Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.19 kDa 
• Atom Count: 9,194 
• Modelled Residue Count: 994 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

 4DCX

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

• PDB DOI: 10.2210/pdb4DCX/pdb

• Classification: METAL TRANSPORT
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-18 Released: 2012-05-09 
• Deposition Author(s): Cherrier, M.V., Girgenti, E., Amara, P., Iannello, M., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S., Cavazza, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Literature

The structure of the periplasmic nickel-binding protein NikA provides insights for artificial metalloenzyme design.

Cherrier, M.V., Girgenti, E., Amara, P., Iannello, M., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S., Cavazza, C.

(2012) J Biol Inorg Chem 17: 817-829

• PubMed: 22526565 
• DOI: 10.1007/s00775-012-0899-7
• Primary Citation of Related Structures:  
  4DCX, 4DCY


• 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.

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Organizational Affiliation: 

Institut de Biologie Structurale Jean-Pierre Ebel, Groupe Métalloproteines, UMR 5075, CEA, CNRS, Université Joseph Fourier Grenoble 1, 41 rue Horowitz, 38027, Grenoble Cedex 1, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-binding periplasmic protein	A, B	502	Escherichia coli K-12	Mutation(s): 0  Gene Names: b3476, JW3441, nikA
UniProt
Find proteins for P33590 (Escherichia coli (strain K12)) Explore P33590  Go to UniProtKB:  P33590

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L2D	FA [auth A], ZA [auth B]	{2,2'-[(1R,2R)-cyclohexane-1,2-diylbis{[(pyridin-2-yl-kappaN)methyl]imino-kappaN}]diacetato-kappaO(2-)}iron C22 H26 Fe N4 O4 RHFVCFXUQWXGET-GZJHNZOKSA-L
SO4	C [auth A], D [auth A], GA [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], RA [auth B], SA [auth B], TA [auth B], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], G [auth A], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], S [auth A], T [auth A], U [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
L2D	PDBBind:  4DCX	Kd: 3.14e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.35	α = 90
b = 95.64	β = 90
c = 125.19	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Cherrier, M.V., Girgenti, E., Amara, P., Iannello, M., Marchi-Delapierre, C., Fontecilla-Camps, J.C., Menage, S., Cavazza, C.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-06-13
  Changes: Database references