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PDBsum entry 2hf9
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Hydrolase, metal binding protein
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PDB id
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2hf9
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References listed in PDB file
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Key reference
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Title
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Structural insights into hypb, A gtp-Binding protein that regulates metal binding.
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Authors
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R.Gasper,
A.Scrima,
A.Wittinghofer.
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Ref.
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J Biol Chem, 2006,
281,
27492-27502.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
27492-27502)
copyright 2006.
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