6K0W

DNA methyltransferase in complex with sinefungin

Summary for 6K0W

• Entry DOI: 10.2210/pdb6k0w/pdb
• Descriptor: Adenine specific DNA methyltransferase (Mod), SINEFUNGIN (3 entities in total)
• Functional Keywords: dna methyltransferase, sinefungin, dna binding protein
• Biological source: Helicobacter pylori 26695
• Total number of polymer chains: 4
• Total formula weight: 284004.61

Authors

Narayanan, N.,Nair, D.T. (deposition date: 2019-05-07, release date: 2019-12-11, Last modification date: 2024-03-27)

Primary citation

Narayanan, N.,Banerjee, A.,Jain, D.,Kulkarni, D.S.,Sharma, R.,Nirwal, S.,Rao, D.N.,Nair, D.T.
Tetramerization at Low pH Licenses DNA Methylation Activity of M.HpyAXI in the Presence of Acid Stress.
J.Mol.Biol., 432:324-342, 2020

PubMed Abstract: Methylation of genomic DNA can influence the transcription profile of an organism and may generate phenotypic diversity for rapid adaptation in a dynamic environment. M.HpyAXI is a Type III DNA methyltransferase present in Helicobacter pylori and is upregulated at low pH. This enzyme may alter the expression of critical genes to ensure the survival of this pathogen at low pH inside the human stomach. M.HpyAXI methylates the adenine in the target sequence (5'-GCAG-3') and shows maximal activity at pH 5.5. Type III DNA methyltransferases are found to form an inverted dimer in the functional form. We observe that M.HpyAXI forms a nonfunctional dimer at pH 8.0 that is incapable of DNA binding and methylation activity. However, at pH 5.5, two such dimers associate to form a tetramer that now includes two functional dimers that can bind and methylate the target DNA sequence. Overall, we observe that the pH-dependent tetramerization of M.HpyAXI ensures that the enzyme is licensed to act only in the presence of acid stress.

PubMed: 31628946
DOI: 10.1016/j.jmb.2019.10.001

Experimental method

X-RAY DIFFRACTION (2.65 Å)