Protein Tunnels: The Case of Urease Accessory Proteins

Abstract

Transition metals are both essential micronutrients and limited in environmental availability. The Ni(II)-dependent urease protein, the most efficient enzyme known to date, is a paradigm for studying the strategies that cells use to handle an essential, yet toxic, metal ion. Urease is a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Ni(II) insertion in the urease active site is performed through the action of three essential accessory proteins: UreD, UreF, and UreG. The crystal structure of the UreD-UreF-UreG complex from the human pathogen Helicobacter pylori (HpUreDFG) revealed the presence of tunnels that cross the entire length of both UreF and UreD, potentially able to deliver Ni(II) ions from UreG to apo-urease. Atomistic molecular dynamics simulations performed on the HpUreDFG complex in explicit solvent and at physiological ionic conditions demonstrate the stability of these protein tunnels in solution and provide insights on the trafficking of water molecules inside the tunnels. The presence of different alternative routes across the identified tunnels for Ni(II) ions, water molecules, and carbonate ions, all involved in urease activation, is highlighted here, and their potential role in the urease activation mechanism is discussed.

The Maturation Pathway of Nickel Urease

“…As the nickel binding site of UreG is far away from the active site of urease, it is not fully understood how the Ni 2+ is transferred from UreG to urease after GTP hydrolysis. One intriguing hypothesis suggested that the Ni 2+ reaches urease through a tunnel within the core of the UreFD complex [82,85,86]. Large cavities have been identified in the structures of H. pylori UreFD complex [82,85,86].…”

“…One intriguing hypothesis suggested that the Ni 2+ reaches urease through a tunnel within the core of the UreFD complex [82,85,86]. Large cavities have been identified in the structures of H. pylori UreFD complex [82,85,86]. The cavities form a tunnel, which is wide enough for Ni 2+ to pass through, connecting the nickel binding site of UreG to an exit at UreD.…”

“…As UreD is responsible for binding urease in the activation complex, the tunnel within the UreFD complex should provide a mechanism for the transfer of Ni 2+ from UreG to the urease within the activation complex. complex [82,85,86]. Large cavities have been identified in the structures of H. pylori UreFD complex [82,85,86].…”

DFT Study of The Interaction between the Ni2+ and Zn2+ Metal Cations and The 1,2-Dithiolene Ligands: Electronic, Geometric and Energetic Analysis

“…1,2 They are used in molecular devices, superconductors, dye-sensitized solar cells, catalyst for molecular hydrogen production, electronic recording disks and model compounds of more elaborated architectures, as in the active sites of pyranopterin molybdenum enzymes. [3][4][5] The dithiolene ligands are studied as elementary building blocks of enzymes, such as ureases (associated with the Ni 2+ cation) 6 and phospholipases (associated with the Zn 2+ cation). 7 They can also act as metalloligands toward other metallic centers.…”

Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data

“…The elucidation of these mechanisms at an atomistic level is of paramount importance to achieve a comprehensive understanding of biological functions. In this context, the Ni(II) trafficking system is an ideal test case because it has all the essential features of other metals, but bacteria that utilize nickel usually use it for a limited number of Ni‐dependent enzymes . In the most studied cases, Escherichia coli requires nickel for hydrogenases, while the pathogen Helicobacter pylori survives the extreme conditions of the gastric mucosa through the action of hydrogenase and urease …”