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PDBsum entry 1a5r
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Targeting protein
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PDB id
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1a5r
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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 determination of the small ubiquitin-Related modifier sumo-1.
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Authors
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P.Bayer,
A.Arndt,
S.Metzger,
R.Mahajan,
F.Melchior,
R.Jaenicke,
J.Becker.
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Ref.
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J Mol Biol, 1998,
280,
275-286.
[DOI no: ]
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PubMed id
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Abstract
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The recently discovered small ubiquitin-related modifier SUMO-1 belongs to the
growing family of ubiquitin-related proteins involved in postranslational
protein modification. Unlike ubiquitin, SUMO-1 does not appear to target
proteins for degradation but seems to be involved in the modulation of
protein-protein interactions. Independent studies demonstrate an essential
function of SUMO-1 in the regulation of nucleo-cytoplasmic transport, and
suggest a role in cell-cycle regulation and apoptosis. Here, we present the
first three-dimensional structure of SUMO-1 solved by NMR. Although having only
18% amino acid sequence identity with ubiquitin, the overall structure closely
resembles that of ubiquitin, featuring the betabetaalphabetabetaalphabeta fold
of the ubiquitin protein family. In addition, the position of the two C-terminal
Gly residues required for isopeptide bond formation is conserved between
ubiquitin and SUMO-1. The most prominent feature of SUMO-1 is a long and highly
flexible N terminus, which protrudes from the core of the protein and which is
absent in ubiquitin. Furthermore, ubiquitin Lys48, required to generate
ubiquitin polymers, is substituted in SUMO-1 by Gln69 at the same position,
which provides an explanation of why SUMO-1 has not been observed to form
polymers. Moreover, the hydrophobic core of SUMO-1 and ubiquitin is maintained
by conserved hydrophobic residues, whereas the overall charge topology of SUMO-1
and ubiquitin differs significantly, suggesting specific modifying enzymes and
target proteins for both proteins.
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Figure 6.
Figure 6. Stereo view of a superposition of the structures
of SUMO-1 (black) and ubiquitin (red) using the Program O [Jones
et al 1991]. The overlay of the C^α backbone shows the
similarity between the two protein cores of SUMO-1 and
ubiquitin, although these proteins share only 18% sequence
identity. Also marked are side-chains of Gln69 of SUMO-1 and
Lys48 of ubiquitin, which is important for the formation of
polyubiquitin and which are located at the same position. The
indicated C-terminal di-glycine motif is localized in a very
flexible region, functionally conserved and located in similar
positions relative to the overall protein fold.
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Figure 7.
Figure 7. Comparison of the surfaces of SUMO-1 (a and b)
and ubiquitin (c and d). Shown are two opposite surface views of
SUMO-1 and ubiquitin rotated around the longitudinal axis by
160° and by ±80° as compared to the front view
shown in Figure 5 and Figure 6. The corresponding orientations
are indicated by the C^α backbone visible underneath the
surface. The charge topology was calculated and coloured
according to the electrostatic potential over a range of
approximately −20 kT/e (in red) to +20 kT/e (in blue) using
the program GRASP [Nicholls et al 1991]. The first view of
SUMO-1 (a) displays positive charged epitopes (Arg54, Lys46,
Lys25, Lys23, Lys17 and Lys16) absent on the corresponding
surface of ubiquitin (c) with the exception of SUMO-1 Lys25 (a),
and ubiquitin Lys6 (c). The second view of SUMO-1 (b) reveals a
large negatively charged surface (Glu89, Asp86, Glu85 and Glu84)
together with a negatively charged pocket (Glu83, Glu18, Glu15,
Asp12, Glu11 and Glu20), which are not conserved on the
corresponding surface of ubiquitin (d).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
280,
275-286)
copyright 1998.
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Secondary reference #1
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Title
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A small ubiquitin-Related polypeptide involved in targeting rangap1 to nuclear pore complex protein ranbp2.
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Authors
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R.Mahajan,
C.Delphin,
T.Guan,
L.Gerace,
F.Melchior.
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Ref.
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Cell, 1997,
88,
97.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. A Novel Ubiquitin-Related Protein (SUMO-1)
Contains Peptide Sequence Present in the 90-kDa RanGAP1(A) cDNA
sequence and deduced amino acid sequence of SUMO-1. The ORF
codes for a protein of 101 amino acids with a predicted
molecular mass of 11.5 kDa. The three unique peptides detected
in the 90-kDa RanGAP protein are present in the ORF (underlined;
see also Table 1).(B) Northern blot analysis of RanGAP1 and
SUMO-1 mRNAs. Hela total RNA (20 μg) was separated on a
formaldehyde gel, transferred onto nitrocellulose, and probed
with ^32P-labeled DNA fragments of RanGAP1 or SUMO-1.(C) SUMO-1
is a member of a ubiquitin-related protein family. The BLAST
search algorithm was used to identify proteins homologous to
SUMO-1. The following proteins were aligned: the deduced
protein sequence of a partially sequenced rat EST cDNA clone
that is virtually identical to human SUMO-1 (Rat SUMO-1,
EST108203); human and S. cerevisiae SMT3; ubiquitins from human,
Dictyostelium discoideum, S. cerevisiae, and Arabidopsis
thaliana; and Nedd-8 from mouse. Dark shading, residues in rat
SUMO-1 and the SMT3 proteins that are identical to corresponding
positions of human SUMO-1. Light shading, residues in ubiquitins
and Nedd-8 that are identical to human ubiquitin. Box, residues
identical among human and rat SUMO-1 and ubiquitins. Asterisks,
residues identical in all proteins compared. Consensus sequence
below is defined by residues that are either identical or highly
homologous among members of the SUMO-1, SMT3, and ubiquitin
families.
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Figure 5.
Figure 5. RanGAP1 Is Localized at the Cytoplasmic Surface
of the NPC(A) Detection of RanGAP1 in NRK cells by
immunofluorescence microscopy. Cells were double stained with
αRanGAP1 (left) and RL1 (right) and analyzed by light
microscopy.(B) Detection of RanGAP1 by confocal
immunofluorescence microscopy of NRK cells. Cells were double
stained with αRanGAP1 (top panels) and RL1 (bottom panels).
Single sections through the equatorial plane (left) or nuclear
surface plane (right) are shown.(C) Immunogold localization of
RanGAP1 in isolated rat liver NEs. Shown are thin section
electron micrographs of isolated rat liver NEs displaying NPCs
either in cross sections (A–E) or in tangential sections
(F–H). Note that gold particles are found exclusively at the
cytoplasmic side of NPCs (arrowheads). Cytoplasmic (C) and
nuclear (N) faces of the NEs are easily distinguished by the
presence of residual chromatin (ch) on the nucleoplasmic
side.Scale bar, 100 nm.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Preferential modification of nuclear proteins by a novel ubiquitin-Like molecule.
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Authors
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T.Kamitani,
H.P.Nguyen,
E.T.Yeh.
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Ref.
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J Biol Chem, 1997,
272,
14001-14004.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Alignment of amino acid sequences of sentrin and
ubiquitin. Identical amino acids were printed in bold type.
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Figure 2.
Fig. 2. Western blot analysis of sentrin expression in human
cell lines. Total cell lysates were analyzed by Western blotting
using antiserum against the N-terminal 21 amino acids of sentrin
preabsorbed with either MBP or MBP-sentrin.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #3
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Title
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A novel ubiquitin-Like modification modulates the partitioning of the ran-Gtpase-Activating protein rangap1 between the cytosol and the nuclear pore complex.
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Authors
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M.J.Matunis,
E.Coutavas,
G.Blobel.
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Ref.
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J Cell Biol, 1996,
135,
1457-1470.
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PubMed id
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