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PDBsum entry 1p98
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* Residue conservation analysis
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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 determinants for the binding of ubiquitin-Like domains to the proteasome.
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Authors
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T.D.Mueller,
J.Feigon.
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Ref.
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Embo J, 2003,
22,
4634-4645.
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PubMed id
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Abstract
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HHR23A, a protein implicated in nucleotide excision repair, belongs to a class
of proteins containing both a ubiquitin-like (Ubl) domain and one or more
ubiquitin-associated (UBA) domains, suggesting a role in the
ubiquitin-proteasome pathway as well. The Ubl domain binds with high affinity to
the second ubiquitin-interacting motif (UIM) of the S5a subunit of the
proteasome. Here we present the solution structures of the HHR23A Ubl domain,
the second UIM of S5a (UIM-2), and the Ubl:S5a-UIM-2 complex. The HHR23A Ubl
domain is structurally similar to ubiquitin. The S5a UIM forms an alpha-helix
with an unexpected hairpin loop that contributes to the binding interface with
Ubl. The molecular determinants of the Ubl-proteasome interaction are revealed
by analysis of the structures, chemical shift mapping, mutant binding studies
and sequence conservation.
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Secondary reference #1
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Title
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Solution structures of uba domains reveal a conserved hydrophobic surface for protein-Protein interactions.
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Authors
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T.D.Mueller,
J.Feigon.
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Ref.
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J Mol Biol, 2002,
319,
1243-1255.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. Stereoviews of the internal UBA domain UBA(1) of
HHR23A (SWISS PROT code R23A_HUMAN) (human homologue of RAD23A)
showing residues Thr156 to Gly204. (a) Ribbon representation.
The three helices are labeled a1, a2, and a3. (b) Superposition
of the ten lowest-energy structures. The backbone atoms are
shown in black for carbon atoms, blue for nitrogen atoms, and
the carbonyl oxygen atoms are omitted. The side-chains for
residues forming the hydrophobic core are shown in green. The
N-terminal residues 155-160 are disordered and are not shown.
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Figure 4.
Figure 4. A potential protein-protein binding interface of
UBA domains is built from hydrophobic residues on the surface.
(a) Surface representation of UBA(1) (left) using the following
color coding: red, acidic amino acid residues Glu and Asp; blue,
basic amino acid residues Arg and Lys, orange, polar amino acid
residues Asn, Gln, His, Ser and Thr; white, hydrophobic residues
Ala, Gly, Phe, Ile, Pro, Met, Leu, Tyr and Val. The major
accessible residues on the hydrophobic surface, Met173, Gly174,
Y175, L199 and I202, are marked. The size of the epitope is
approximately 470 Å2. The right picture shows the
orientation of the helical bundle with respect to the surface
representation. The hydrophobic surface patch consists mainly of
residues from loop 1 between helices 1 and 2 as well as residues
from helix 3. (b) For comparison, the surface of UBA(2) is shown
in the same orientation as UBA(1), revealing that the location
of the hydrophobic epitope is indeed conserved and consists of
identical or homologous residues. The C terminus of UBA(2) is
not shown, due to its flexibility.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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