4I8C

X-ray structure of NikA in complex with Ni-(L-His)2

PDB DOI: https://doi.org/10.2210/pdb4I8C/pdb

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

Deposited: 2012-12-03 Released: 2013-01-30
Deposition Author(s): Lebrette, H., Iannello, M., Fontecilla-Camps, J.C., Cavazza, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.234
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The binding mode of Ni-((L)-His)(2) in NikA revealed by X-ray crystallography.

Lebrette, H., Iannello, M., Fontecilla-Camps, J.C., Cavazza, C.

(2012) J Inorg Biochem 121C: 16-18

PubMed: 23314594 Search on PubMed
DOI: https://doi.org/10.1016/j.jinorgbio.2012.12.010
Primary Citation of Related Structures:
4I8C

PubMed Abstract:
The ABC-type importer NikABCDE mediates nickel acquisition in Escherichia coli. The periplasmic nickel-binding component NikA has a folding similar to that of the peptide transporter OppA and does not bind free nickel. Instead, we showed that the metal is tetra-coordinated by an organic tri-dentate molecule and His416. Conversely, it has been recently reported that NikA binds Ni-(L-His)2 and that addition of histidine increases the rate of nickel uptake in vivo. Here, we report the structure of NikA/Ni-(L-His)2 and show that histidine binding differs from peptide binding in OppA. The structure also confirms the central role of His416 in nickel binding.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 172.1 kDa
Atom Count: 12,432
Modelled Residue Count: 1,494
Deposited Residue Count: 1,506
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-binding periplasmic protein	A, B, C	502	Escherichia coli K-12	Mutation(s): 0 Gene Names: nikA, b3476, JW3441
UniProt
Find proteins for P33590 (Escherichia coli (strain K12)) Explore P33590 Go to UniProtKB: P33590
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33590
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HIS Query on HIS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain D [auth A]	D [auth A] E [auth A] EA [auth C] FA [auth C] Q [auth B] D [auth A], E [auth A], EA [auth C], FA [auth C], Q [auth B], R [auth B]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain Q [auth B] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain MA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain MA [auth C]	CA [auth B], MA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain MA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain MA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain KA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] KA [auth C] LA [auth C] N [auth A] AA [auth B], BA [auth B], KA [auth C], LA [auth C], N [auth A], O [auth A], P [auth A], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain Y [auth B] SDF format, chain DA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	DA [auth B] G [auth A] H [auth A] HA [auth C] I [auth A] DA [auth B], G [auth A], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], L [auth A], M [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain DA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain GA [auth C] SDF format, chain S [auth B] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain S [auth B]	F [auth A], GA [auth C], S [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain GA [auth C] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain GA [auth C] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.234
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.63	α = 90
b = 158.63	β = 90
c = 135.82	γ = 120

Software Package:

Software Name	Purpose
MX	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-30

Deposition Author(s):

Lebrette, H.

Iannello, M.

Fontecilla-Camps, J.C.

Cavazza, C.

Revision History (Full details and data files)

Version 1.0: 2013-01-30
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description