Molecular Playground/HypA

One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.

Introduction

Helicobacter pylori is a pathogenic bacterium that colonizes the human gastric mucosa, which can cause peptic ulcers and has been linked to stomach cancers.^[1] H. pylori requires the activity of nickel-dependent enzymes, [NiFe]-Hydrogenase (H₂ase) and urease, to survive in the acidic environment of the stomach.^[2][3][4] Thus nickel is an important nutrient for H. pylori.

Accessory proteins HypABCDEF and UreIEFGH facilitate the maturation of [NiFe]-H₂ase and urease respectively^[5]. HypA is a nickel metallochaperone normally associated with the maturation of [NiFe]-H₂ase^[6]. In H. pylori, however, it is also require for the full activy of urease, despite the presence of the urease-specific Ni-chaperone, UreE^[7].

HypA

The H. pyloriHypA (HpHypA) is a 13.2kDa Ni-chaperone with both a nickel binding site and and structural zinc site. Zn(II) is coordinated by two CXXC motif each with a flanking histidine, whereas the Ni(II) is known to bind to the N-terminus MHE motif^[8]. The HpHypA protein has also been characterized as a monomer and a homodimer. The (N-terminal tag colored in red) has been solved by NMR (PDB ID: 2KDX)^[9]. The monomeric structure shows an containing the N- and C-termini well separated from the . The homodimeric HpHypA has been characterized by NMR to have the similar overall structure with discrepancies to the metal binding sites^[8]. The metal sites in HpHypA have been characterized by X-ray absorption spectroscopy (XAS) at pH 6.3 and 7.2 to similate the internal pH of H. pylori under acid shock or at neutral pH conditions^[8] respectively. While the Ni(II) site is 6-coordinate N/O under both pH conditions, the Zn(II) coordination changes from Cys₄ at neutral pH to Cys₂His₂ at acidic pH with nickel-bound^[8] (Fig. 1). Changes to the coordination of structural Zinc site in response to pH has been hypothesized to be linked to changes in HypA conformations and protein interaction partners^[8].

Fig. 1: Diagram of Ni- and pH-dependent structural changes to Zn(II) site of HpHypA (adapted figure^[8])

The crystal structure of (PDB ID: 3A43) and (PDB ID: 3A44) HypA from Thermococcus kodakarensis has been solved^[10]. The HypA homodimer from T. kodakarensis shows a switch dimer, where one beta strand of each alpha/beta lobe comes from the opposite subunit. Additionally, each is coordinated by CXXC motifs from a different subunit. These observations were consistent with the H. pylori homodimeric HypA NMR data^[8].

Research Interests

The Ni- and pH-dependent changes in the H. pylori HypA structural zinc site suggests multiple conformations of this protein. Thus HypA is likely interfacing between the maturation of [NiFe]-H₂ase and/or urease in H. pylori in a pH-dependent manner, as it is required for the full activation of both of these nickel enzymes. The Maroney Lab at the University of Massachusetts Amherst is interested in characterizing the conformational changes in HypA and its interaction partners under neutral and acid shock conditions.