PDBsum entry 2noo

Hydrolase

PDB id: 2noo

Contents

Protein chain

496 a.a. *

Metals

_NI

IOD ×2

Waters ×348

* Residue conservation analysis

PDB id:

2noo

Name:

Hydrolase

Title:

Crystal structure of mutant nika

Structure:

Nickel-binding periplasmic protein. Chain: a. Synonym: nika. Engineered: yes. Mutation: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: nika. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.65Å R-factor: 0.179 R-free: 0.210

Authors:

C.Addy,M.Ohara,F.Kawai,A.Kidera,M.Ikeguchi,S.Fuchigami,M.Osawa, I.Shimada,S.Y.Park,J.R.H.Tame,J.G.Heddle

Key ref:

C.Addy et al. (2007). Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography. Acta Crystallogr D Biol Crystallogr, 63, 221-229. PubMed id: 17242515 DOI: 10.1107/S0907444906048712

Date:

26-Oct-06 Release date: 23-Jan-07

Protein chain

P33590  (NIKA_ECOLI) -  Nickel-binding periplasmic protein from Escherichia coli (strain K12)

Seq: 524 a.a.

Struc: 496 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.6.3.24 - Transferred entry: 7.2.2.11.
• Reaction: ATP + H₂O + Ni²⁺(Out) = ADP + phosphate + Ni²⁺(In)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444906048712

Acta Crystallogr D Biol Crystallogr 63:221-229 (2007)

PubMed id: 17242515

Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.

C.Addy, M.Ohara, F.Kawai, A.Kidera, M.Ikeguchi, S.Fuchigami, M.Osawa, I.Shimada, S.Y.Park, J.R.Tame, J.G.Heddle.

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.

Selected figure(s)

Figure 3.
Figure 3 ITC traces of (a) 10 µl injections of 1.1 mM NiCl[2] into 180 µM EDTA. (b) 10 µl injections of 5 mM EDTA, 1.8 mM NiCl[2] into 180 µM NikA H56A. (c) 10 µl injections of 5 mM EDTA, 1.8 mM NiCl[2] into 180 µM wild-type NikA. (d) 10 µl injections of 5 mM EDTA, 1.8 mM NiCl[2] into 180 µM 6-mutant NikA. 1 cal = 4.186 J.

Figure 4.
Figure 4 (a) Crystal structure of 6-mutant NikA. The mutated residues around the binding cleft are shown as cyan sticks. The nickel-binding histidine residues are shown as yellow sticks. (b) Ribbon representations of NikA (red) and 6-mutant NikA (yellow) after alignment of the C^ backbones of lobe 1 (residues 4-245 and 471-499) of the two proteins.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 221-229) copyright 2007.

Figures were selected by an automated process.