5HEK

crystal structure of M1.HpyAVI

Summary for 5HEK

• Entry DOI: 10.2210/pdb5hek/pdb
• Related: 5HFJ
• Descriptor: Adenine specific DNA methyltransferase (DpnA) (1 entity in total)
• Functional Keywords: m1.hpyavi, dna binding protein
• Biological source: Helicobacter pylori (strain ATCC 700392 / 26695)
• Total number of polymer chains: 4
• Total formula weight: 112846.79

Authors

Ma, B.,Zhang, H.,Liu, W. (deposition date: 2016-01-06, release date: 2016-11-16, Last modification date: 2023-11-08)

Primary citation

Ma, B.,Ma, J.,Liu, D.,Guo, L.,Chen, H.,Ding, J.,Liu, W.,Zhang, H.
Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori
Oncotarget, 7:40965-40977, 2016

PubMed Abstract: DNA N6-methyladenine modification plays an important role in regulating a variety of biological functions in bacteria. However, the mechanism of sequence-specific recognition in N6-methyladenine modification remains elusive. M1.HpyAVI, a DNA N6-adenine methyltransferase from Helicobacter pylori, shows more promiscuous substrate specificity than other enzymes. Here, we present the crystal structures of cofactor-free and AdoMet-bound structures of this enzyme, which were determined at resolutions of 3.0 Å and 3.1 Å, respectively. The core structure of M1.HpyAVI resembles the canonical AdoMet-dependent MTase fold, while the putative DNA binding regions considerably differ from those of the other MTases, which may account for the substrate promiscuity of this enzyme. Site-directed mutagenesis experiments identified residues D29 and E216 as crucial amino acids for cofactor binding and the methyl transfer activity of the enzyme, while P41, located in a highly flexible loop, playing a determinant role for substrate specificity. Taken together, our data revealed the structural basis underlying DNA N6-adenine methyltransferase substrate promiscuity.

PubMed: 27259995
DOI: 10.18632/oncotarget.9692

Experimental method

X-RAY DIFFRACTION (3 Å)