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PDBsum entry 3c0r
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Cell cycle, hydrolase
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PDB id
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3c0r
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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 basis for ubiquitin recognition by the otu1 ovarian tumor domain protein.
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Authors
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T.E.Messick,
N.S.Russell,
A.J.Iwata,
K.L.Sarachan,
R.Shiekhattar,
J.R.Shanks,
F.E.Reyes-Turcu,
K.D.Wilkinson,
R.Marmorstein.
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Ref.
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J Biol Chem, 2008,
283,
11038-11049.
[DOI no: ]
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PubMed id
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Abstract
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Ubiquitination of proteins modifies protein function by either altering their
activities, promoting their degradation, or altering their subcellular
localization. Deubiquitinating enzymes are proteases that reverse this
ubiquitination. Previous studies demonstrate that proteins that contain an
ovarian tumor (OTU) domain possess deubiquitinating activity. This domain of
approximately 130 amino acids is weakly similar to the papain family of
proteases and is highly conserved from yeast to mammals. Here we report
structural and functional studies on the OTU domain-containing protein from
yeast, Otu1. We show that Otu1 binds polyubiquitin chain analogs more tightly
than monoubiquitin and preferentially hydrolyzes longer polyubiquitin chains
with Lys(48) linkages, having little or no activity on Lys(63)- and
Lys(29)-linked chains. We also show that Otu1 interacts with Cdc48, a regulator
of the ER-associated degradation pathway. We also report the x-ray crystal
structure of the OTU domain of Otu1 covalently complexed with ubiquitin and
carry out structure-guided mutagenesis revealing a novel mode of ubiquitin
recognition and a variation on the papain protease catalytic site configuration
that appears to be conserved within the OTU family of ubiquitin hydrolases.
Together, these studies provide new insights into ubiquitin binding and
hydrolysis by yeast Otu1 and other OTU domain-containing proteins.
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Figure 4.
FIGURE 4. The Otu1-ubiquitin interface. A, three regions of
interaction between Otu1 and ubiquitin. The figure is rendered
in a surface representation and shown in "open book" format
highlighting contact regions 1 (blue), 2 (green), and 3 (red).
B, close-up of Otu1-ubiquitin interactions in region 1. Side
chains that mediate hydrogen bonds (dotted line) and van der
Waals interactions are shown. C, close-up of Otu1-ubiquitin
interactions in region 2. Water molecules are indicated as white
spheres. D, close-up of Otu1-ubiquitin interactions in region 3.
E, superimposed active sites of deubiquitinating enzymes. The
catalytic triad cysteine, histidine, and aspartate as well as
ubiquitin (magenta) are shown as a stick models. Otu1 is shown
as cyan, UCH-L3 (Protein Data Bank code 1xd3) is shown in
violet, and HAUSP/USP7 (Protein Data Bank code 1nbf) is shown in
green.
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Figure 6.
FIGURE 6. Comparison of the Otu1-ubiquitin complex with
otubain 2. A, superposition of the Otu1-ubiquitin complex (cyan
and magenta, respectively) with nascent otubain 2 (yellow). B,
close-up view of the β4-loop region of Otu1 (cyan) with bound
ubiquitin (magenta) with the corresponding region of nascent
otubain 2 (yellow).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2008,
283,
11038-11049)
copyright 2008.
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