6M2V

Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA.

Summary for 6M2V

• Entry DOI: 10.2210/pdb6m2v/pdb
• Descriptor: DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3'), E3 ubiquitin-protein ligase UHRF1 (3 entities in total)
• Functional Keywords: 5-methyl-cytosine, complex, epigenetics, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Mus musculus (Mouse); More
• Total number of polymer chains: 4
• Total formula weight: 55680.54

Authors

Abhishek, S.,Nakarakanti, N.K.,Deeksha, W.,Rajakumara, E. (deposition date: 2020-03-01, release date: 2021-01-13, Last modification date: 2023-11-29)

Primary citation

Abhishek, S.,Nakarakanti, N.K.,Deeksha, W.,Rajakumara, E.
Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA.
Int.J.Biol.Macromol., 170:514-522, 2021

PubMed Abstract: Non-CpG DNA methylation (non-mCpG) is enriched in the genome of brain neurons and germline cells in mammals. Accumulation of non-mCpG during postnatal brain development correlates with gene regulation and inactivation of distal regulatory elements. Recently, UHRF1 has been found to contribute to de novo non-CpG methylation, however, whether UHRF1 could recognize non-mCpG is unknown. Here, we have demonstrated through calorimetric measurements that the UHRF1 SRA can recognize mCpH and fully-mCpHpG, types of non-mCpG. Our ITC binding studies endorse the preferential reading of hemi-mCpG by UHRF1 SRA and also show 6-fold weaker binding for fully-mCpG than hemi-mCpG. Despite presence of symmetrical (5-methyl cytosine) 5mCs, stoichiometry of 1:1 for UHRF1 SRA binding to fully-mCpG indicates that UHRF1 SRA may not form a stable complex with fully-mCpG DNA. Contrarily, UHRF1 SRA recognizes fully-mCpHpG with a stoichiometry of 2:1 protein to DNA duplex with binding affinity higher than fully-mCpG. Our crystal structure of UHRF1 SRA bound to fully-mCpHpG DNA reveals dual flip-out mechanism of 5mC recognition. Metadynamics studies corroborates with ITC data that UHRF1 SRA could not form a stable complex with fully-mCpG DNA. Altogether, this study demonstrates that UHRF1 SRA recognizes non-mCpG DNA and exhibits contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition.

PubMed: 33359809
DOI: 10.1016/j.ijbiomac.2020.12.149

Experimental method

X-RAY DIFFRACTION (3 Å)