 |
PDBsum entry 1vdr
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxidoreductase
|
PDB id
|
|
|
|
1vdr
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the dead sea halophilic archaeon, Haloferax volcanii.
|
|
|
Authors
|
|
U.Pieper,
G.Kapadia,
M.Mevarech,
O.Herzberg.
|
|
|
Ref.
|
|
Structure, 1998,
6,
75-88.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
BACKGROUND: The proteins of halophilic archaea require high salt concentrations
both for stability and for activity, whereas they denature at low ionic
strength. The structural basis for this phenomenon is not yet well understood.
The crystal structure of dihydrofolate reductase (DHFR) from Haloferax volcanii
(hv-DHFR) reported here provides the third example of a structure of a protein
from a halophilic organism. The enzyme is considered moderately halophilic, as
it retains activity and secondary structure at monovalent salt concentrations as
low as 0.5 M. RESULTS: The crystal structure of hv-DHFR has been determined at
2.6 A resolution and reveals the same overall fold as that of other DHFRs. The
structure is in the apo state, with an open conformation of the active-site
gully different from the open conformation seen in other DHFR structures. The
unique feature of hv-DHFR is a shift of the alpha helix encompassing residues
46-51 and an accompanied altered conformation of the ensuing loop relative to
other DHFRs. Analysis of the charge distribution, amino acid composition,
packing and hydrogen-bonding pattern in hv-DHFR and its non-halophilic homologs
has been performed. CONCLUSIONS: The moderately halophilic behavior of hv-DHFR
is consistent with the lack of striking structural features expected to occur in
extremely halophilic proteins. The most notable feature of halophilicity is the
presence of clusters of non-interacting negatively charged residues. Such
clusters are associated with unfavorable electrostatic energy at low salt
concentrations, and may account for the instability of hv-DHFR at salt
concentrations lower than 0.5 M. With respect to catalysis, the open
conformation seen here is indicative of a conformational transition not reported
previously. The impact of this conformation on function and/or halophilicity is
unknown.
|
|
|
|
|
|
|
|
Figure 3.
Figure 3. Superposition of the Cα trace of hv-DHFR (solid
line), ec-DHFR in the closed conformation (long dashes; PDB
entry code 1rx9) and ec-DHFR in the occluded conformation (short
dashes; PDB entry code 1rx5). Every tenth residue of hv-DHFR is
labeled.
|
|
Figure 6.
Figure 6. Stereo representation of two clusters of negatively
charged residues in hv-DHFR. Water molecules are depicted as
black spheres and hydrogen bonds as dashed lines. (a)
Intramolecular cluster; (b) intermolecular cluster at the
interface of three molecules.
|
|
|
|
|
|
The above figures are
reprinted
by permission from Cell Press:
Structure
(1998,
6,
75-88)
copyright 1998.
|
|
|
|
|
|
|
