5W1F

Crystal structure of Ni(II)- and Ca(II)-bound human calprotectin

Summary for 5W1F

• Entry DOI: 10.2210/pdb5w1f/pdb
• Descriptor: Protein S100-A8, Protein S100-A9, SODIUM ION, ... (6 entities in total)
• Functional Keywords: calprotectin, innate immunity, metal sequestration, nickel, calcium, s100 protein, metal binding protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 8
• Total formula weight: 97232.55

Authors

Nakashige, T.G.,Drennan, C.L.,Nolan, E.M. (deposition date: 2017-06-03, release date: 2017-06-14, Last modification date: 2023-10-04)

Primary citation

Nakashige, T.G.,Zygiel, E.M.,Drennan, C.L.,Nolan, E.M.
Nickel Sequestration by the Host-Defense Protein Human Calprotectin.
J. Am. Chem. Soc., 139:8828-8836, 2017

PubMed Abstract: The human innate immune protein calprotectin (CP, S100A8/S100A9 oligomer, calgranulin A/calgranulin B oligomer, MRP-8/MRP-14 oligomer) chelates a number of first-row transition metals, including Mn(II), Fe(II), and Zn(II), and can withhold these essential nutrients from microbes. Here we elucidate the Ni(II) coordination chemistry of human CP. We present a 2.6-Å crystal structure of Ni(II)- and Ca(II)-bound CP, which reveals that CP binds Ni(II) ions at both its transition-metal-binding sites: the HisAsp motif (site 1) and the His motif (site 2). Further biochemical studies establish that coordination of Ni(II) at the hexahistidine site is thermodynamically preferred over Zn(II). We also demonstrate that CP can sequester Ni(II) from two human pathogens, Staphylococcus aureus and Klebsiella pneumoniae, that utilize this metal nutrient during infection, and inhibit the activity of the Ni(II)-dependent enzyme urease in bacterial cultures. In total, our findings expand the biological coordination chemistry of Ni(II)-chelating proteins in nature and provide a foundation for evaluating putative roles of CP in Ni(II) homeostasis at the host-microbe interface and beyond.

PubMed: 28573847
DOI: 10.1021/jacs.7b01212

Experimental method

X-RAY DIFFRACTION (2.6 Å)