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PDBsum entry 1umh
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Contents |
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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 basis of sugar-Recognizing ubiquitin ligase.
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Authors
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T.Mizushima,
T.Hirao,
Y.Yoshida,
S.J.Lee,
T.Chiba,
K.Iwai,
Y.Yamaguchi,
K.Kato,
T.Tsukihara,
K.Tanaka.
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Ref.
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Nat Struct Mol Biol, 2004,
11,
365-370.
[DOI no: ]
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PubMed id
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Abstract
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SCF(Fbs1) is a ubiquitin ligase that functions in the endoplasmic reticulum
(ER)-associated degradation pathway. Fbs1/Fbx2, a member of the F-box proteins,
recognizes high-mannose oligosaccharides. Efficient binding to an N-glycan
requires di-N-acetylchitobiose (chitobiose). Here we report the crystal
structures of the sugar-binding domain (SBD) of Fbs1 alone and in complex with
chitobiose. The SBD is composed of a ten-stranded antiparallel beta-sandwich.
The structure of the SBD-chitobiose complex includes hydrogen bonds between Fbs1
and chitobiose and insertion of the methyl group of chitobiose into a small
hydrophobic pocket of Fbs1. Moreover, NMR spectroscopy has demonstrated that the
amino acid residues adjoining the chitobiose-binding site interact with the
outer branches of the carbohydrate moiety. Considering that the innermost
chitobiose moieties in N-glycans are usually involved in intramolecular
interactions with the polypeptide moieties, we propose that Fbs1 interacts with
the chitobiose in unfolded N-glycoprotein, pointing the protein moiety toward E2
for ubiquitination.
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Figure 1.
Figure 1. Tertiary structure of SBD in Fbs1. (a) Overall
structure of SBD of Fbs1 shown as a ribbon diagram.  -strands
belonging to S1 and S2 are blue and red, respectively. Loops and
helices are black and yellow, respectively. (b) A topology
diagram of SBD. The  -helices
are yellow cylinders labeled 1
and 2.
The -strands
are arrows labeled 1
- 10.
The left and right forms of -strands
correspond to S1 and S2, respectively, as in a. N and C, N and C
termini, respectively. (c) Amino acid sequences of SBD in Fbs1
and corresponding region of Fbs2. Amino acid residues are
numbered in the N-to-C direction, for example, from position 117
to position 297 (C-terminal end) of Fbs1, and from 69 to 295
(C-terminal end) of Fbs2. Identical residues are boxed.
Secondary structure elements are colored as a. Substrate-binding
residues are red characters.
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Figure 2.
Figure 2. Structure of SBD in complex with chitobiose. (a)
Stereo view of the difference-density map (F[o] - F[c] with
phase from the Fbs1 model) of binding chitobiose, contoured at
2.1  ,
modeled into the electron density. -strands
belonging to S1 and S2 are blue and red, respectively. Loops are
black. The bound chitobiose is orange, and the residues involved
in the substrate binding (FYWK, see Fig. 1c) are green. (b)
Molecular surface representation of the chitobiose-binding
region. The bound chitobiose is shown in ball-and-stick
representation. Two GlcNAc residues are represented by A and B.
Cyan spheres are two water molecules of wild type SBD that are
fixed on the molecular surface through hydrogen bonds with the
backbone N and O of Lys281, respectively. These water molecules
are replaced by O3 and O6 of the chitobiose upon formation of
the SBD -chitobiose complex. (c) Stick representation of the
amino acids involved in binding. Hydrogen bonds are dashed
lines. Oxygen and nitrogen are red and blue, respectively.
Symbols of two water molecules are as in b.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2004,
11,
365-370)
copyright 2004.
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