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PDBsum entry 3ebb
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References listed in PDB file
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Key reference
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Title
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Structure and function of the plaa/ufd3-P97/cdc48 complex.
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Authors
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L.Qiu,
N.Pashkova,
J.R.Walker,
S.Winistorfer,
A.Allali-Hassani,
M.Akutsu,
R.Piper,
S.Dhe-Paganon.
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Ref.
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J Biol Chem, 2010,
285,
365-372.
[DOI no: ]
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PubMed id
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Abstract
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PLAA (ortholog of yeast Doa1/Ufd3, also know as human PLAP or phospholipase
A2-activating protein) has been implicated in a variety of disparate biological
processes that involve the ubiquitin system. It is linked to the maintenance of
ubiquitin levels, but the mechanism by which it accomplishes this is unclear.
The C-terminal PUL (PLAP, Ufd3p, and Lub1p) domain of PLAA binds p97, an AAA
ATPase, which among other functions helps transfer ubiquitinated proteins to the
proteasome for degradation. In yeast, loss of Doa1 is suppressed by altering
p97/Cdc48 function indicating that physical interaction between PLAA and p97 is
functionally important. Although the overall regions of interaction between
these proteins are known, the structural basis has been unavailable. We solved
the high resolution crystal structure of the p97-PLAA complex showing that the
PUL domain forms a 6-mer Armadillo-containing domain. Its N-terminal extension
folds back onto the inner curvature forming a deep ridge that is positively
charged with residues that are phylogenetically conserved. The C terminus of p97
binds in this ridge, where the side chain of p97-Tyr(805), implicated in
phosphorylation-dependent regulation, is buried. Expressed in doa1Delta null
cells, point mutants of the yeast ortholog Doa1 that disrupt this interaction
display slightly reduced ubiquitin levels, but unlike doa1Delta null cells,
showed only some of the growth phenotypes. These data suggest that the p97-PLAA
interaction is important for a subset of PLAA-dependent biological processes and
provides a framework to better understand the role of these complex molecules in
the ubiquitin system.
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Figure 1.
Structure of the PUL domain. A, domain map of PLAA that
defines N-terminal WD40 β-propeller (yellow), central PFU
domain (blue), and C-terminal PUL domain (gray). Secondary
structure elements are shown colored according to their ARM. B,
overall structure of PUL domain containing six Armadillo repeats
individually colored and labeled. All figures were generated
with PyMol. C, stereoscopic view of the N-terminal extension in
yellow stick format bound across the concave surface of the
Armadillo fold, shown as light blue cylinders. The third helices
of each Armadillo unit is labeled.
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Figure 2.
Co-structure of the PUL domain with the C-terminal p97
peptide. A, electrostatic surface representation was generated
with a gradient from −10 (red) to 10 (blue) kT/e of the PUL
domain only. The bound p97 peptide is show in green stick
format. B, surface representation of the PUL domain is shown in
light gray with conserved residues in purple. C, stereoscopic
view of the terminal p97 peptide residues LYG^806 bound to the
PUL domain shown with helices in schematic format and labeled.
PUL residues within proximity are shown in stick format and
labeled. The hydrogen bond is shown as a black dashed line;
water molecules are shown as red cross-hairs. D, schematic
representation of p97 (black) interactions with PLAA (blue). E,
three-dimensional alignment of the PLAA (green) and PNGase
(cyan)-bound p97 peptides.
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The above figures are
reprinted
from an Open Access publication published by the ASBMB:
J Biol Chem
(2010,
285,
365-372)
copyright 2010.
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