4DCX

X-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamine

Summary for 4DCX

• Entry DOI: 10.2210/pdb4dcx/pdb
• Related: 1ZLQ 4DCY
• Descriptor: Nickel-binding periplasmic protein, SULFATE ION, ACETATE ION, ... (6 entities in total)
• Functional Keywords: transport protein, protein-bound iron complex, metal transport
• Biological source: Escherichia coli
• Cellular location: Periplasm (Probable): P33590
• Total number of polymer chains: 2
• Total formula weight: 117194.16

Authors

Cherrier, M.V.,Girgenti, E.,Amara, P.,Iannello, M.,Marchi-Delapierre, C.,Fontecilla-Camps, J.C.,Menage, S.,Cavazza, C. (deposition date: 2012-01-18, release date: 2012-05-09, Last modification date: 2023-09-13)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2 Å)