5KZJ

Loop Deletion mutant of Paracoccus denitrificans AztC

Summary for 5KZJ

• Entry DOI: 10.2210/pdb5kzj/pdb
• Related: 4XRV
• Descriptor: Periplasmic solute binding protein, ZINC ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: zinc binding protein, periplasm, deletion mutant, metal binding protein
• Biological source: Paracoccus denitrificans (strain Pd 1222)
• Total number of polymer chains: 2
• Total formula weight: 62062.19

Authors

Yukl, E. (deposition date: 2016-07-25, release date: 2017-07-05, Last modification date: 2024-10-23)

Primary citation

Neupane, D.P.,Avalos, D.,Fullam, S.,Roychowdhury, H.,Yukl, E.T.
Mechanisms of zinc binding to the solute-binding protein AztC and transfer from the metallochaperone AztD.
J. Biol. Chem., 292:17496-17505, 2017

PubMed Abstract: Bacteria can acquire the essential metal zinc from extremely zinc-limited environments by using ATP-binding cassette (ABC) transporters. These transporters are critical virulence factors, relying on specific and high-affinity binding of zinc by a periplasmic solute-binding protein (SBP). As such, the mechanisms of zinc binding and release among bacterial SBPs are of considerable interest as antibacterial drug targets. Zinc SBPs are characterized by a flexible loop near the high-affinity zinc-binding site. The function of this structure is not always clear, and its flexibility has thus far prevented structural characterization by X-ray crystallography. Here, we present intact structures for the zinc-specific SBP AztC from the bacterium in the zinc-bound and apo-states. A comparison of these structures revealed that zinc loss prompts significant structural rearrangements, mediated by the formation of a sodium-binding site in the apo-structure. We further show that the AztC flexible loop has no impact on zinc-binding affinity, stoichiometry, or protein structure, yet is essential for zinc transfer from the metallochaperone AztD. We also found that 3 His residues in the loop appear to temporarily coordinate zinc and then convey it to the high-affinity binding site. Thus, mutation of any of these residues to Ala abrogated zinc transfer from AztD. Our structural and mechanistic findings conclusively identify a role for the AztC flexible loop in zinc acquisition from the metallochaperone AztD, yielding critical insights into metal binding by AztC from both solution and AztD. These proteins are highly conserved in human pathogens, making this work potentially useful for the development of novel antibiotics.

PubMed: 28887302
DOI: 10.1074/jbc.M117.804799

Experimental method

X-RAY DIFFRACTION (2.2 Å)