domain (SRA) of the SUVH5 protein (SUVH5 SRA). Using calorimetric measurements, we demonstrate that the SRA domain binds to the hydroxymethylated CG (5hmCG) DNA duplex in a similar manner to methylated CG (5mCG). Interestingly, the SUVH5 SRA domain exhibits weaker affinity towards carboxylated CG (5caCG) and formylated CG (5fCG). We report the 2.6 Å resolution crystal structure of the SUVH5 SRA domain in a complex with fully hydroxymethyl-CG and demonstrate a dual flip-out mechanism, whereby the symmetrical 5hmCs are simultaneously extruded from the partner strands of the DNA duplex and are positioned within the binding pockets of individual SRA domains. The hydroxyl group of 5hmC establishes both intra- and intermolecular interactions in the binding pocket. Collectively, we show that SUVH5 SRA recognizes 5hmC in a similar manner to 5 mC, but exhibits weaker affinity towards 5 hmC oxidation derivatives.

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IITH Creators:

IITH Creators	ORCiD
Eerappa, Rajakumara	http://orcid.org/0000-0002-9341-0070

Item Type:

Article

Additional Information:

E.R. acknowledges Prof. Dinshaw J. Patel, Sloan-Kettering Institute, New York, USA, for access to the crystallization and other facilities and Dr. Dana Branzei, Principal Investigator, IFOM Foundation-The FIRC Institute of Molecular Oncology Foundation, Milan, Italy, for providing access to the ITC instrument and the Typhoon TRIO Variable Mode Imager at the European Institute of Oncology and IFOM. We thank the personnel of beam-line X29 at the Brookhaven National Laboratory, funded by the US Department of Energy, for assistance in data collection. E.R. is a Ramalingaswami Re-entry fellow in the Department of Biotechnology, Government of India. N.K.N., M.A.N. and M.S. are supported by research fellowships from the Ministry of Human Resource Development, Government of India.

Uncontrolled Keywords:

Dependent Restriction-Endonuclease; Hemi-Methylated DNA; Flips 5-Methylcytosine; Structural Basis; Mammalian DNA; Human Uhrf1; 5-Carboxylcytosine; 5-Formylcytosine; Helix; Base

Subjects:

Others > Biotechnology

Divisions:

Department of Biotechnology

Depositing User:

Team Library

Date Deposited:

26 Feb 2016 04:58

Last Modified:

04 Dec 2018 09:33

URI:

http://raiithold.iith.ac.in/id/eprint/2220