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PDBsum entry 3d57
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Hormone, transcription receptor
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PDB id
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3d57
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References listed in PDB file
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Key reference
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Title
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Molecular basis for dimer formation of trbeta variant d355r.
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Authors
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N.Jouravel,
E.Sablin,
M.Togashi,
J.D.Baxter,
P.Webb,
R.J.Fletterick.
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Ref.
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Proteins, 2008,
75,
111-117.
[DOI no: ]
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PubMed id
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Abstract
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Protein quality and stability are critical during protein purification for X-ray
crystallography. A target protein that is easy to manipulate and crystallize
becomes a valuable product useful for high-throughput crystallography for drug
design and discovery. In this work, a single surface mutation, D355R, was shown
to be crucial for converting the modestly stable monomeric ligand binding domain
of the human thyroid hormone receptor (TR LBD) into a stable dimer. The
structure of D335R TR LBD mutant was solved using X-ray crystallography and
refined to 2.2 A resolution with R(free)/R values of 24.5/21.7. The crystal
asymmetric unit reveals the TR dimer with two molecules of the hormone-bound LBD
related by twofold symmetry. The ionic interface between the two LBDs comprises
residues within loop H10-H11 and loop H6-H7 as well as the C-terminal halves of
helices 8 of both protomers. Direct intermolecular contacts formed between the
introduced residue Arg 355 of one TR molecule and Glu 324 of the second molecule
become a part of the extended dimerization interface of 1330 A(2) characteristic
for a strong complex assembly that is additionally strengthened by buffer
solutes. Proteins 2009. (c) 2008 Wiley-Liss, Inc.
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Figure 1.
Figure 1. Size exclusion chromatography of D355R TR LBD. Each
protein peak is labeled with its apparent molecular mass (kDa).
Panels (A) and (B) represent runs from independent protein
preparations. (A) Initial run is shown in gray,
rechromatographed fraction of dimeric TR is in black. (B)
Protein was prepared in the presence (black line) or absence
(gray line) of 50 mM lithium sulfate.
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Figure 2.
Figure 2. Structure of the TR  D355R
mutant dimer. (A) Cartoon representation of the dimer. The two
TR monomers are shown in green (helixes are numbered) and
yellow. The N- and C-termini of each LBD are labeled. Residues
H412, H413, R355, E324, E326, R338, and sulfate ion at the dimer
interface are shown as stick models and orange sphere,
respectively. The bound hormone is shown as space-filling model
in dark gray. The two boxed regions indicate the crucial polar
interactions at the dimer interface (shown in detail on Panel
B). (B) Network of contacting interfacial residues from two
sites at the dimer interface. Residues are shown as stick
models. Sulfate ion and water are drawn as stick model and
sphere, respectively. Contacts between interacting residues and
ions are indicated. The electron density corresponding to the
sulfate ion (black mesh) in the 2Fo-Fc map is contoured at 2.0
 .
(C) Polar dimer interface. The intermolecular residues are in
surface representation for the green monomer, and in stick
representation for the yellow monomer. Shared at interface water
molecules are depicted as cyan dotted spheres. Figures were
prepared with PyMOL from DeLano Scientific
(http://www.pymol.org).
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2008,
75,
111-117)
copyright 2008.
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