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PDBsum entry 3h7p
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Signaling protein
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PDB id
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3h7p
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References listed in PDB file
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Key reference
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Title
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Crystal structures of lys-63-Linked tri- And di-Ubiquitin reveal a highly extended chain architecture.
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Authors
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S.D.Weeks,
K.C.Grasty,
L.Hernandez-Cuebas,
P.J.Loll.
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Ref.
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Proteins, 2009,
77,
753-759.
[DOI no: ]
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PubMed id
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Abstract
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The covalent attachment of different types of poly-ubiquitin chains signal
different outcomes for the proteins so targeted. For example, a protein modified
with Lys-48-linked poly-ubiquitin chains is targeted for proteasomal
degradation, whereas Lys-63-linked chains encode nondegradative signals. The
structural features that enable these different types of chains to encode
different signals have not yet been fully elucidated. We report here the X-ray
crystal structures of Lys-63-linked tri- and di-ubiquitin at resolutions of 2.3
and 1.9 A, respectively. The tri- and di-ubiquitin species adopt essentially
identical structures. In both instances, the ubiquitin chain assumes a highly
extended conformation with a left-handed helical twist; the helical chain
contains four ubiquitin monomers per turn and has a repeat length of
approximately 110 A. Interestingly, Lys-48 ubiquitin chains also adopt a
left-handed helical structure with a similar repeat length. However, the Lys-63
architecture is much more open than that of Lys-48 chains and exposes much more
of the ubiquitin surface for potential recognition events. These new crystal
structures are consistent with the results of solution studies of Lys-63 chain
conformation, and reveal the structural basis for differential recognition of
Lys-63 versus Lys-48 chains.
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Figure 1.
Figure 1. (a) Verification of the ubiquitin species contained
within our crystals. Lane 1, purified tri-ubiquitin; Lane 2,
purified di-ubiquitin; Lanes 3 and 4, molecular weight markers
(molecular weights are shown in the space between the two gels);
Lane 5, a different sample of purified di-ubiquitin that was
used for crystallization experiments; Lane 6, washed and
dissolved di-ubiquitin crystals; Lane 7, washed and dissolved
tri-ubiquitin crystals. Crystals were washed repeatedly with
protein-free mother liquor, transferred to sample buffer and run
on a 12-20% SDS-PAGE gradient gel, which was fixed and stained
with Coomassie Brilliant Blue. The formation of SDS-resistant
higher molecular weight species is likely due to residual PEG in
the dissolved crystals. (b) Structure of the di-ubiquitin chain
found in the asymmetric unit of both the di- and tri-ubiquitin
crystals. The distal molecule is colored cyan and the proximal
molecule yellow. The side chains of Lys-63 (on the proximal
molecule) and Arg-63 (on the distal molecule) are shown in
ball-and-stick representation. (c) Positional disorder in the
tri-ubiquitin structure. At top is shown a portion of one of the
extended ubiquitin chains running throughout the crystal; the
distal and proximal ends of the chain are marked. Three adjacent
asymmetric units are shown (A  -B
,
A-B, and A -B
),
separated by dotted lines. Below is a schematic representation
of the packing of the tri-ubiquitin species. The distal-most
subunit of the trimer will alternately occupy the A and B
positions in the asymmetric unit. Figures 1 and 2 were prepared
using MacPyMol (http://www.pymol.org).
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Figure 2.
Figure 2. Stereo views of K63- and K48-linked ubiquitin chains.
Upper panel: The extended K63-linked ubiquitin chain that runs
through the di- and tri-ubiquitin crystals. Shown are surface
representations for six monomers (three adjacent asymmetric
units). Molecules occupying the distal position are colored blue
and molecules in the proximal position are colored yellow. The
proximal end of the chain is at the bottom of the figure, and
the distal end at the top. On each molecule, the hydrophobic
patch comprising residues Leu-8, Ile-44, and Val-70 is colored
red. Lower panel: A tetramer of K48-linked ubiquitin molecules.
Starting from the distal end and moving toward the proximal end
of the chain, the monomers are colored cyan, magenta, blue, and
yellow, respectively. The hydrophobic patch on each monomer is
colored red, as in the upper panel.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2009,
77,
753-759)
copyright 2009.
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