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PDBsum entry 2jnh
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References listed in PDB file
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Key reference
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Title
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Differential ubiquitin binding of the uba domains from human c-Cbl and cbl-B: nmr structural and biochemical insights.
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Authors
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Z.R.Zhou,
H.C.Gao,
C.J.Zhou,
Y.G.Chang,
J.Hong,
A.X.Song,
D.H.Lin,
H.Y.Hu.
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Ref.
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Protein Sci, 2008,
17,
1805-1814.
[DOI no: ]
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PubMed id
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Abstract
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The Cbl proteins, RING-type E3 ubiquitin ligases, are responsible for
ubiquitinating the activated tyrosine kinases and targeting them for
degradation. Both c-Cbl and Cbl-b have a UBA (ubiquitin-associated) domain at
their C-terminal ends, and these two UBA domains share a high sequence
similarity (75%). However, only the UBA from Cbl-b, but not from c-Cbl, can bind
ubiquitin (Ub). To understand the mechanism by which the UBA domains
specifically interact with Ub with different affinities, we determined the
solution NMR structures of these two UBA domains, cUBA from human c-Cbl and UBAb
from Cbl-b. Their structures show that these two UBA domains share the same
fold, a compact three-helix bundle, highly resembling the typical UBA fold.
Chemical shift perturbation experiments reveal that the helix-1 and loop-1 of
UBAb form a predominately hydrophobic surface for Ub binding. By comparing the
Ub-interacting surface on UBAb and its counterpart on cUBA, we find that the
hydrophobic patch on cUBA is interrupted by a negatively charged residue Glu12.
Fluorescence titration data show that the Ala12Glu mutant of UBAb completely
loses the ability to bind Ub, whereas the mutation disrupting the dimerization
has no significant effect on Ub binding. This study provides structural and
biochemical insights into the Ub binding specificities of the Cbl UBA domains,
in which the hydrophobic surface distribution on the first helix plays crucial
roles in their differential affinities for Ub binding. That is, the amino acid
residue diversity in the helix-1 region, but not the dimerization, determines
the abilities of various UBA domains binding with Ub.
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Figure 3.
Both cUBA and UBAb domain structures are stabilized by a
hydrophobic core. (A) Hydrophobic core of cUBA. The side chains
of the residues in the hydrophobic core are displayed in neon
style (orange); these residues include Leu7, Ile11, Leu14,
Ile24, Leu28, Ile35, Ala38, and Leu42. (B) Hydrophobic core of
UBAb. The core residues are Val7, Ile11, Leu14, Val24, Leu28,
Val35, Ala38, and Leu42. (C) Overlay of the secondary structure
elements of cUBA (cyan) and UBAb (red).
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Figure 6.
Comparison of the electrostatic surfaces of cUBA (A) and UBAb
(B). The orientation of both cUBA and UBAb is identical to that
of panels C and D in Figure 4 Figure 4.- .
The positive charges are shown in blue, and the negative charges
are colored in red. The surface presentation shows that the Ub
recognition surface on UBAb is predominately hydrophobic with
positively charged edges while the corresponding surface on cUBA
is something negatively charged in the center. The Ub
recognition surface on UBAb and its counterpart on cUBA are
highlighted by green parallelograms and labeled with amino acid
residues. The dimeric interfaces (indicated by green circles) of
cUBA (C) and UBAb (D) are rotated by [similar]180[deg] relative
to those in A and B, respectively. Residues I30 and I41 that are
involved in homodimerization are labeled. The PDB codes for the
structures are 2JUJ for cUBA and 2JNH for UBAb. (E) Glutamic
acid; (A) alanine; (I) isoleucine.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(2008,
17,
1805-1814)
copyright 2008.
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