4DCY

X-ray structure of NikA in complex with Fe(1S,2S)-N,N-kappa-Bis(2-pyridylmethyl)-N-carboxymethyl-N-kappa-methyl-1,2-cyclohexanediamine

4DCY の概要

• エントリーDOI: 10.2210/pdb4dcy/pdb
• 関連するPDBエントリー: 1ZLQ
• 分子名称: Nickel-binding periplasmic protein, ACETATE ION, GLYCEROL, ... (7 entities in total)
• 機能のキーワード: transport protein, protein-bound iron complex, metal transport
• 由来する生物種: Escherichia coli
• 細胞内の位置: Periplasm (Probable): P33590
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 116598.79

構造登録者

Cherrier, M.V.,Girgenti, E.,Amara, P.,Iannello, M.,Marchi-Delapierre, C.,Fontecilla-Camps, J.C.,Menage, S.,Cavazza, C. (登録日: 2012-01-18, 公開日: 2012-05-09, 最終更新日: 2023-09-13)

主引用文献

Cherrier, M.V.,Girgenti, E.,Amara, P.,Iannello, M.,Marchi-Delapierre, C.,Fontecilla-Camps, J.C.,Menage, S.,Cavazza, C.
The structure of the periplasmic nickel-binding protein NikA provides insights for artificial metalloenzyme design.
J.Biol.Inorg.Chem., 17:817-829, 2012

PubMed Abstract: Understanding the interaction of a protein with a relevant ligand is crucial for the design of an artificial metalloenzyme. Our own interest is focused on the synthesis of artificial monooxygenases. In an initial effort, we have used the periplasmic nickel-binding protein NikA from Escherichia coli and iron complexes in which N(2)Py(2) ligands (where Py is pyridine) have been varied in terms of charge, aromaticity, and size. Six "NikA/iron complex" hybrids have been characterized by X-ray crystallography, and their interactions and solution properties have been studied. The hybrids are stable as indicated by their K (d) values, which are all in the micromolar range. The X-ray structures show that the ligands interact with NikA through salt bridges with arginine residues and π-stacking with a tryptophan residue. We have further characterized these interactions using quantum mechanical calculations and determined that weak CH/π hydrogen bonds finely modulate the stability differences between hybrids. We emphasize the important role of the tryptophan residues. Thus, our study aims at the complete characterization of the factors that condition the interaction of an artificial ligand and a protein and their implications for catalysis. Besides its potential usefulness in the synthesis of artificial monooxygenases, our approach should be generally applicable in the field of artificial metalloenzymes.

PubMed: 22526565
DOI: 10.1007/s00775-012-0899-7

実験手法

X-RAY DIFFRACTION (2 Å)