2HF9

Crystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form

Summary for 2HF9

• Entry DOI: 10.2210/pdb2hf9/pdb
• Descriptor: Probable hydrogenase nickel incorporation protein hypB, MAGNESIUM ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: alpha and beta protein, p-loop containing nucleoside triphosphate hydrolase, hydrolase, metal binding protein
• Biological source: Methanocaldococcus jannaschii
• Total number of polymer chains: 2
• Total formula weight: 50765.83

Authors

Gasper, R.,Scrima, A.,Wittinghofer, A. (deposition date: 2006-06-23, release date: 2006-07-04, Last modification date: 2024-10-16)

Primary citation

Gasper, R.,Scrima, A.,Wittinghofer, A.
Structural insights into HypB, a GTP-binding protein that regulates metal binding.
J.Biol.Chem., 281:27492-27502, 2006

PubMed Abstract: 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.

PubMed: 16807243
DOI: 10.1074/jbc.M600809200

Experimental method

X-RAY DIFFRACTION (1.9 Å)