3DP8

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

Summary for 3DP8

• Entry DOI: 10.2210/pdb3dp8/pdb
• Related: 1UIU 1UIV 1ZLQ 2NOO
• Descriptor: Nickel-binding periplasmic protein, NICKEL (II) ION, ACETATE ION, ... (8 entities in total)
• Functional Keywords: nickel, nickellophore, butane-1, 2, 4-tricarboxylate, transport, metal transport
• Biological source: Escherichia coli
• Cellular location: Periplasm (Probable): P33590
• Total number of polymer chains: 3
• Total formula weight: 171559.20

Authors

Cherrier, M.V.,Cavazza, C.,Bochot, C.,Lemaire, D.,Fontecilla-Camps, J.C. (deposition date: 2008-07-07, release date: 2008-09-16, Last modification date: 2023-11-01)

Primary citation

Cherrier, M.V.,Cavazza, C.,Bochot, C.,Lemaire, D.,Fontecilla-Camps, J.C.
Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA
Biochemistry, 47:9937-9943, 2008

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) (-). 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.

PubMed: 18759453
DOI: 10.1021/bi801051y

Experimental method

X-RAY DIFFRACTION (2.5 Å)