2KKD

NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin

「2QKZ」から置き換えられました

2KKD の概要

• エントリーDOI: 10.2210/pdb2kkd/pdb
• 関連するPDBエントリー: 2QL0 8RXN
• NMR情報: BMRB: 15375,16849
• 分子名称: Rubredoxin, NICKEL (II) ION (2 entities in total)
• 機能のキーワード: electron transport, [fe-4s], iron, metal-binding, cytoplasm, transport
• 由来する生物種: Desulfovibrio vulgaris str. Hildenborough
• 細胞内の位置: Cytoplasm: P00269
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 5636.87

構造登録者

Nunes, S.G.,Volkman, B.F.,Moura, J.J.G.,Moura, I.,Macedo, A.L.,Markley, J.L.,Duarte, I.C. (登録日: 2009-06-18, 公開日: 2009-12-22, 最終更新日: 2024-05-22)

主引用文献

Goodfellow, B.J.,Duarte, I.C.,Macedo, A.L.,Volkman, B.F.,Nunes, S.G.,Moura, I.,Markley, J.L.,Moura, J.J.
An NMR structural study of nickel-substituted rubredoxin
J.Biol.Inorg.Chem., 15:409-420, 2010

PubMed Abstract: The Ni(II) and Zn(II) derivatives of Desulfovibrio vulgaris rubredoxin (DvRd) have been studied by NMR spectroscopy to probe the structure at the metal centre. The beta CH(2) proton pairs from the cysteines that bind the Ni(II) atom have been identified using 1D nuclear Overhauser enhancement (NOE) difference spectra and sequence specifically assigned via NOE correlations to neighbouring protons and by comparison with the published X-ray crystal structure of a Ni(II) derivative of Clostridium pasteurianum rubredoxin. The solution structures of DvRd(Zn) and DvRd(Ni) have been determined and the paramagnetic form refined using pseudocontact shifts. The determination of the magnetic susceptibility anisotropy tensor allowed the contact and pseudocontact contributions to the observed chemical shifts to be obtained. Analysis of the pseudocontact and contact chemical shifts of the cysteine H beta protons and backbone protons close to the metal centre allowed conclusions to be drawn as to the geometry and hydrogen-bonding pattern at the metal binding site. The importance of NH-S hydrogen bonds at the metal centre for the delocalization of electron spin density is confirmed for rubredoxins and can be extrapolated to metal centres in Cu proteins: amicyanin, plastocyanin, stellacyanin, azurin and pseudoazurin.

PubMed: 19997764
DOI: 10.1007/s00775-009-0613-6

実験手法

SOLUTION NMR