Structural insights into HypB, a GTP-binding protein that regulates metal binding

Area of Science:

• Biochemistry
• Structural Biology
• Microbiology

Background:

• HypB is a prokaryotic metal-binding guanine nucleotide-binding protein.
• It is essential for nickel incorporation into hydrogenases, which are vital enzymes.
• Understanding HypB's structure and function is key to understanding hydrogenase maturation.

Purpose of the Study:

• To determine the x-ray structure of HypB from Methanocaldococcus jannaschii.
• To elucidate the mechanism of nucleotide-dependent dimerization and metal-binding.
• To propose a model for metal ion incorporation into hydrogenases.

Main Methods:

• X-ray crystallography to solve the structure of HypB.
• Biochemical assays to study nucleotide-dependent dimerization and metal binding.
• Comparative analysis with homologous proteins like NifH.

Main Results:

• The G-domain of HypB exhibits a unique topology, classifying it within the SIMIBI class of NTP-binding proteins.
• HypB undergoes nucleotide-dependent dimerization, with nucleotides at the dimer interface.
• Two metal-binding sites were identified, one sensitive to the nucleotide-bound state, and a conserved motif links nucleotide binding to metal sites.

Conclusions:

• HypB's distinct structure and nucleotide-dependent dimerization are critical for its function in nickel incorporation.
• Dimerization is essential for both nucleotide binding and likely hydrolysis.
• The findings provide insights into the mechanism of metal ion insertion into hydrogenases, potentially through a switch-dependent process.