3DP8: Structural Characterization Of A Putative Endogenous Metal Chelator In The Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)

Citation:
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) (-). 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.
PDB ID: 3DP8Download
MMDB ID: 66768
PDB Deposition Date: 2008/7/7
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.5  Å
Source Organism:
Similar Structures:
Biological Unit for 3DP8: monomeric; determined by author and by software (PISA)
Molecular Components in 3DP8
Label Count Molecule
Protein (1 molecule)
1
Nickel-binding Periplasmic Protein(Gene symbol: nikA)
Molecule annotation
Chemicals (11 molecules)
1
4
2
1
3
2
4
1
5
3
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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