5HFJ

crystal structure of M1.HpyAVI-SAM complex

5HFJ の概要

• エントリーDOI: 10.2210/pdb5hfj/pdb
• 関連するPDBエントリー: 5HEK
• 分子名称: Adenine specific DNA methyltransferase (DpnA), S-ADENOSYLMETHIONINE (2 entities in total)
• 機能のキーワード: m1.hpyavi, sam, dna binding protein
• 由来する生物種: Helicobacter pylori (strain ATCC 700392 / 26695)
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 220311.84

構造登録者

Ma, B.,Liu, W.,Zhang, H. (登録日: 2016-01-07, 公開日: 2016-11-16, 最終更新日: 2023-11-08)

主引用文献

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

実験手法

X-RAY DIFFRACTION (3.1 Å)