6G81

Solution structure of the Ni metallochaperone HypA from Helicobacter pylori

6G81 の概要

• エントリーDOI: 10.2210/pdb6g81/pdb
• NMR情報: BMRB: 34257
• 分子名称: Hydrogenase maturation factor HypA, ZINC ION (2 entities in total)
• 機能のキーワード: metallochaperone metal-binding nickel hydrogenase, metal binding protein
• 由来する生物種: Helicobacter pylori J99 (Campylobacter pylori J99)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 13286.66

構造登録者

Spronk, C.A.E.M.,Zerko, S.,Gorka, M.,Kozminski, W.,Bardiaux, B.,Zambelli, B.,Musiani, F.,Piccioli, M.,Hu, H.,Maroney, M.,Ciurli, S. (登録日: 2018-04-07, 公開日: 2018-10-10, 最終更新日: 2024-06-19)

主引用文献

Spronk, C.A.E.M.,Zerko, S.,Gorka, M.,Kozminski, W.,Bardiaux, B.,Zambelli, B.,Musiani, F.,Piccioli, M.,Basak, P.,Blum, F.C.,Johnson, R.C.,Hu, H.,Merrell, D.S.,Maroney, M.,Ciurli, S.
Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools.
J. Biol. Inorg. Chem., 23:1309-1330, 2018

PubMed Abstract: Helicobacter pylori HypA (HpHypA) is a metallochaperone necessary for maturation of [Ni,Fe]-hydrogenase and urease, the enzymes required for colonization and survival of H. pylori in the gastric mucosa. HpHypA contains a structural Zn(II) site and a unique Ni(II) binding site at the N-terminus. X-ray absorption spectra suggested that the Zn(II) coordination depends on pH and on the presence of Ni(II). This study was performed to investigate the structural properties of HpHypA as a function of pH and Ni(II) binding, using NMR spectroscopy combined with DFT and molecular dynamics calculations. The solution structure of apo,Zn-HpHypA, containing Zn(II) but devoid of Ni(II), was determined using 2D, 3D and 4D NMR spectroscopy. The structure suggests that a Ni-binding and a Zn-binding domain, joined through a short linker, could undergo mutual reorientation. This flexibility has no physiological effect on acid viability or urease maturation in H. pylori. Atomistic molecular dynamics simulations suggest that Ni(II) binding is important for the conformational stability of the N-terminal helix. NMR chemical shift perturbation analysis indicates that no structural changes occur in the Zn-binding domain upon addition of Ni(II) in the pH 6.3-7.2 range. The structure of the Ni(II) binding site was probed using H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals around the paramagnetic metal ion. On this basis, two possible models were derived using quantum-mechanical DFT calculations. The results provide a comprehensive picture of the Ni(II) mode to HpHypA, important to rationalize, at the molecular level, the functional interactions of this chaperone with its protein partners.

PubMed: 30264175
DOI: 10.1007/s00775-018-1616-y

実験手法

SOLUTION NMR