2MX0

Solution structure of HP0268 from Helicobacter pylori

2MX0 の概要

• エントリーDOI: 10.2210/pdb2mx0/pdb
• NMR情報: BMRB: 25380
• 分子名称: Uncharacterized protein HP_0268 (1 entity in total)
• 機能のキーワード: smr domain-like, unknown function
• 由来する生物種: Helicobacter pylori 26695 (Campylobacter pylori)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 9699.98

構造登録者

Lee, K.Y. (登録日: 2014-12-05, 公開日: 2015-12-09, 最終更新日: 2024-05-15)

主引用文献

Lee, K.Y.,Lee, K.Y.,Kim, J.H.,Lee, I.G.,Lee, S.H.,Sim, D.W.,Won, H.S.,Lee, B.J.
Structure-based functional identification of Helicobacter pylori HP0268 as a nuclease with both DNA nicking and RNase activities
Nucleic Acids Res., 43:5194-5207, 2015

PubMed Abstract: HP0268 is a conserved, uncharacterized protein from Helicobacter pylori. Here, we determined the solution structure of HP0268 using three-dimensional nuclear magnetic resonance (NMR) spectroscopy, revealing that this protein is structurally most similar to a small MutS-related (SMR) domain that exhibits nicking endonuclease activity. We also demonstrated for the first time that HP0268 is a nicking endonuclease and a purine-specific ribonuclease through gel electrophoresis and fluorescence spectroscopy. The nuclease activities for DNA and RNA were maximally increased by Mn(2+) and Mg(2+) ions, respectively, and decreased by Cu(2+) ions. Using NMR chemical shift perturbations, the metal and nucleotide binding sites of HP0268 were determined to be spatially divided but close to each other. The lysine residues (Lys7, Lys11 and Lys43) are clustered and form the nucleotide binding site. Moreover, site-directed mutagenesis was used to define the catalytic active site of HP0268, revealing that this site contains two acidic residues, Asp50 and Glu54, in the metal binding site. The nucleotide binding and active sites are not conserved in the structural homologues of HP0268. This study will contribute to improving our understanding of the structure and functionality of a wide spectrum of nucleases.

PubMed: 25916841
DOI: 10.1093/nar/gkv348

実験手法

SOLUTION NMR