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

J Biol Chem. 2006 Sep 15;281(37):27492-502. doi: 10.1074/jbc.M600809200. Epub 2006 Jun 28.


HypB is a prokaryotic metal-binding guanine nucleotide-binding protein that is essential for nickel incorporation into hydrogenases. Here we solved the x-ray structure of HypB from Methanocaldococcus jannaschii. It shows that the G-domain has a different topology than the Ras-like proteins and belongs to the SIMIBI (after Signal Recognition Particle, MinD and BioD) class of NTP-binding proteins. We show that HypB undergoes nucleotide-dependent dimerization, which is apparently a common feature of SIMIBI class G-proteins. The nucleotides are located in the dimer interface and are contacted by both subunits. The active site features residues from both subunits arguing that hydrolysis also requires dimerization. Two metal-binding sites are found, one of which is dependent on the state of bound nucleotide. A totally conserved ENV/IGNLV/ICP motif in switch II relays the nucleotide binding with the metal ionbinding site. The homology with NifH, the Fe protein subunit of nitrogenase, suggests a mechanistic model for the switch-dependent incorporation of a metal ion into hydrogenases.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / physiology*
  • Binding Sites
  • Chromatography
  • Crystallography, X-Ray
  • Dimerization
  • GTP-Binding Proteins / chemistry*
  • GTP-Binding Proteins / physiology*
  • Guanosine Triphosphate / chemistry*
  • Metals / chemistry
  • Methanococcus / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid


  • Bacterial Proteins
  • HypB protein, bacteria
  • Metals
  • Guanosine Triphosphate
  • GTP-Binding Proteins

Associated data

  • PDB/2HF8
  • PDB/2HF9