2NOO

Crystal Structure of Mutant NikA

Summary for 2NOO

• Entry DOI: 10.2210/pdb2noo/pdb
• Descriptor: Nickel-binding periplasmic protein, IODIDE ION, NICKEL (II) ION, ... (4 entities in total)
• Functional Keywords: nickel-bound, transport, iodine, periplasm, hydrolase
• Biological source: Escherichia coli K12
• Cellular location: Periplasm : P33590
• Total number of polymer chains: 1
• Total formula weight: 56590.14

Authors

Addy, C.,Ohara, M.,Kawai, F.,Kidera, A.,Ikeguchi, M.,Fuchigami, S.,Osawa, M.,Shimada, I.,Park, S.Y.,Tame, J.R.H.,Heddle, J.G. (deposition date: 2006-10-26, release date: 2007-01-23, Last modification date: 2024-10-30)

Primary citation

Addy, C.,Ohara, M.,Kawai, F.,Kidera, A.,Ikeguchi, M.,Fuchigami, S.,Osawa, M.,Shimada, I.,Park, S.Y.,Tame, J.R.,Heddle, J.G.
Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.
Acta Crystallogr.,Sect.D, 63:221-229, 2007

PubMed Abstract: Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wild-type NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed.

PubMed: 17242515
DOI: 10.1107/S0907444906048712

Experimental method

X-RAY DIFFRACTION (1.65 Å)