3QIM | pdb_00003qim

Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb3QIM/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-01-27 Released: 2011-03-02
Deposition Author(s): Cavazza, C., Martin, L., Laffly, E., Lebrette, H., Cherrier, M.V., Zeppieri, L., Richaud, P., Carriere, M., Fontecilla-Camps, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.237 (Depositor), 0.221 (DCC)
R-Value Work:
0.176 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Histidine 416 of the periplasmic binding protein NikA is essential for nickel uptake in Escherichia coli

Cavazza, C., Martin, L., Laffly, E., Lebrette, H., Cherrier, M.V., Zeppieri, L., Richaud, P., Carriere, M., Fontecilla-Camps, J.C.

(2011) FEBS Lett 585: 711-715

PubMed: 21281641 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2011.01.038
Primary Citation Related Structures:
3QIM

PubMed Abstract:
Escherichia coli require nickel for the synthesis of [NiFe] hydrogenases under anaerobic growth conditions. Nickel import depends on the specific ABC-transporter NikABCDE encoded by the nik operon, which deletion causes the complete abolition of hydrogenase activity. We have previously postulated that the periplasmic binding protein NikA binds a natural metallophore containing three carboxylate functions that coordinate a Ni(II) ion, the fourth ligand being His416, the only direct metal-protein contact, completing a square-planar coordination for the metal. The crystal structure of the H416I mutant showed no electron density corresponding to a metal-chelator complex. In vivo experiments indicate that the mutation causes a significant decrease in nickel uptake and hydrogenase activity. These results confirm the essential role of His416 in nickel transport by NikA.

Organizational Affiliation

Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, CEA, CNRS, Université Joseph Fourier-Grenoble 1, Grenoble, France. christine.cavazza@ibs.fr

Macromolecule Content

Total Structure Weight: 114.56 kDa
Atom Count: 8,617
Modeled Residue Count: 996
Deposited Residue Count: 1,004
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-binding periplasmic protein	A, B	502	Escherichia coli K-12	Mutation(s): 1 Gene Names: b3476, JW3441, nikA
UniProt
Find proteins for P33590 (Escherichia coli (strain K12)) Explore P33590 Go to UniProtKB: P33590
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33590
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain AA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain AA [auth B]	AA [auth B], Q [auth A], R [auth A], S [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain AA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain O [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain T [auth B] mmCIF format, chain O [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth A] C [auth A], D [auth A], E [auth A], F [auth A], H [auth A], J [auth A], O [auth A], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain O [auth A] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain O [auth A] Focus chain T [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A] I [auth A] K [auth A] L [auth A] M [auth A] G [auth A], I [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [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] Focus chain Z [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [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] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.237 (Depositor), 0.221 (DCC)
R-Value Work: 0.176 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.731	α = 90
b = 94.005	β = 90
c = 124.33	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-03-02

Deposition Author(s):

Fontecilla-Camps, J.C.

Revision History (Full details and data files)

Version 1.0: 2011-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description