PDBsum entry 2hf9

Hydrolase, metal binding protein

PDB id: 2hf9

Contents

Protein chains

211 a.a. *

Ligands

GSP ×2

Metals

_MG ×2

_ZN ×2

Waters ×174

* Residue conservation analysis

PDB id:

2hf9

Name:

Hydrolase, metal binding protein

Title:

Crystal structure of hypb from methanocaldococcus jannaschii in the triphosphate form

Structure:

Probable hydrogenase nickel incorporation protein hypb. Chain: a, b. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: hypb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.217 R-free: 0.241

Authors:

R.Gasper,A.Scrima,A.Wittinghofer

Key ref:

R.Gasper et al. (2006). Structural insights into HypB, a GTP-binding protein that regulates metal binding. J Biol Chem, 281, 27492-27502. PubMed id: 16807243 DOI: 10.1074/jbc.M600809200

Date:

23-Jun-06 Release date: 04-Jul-06

Protein chains

Q57884  (HYPB_METJA) -  Probable hydrogenase maturation factor HypB from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 221 a.a.

Struc: 211 a.a.

DOI no: 10.1074/jbc.M600809200

J Biol Chem 281:27492-27502 (2006)

PubMed id: 16807243

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

R.Gasper, A.Scrima, A.Wittinghofer.

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.

Selected figure(s)

Figure 5.
FIGURE 5. The switch regions. A, overlay of different proteins showing the switch regions and the P-loop. Switch I is underlined in red, switch II in blue, and the P-loop in green. The NH groups of the invariant switch II glycines are shown in black. B, detailed representation of the switch II loop (green) of HypB, with switch I and the P-loop shown as brown and red lines, respectively.

Figure 6.
FIGURE 6. Comparison to other nucleotide-binding proteins. A, superimposition of HypB and SRP (PDB code 1RJ9) as green (HypB) and blue (SRP) ribbons, with nucleotides from HypB and SRP in orange and red, respectively. Differences between HypB and SRP are shown in cyan (HypB) and light blue (SRP). B, active site of the Soj homodimer. Monomer A and B are shown in cyan and light cyan, respectively (PDB code 2BEK; r.m.s.d.: 3.0 Å over 167 residues). C, stereoview of a superimposition of HypB and the SIMIBI-ATPase Soj (PDB code 2BEK). HypB is shown in green, Soj in cyan, ATP in red, and GTP Sin orange. The comparison shows a similar positioning of the dimer and the nucleotides. D, van der Waals surface overlay of HypB and nitrogenase iron protein NifH bound to ADP-AlF^-[4] (PDB code 1M34). HypB is shown in green, NifH in blue, and the nucleotides of HypB and NifH in orange and red, respectively. Zinc ions of HypB are shown in orange and the 4Fe:4S cluster of NifH in red. The binding site of the MoFe nitrogenase protein is shown schematically as a violet band.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 27492-27502) copyright 2006.

Figures were selected by an automated process.