8ETB

the crystal structure of a rationally designed zinc sensor based on maltose binding protein - Zn binding conformation

Summary for 8ETB

• Entry DOI: 10.2210/pdb8etb/pdb
• Descriptor: Zinc Sensor protein, ZINC ION, ACETATE ION, ... (4 entities in total)
• Functional Keywords: zinc, sensing, xe nmr, metal binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 40346.91

Authors

Zhao, Z.,Zhou, M.,Zemerov, S.D.,Marmorstein, R.,Dmochowski, I.J. (deposition date: 2022-10-16, release date: 2023-03-22, Last modification date: 2024-05-22)

Primary citation

Zhao, Z.,Zhou, M.,Zemerov, S.D.,Marmorstein, R.,Dmochowski, I.J.
Rational design of a genetically encoded NMR zinc sensor.
Chem Sci, 14:3809-3815, 2023

PubMed Abstract: Elucidating the biochemical roles of the essential metal ion, Zn, motivates detection strategies that are sensitive, selective, quantitative, and minimally invasive in living systems. Fluorescent probes have identified Zn in cells but complementary approaches employing nuclear magnetic resonance (NMR) are lacking. Recent studies of maltose binding protein (MBP) using ultrasensitive Xe NMR spectroscopy identified a switchable salt bridge which causes slow xenon exchange and elicits strong hyperpolarized Xe chemical exchange saturation transfer (hyper-CEST) NMR contrast. To engineer the first genetically encoded, NMR-active sensor for Zn, we converted the MBP salt bridge into a Zn binding site, while preserving the specific xenon binding cavity. The zinc sensor (ZS) at only 1 μM achieved 'turn-on' detection of Zn with pronounced hyper-CEST contrast. This made it possible to determine different Zn levels in a biological fluid hyper-CEST. ZS was responsive to low-micromolar Zn, only modestly responsive to Cu, and nonresponsive to other biologically important metal ions, according to hyper-CEST NMR spectroscopy and isothermal titration calorimetry (ITC). Protein X-ray crystallography confirmed the identity of the bound Zn ion using anomalous scattering: Zn was coordinated with two histidine side chains and three water molecules. Penta-coordinate Zn forms a hydrogen-bond-mediated gate that controls the Xe exchange rate. Metal ion binding affinity, Xe NMR chemical shift, and exchange rate are tunable parameters protein engineering, which highlights the potential to develop proteins as selective metal ion sensors for NMR spectroscopy and imaging.

PubMed: 37035699
DOI: 10.1039/d3sc00437f

Experimental method

X-RAY DIFFRACTION (1.63 Å)