3DP8

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA

Cherrier, M.V., Cavazza, C., Bochot, C., Lemaire, D., Fontecilla-Camps, J.C.

(2008) Biochemistry 47: 9937-9943

  • DOI: 10.1021/bi801051y
  • Primary Citation of Related Structures:  
    3DP8, 3E3K

  • PubMed Abstract: 

    • Escherichia coli and related bacteria require nickel for the synthesis of hydrogenases, enzymes involved in hydrogen oxidation and proton reduction. Nickel transport to the cytoplasm depends on five proteins, NikA-E. We have previously reported the three-dimensional structure of the soluble periplasmic nickel transporter NikA in a complex with FeEDTA(H 2O) (-) ...

    Escherichia coli and related bacteria require nickel for the synthesis of hydrogenases, enzymes involved in hydrogen oxidation and proton reduction. Nickel transport to the cytoplasm depends on five proteins, NikA-E. We have previously reported the three-dimensional structure of the soluble periplasmic nickel transporter NikA in a complex with FeEDTA(H 2O) (-). We have now determined the structure of EDTA-free NikA and have found that it binds a small organic molecule that contributes three ligands to the coordination of a transition metal ion. Unexpectedly, His416, which was far from the metal-binding site in the FeEDTA(H 2O) (-)-NikA complex, becomes the fourth observed ligand to the metal. The best match to the omit map electron density is obtained for butane-1,2,4-tricarboxylate (BTC). Our attempts to obtain a BTC-Ni-NikA complex using apo protein and commercial reagents resulted in nickel-free BTC-NikA. Overall, our results suggest that nickel transport in vivo requires a specific metallophore that may be BTC.

    Organizational Affiliation: 

    Laboratoire de Cristallographie et de Cristallogenese des Proteines, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Universite J. Fourier, 41 rue J. Horowitz, 38027 Grenoble Cedex 1, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nickel-binding periplasmic proteinA, B, C502Escherichia coli K-12Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33590
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HCT
Query on HCT
Download Ideal Coordinates CCD File 
JA [auth C],
L [auth A],
Y [auth B]		(2R)-butane-1,2,4-tricarboxylic acid
C7 H10 O6
LOGBRYZYTBQBTB-SCSAIBSYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
M [auth A],
N [auth A],
AA [auth B],
BA [auth B],
CA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
NI
Query on NI
Download Ideal Coordinates CCD File 
D [auth A],
DA [auth C],
Q [auth B]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
HA [auth C],
IA [auth C],
J [auth A],
K [auth A],
V [auth B],
HA [auth C],
IA [auth C],
J [auth A],
K [auth A],
V [auth B],
W [auth B],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.57α = 90
b = 158.57β = 90
c = 134.94γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance