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* Residue conservation analysis
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Enzyme class:
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Chains A, B:
E.C.?
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DOI no:
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Structure
8:329-338
(2000)
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PubMed id:
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Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha.
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E.Conti,
J.Kuriyan.
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ABSTRACT
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BACKGROUND: Karyopherin alpha (importin alpha) is an adaptor molecule that
recognizes proteins containing nuclear localization signals (NLSs). The
prototypical NLS that is able to bind to karyopherin alpha is that of the SV40 T
antigen, and consists of a short positively charged sequence motif. Distinct
classes of NLSs (monopartite and bipartite) have been identified that are only
partly conserved with respect to one another but are nevertheless recognized by
the same receptor. RESULTS: We report the crystal structures of two peptide
complexes of yeast karyopherin alpha (Kapalpha): one with a human c-myc NLS
peptide, determined at 2.1 A resolution, and one with a Xenopus nucleoplasmin
NLS peptide, determined at 2.4 A resolution. Analysis of these structures
reveals the determinants of specificity for the binding of a relatively
hydrophobic monopartite NLS and of a bipartite NLS peptide. The peptides bind
Kapalpha in its extended surface groove, which presents a modular array of
tandem binding pockets for amino acid residues. CONCLUSIONS: Monopartite and
bipartite NLSs bind to a different number of amino acid binding pockets and make
different interactions within them. The relatively hydrophobic monopartite c-myc
NLS binds extensively at a few binding pockets in a similar manner to that of
the SV40 T antigen NLS. In contrast, the bipartite nucleoplasmin NLS engages the
whole array of pockets with individually more limited but overall more abundant
interactions, which include the NLS two basic clusters and the backbone of its
non-conserved linker region. Versatility in the specific recognition of NLSs
relies on the modular.
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Selected figure(s)
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Figure 2.
Figure 2. Interactions of distinct NLSs with Kapa. The NLS
peptides (shown in colour) nestle between the conserved Trp-Asn
pairs of residues that line the surface of Kapa. Each pair is
provided by a single ARM repeat, shaping the regularly spaced P
and P' specificity pockets at the large and small binding sites,
respectively. The polar and electrostatic interactions between
conserved protein and NLS residues are indicated with dotted
lines. (a) Schematic diagram of the interactions between the
human c-myc NLS peptide (highlighted in blue) and yeast Kapa.
The monopartite NLS binds at the large (functional) and small
sites with mainchain and sidechain interactions. (b) Schematic
diagram of the interactions between the Xenopus nucleoplasmin
NLS peptide (highlighted in pink) and protein residues. The
bipartite NLS binds along the whole surface groove with
mainchain and sidechain interactions at the small site, and with
mainly backbone interactions of the linker and the downstream
cluster.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2000,
8,
329-338)
copyright 2000.
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Figure was
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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Structure,
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PDB code:
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PDB code:
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Kap104p imports the PY-NLS-containing transcription factor Tfg2p into the nucleus.
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J Biol Chem,
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PDB code:
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Nat Struct Mol Biol,
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PDB codes:
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Y.An,
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PDB codes:
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B.Ding,
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Structure of an O-GlcNAc transferase homolog provides insight into intracellular glycosylation.
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Nat Struct Mol Biol,
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PDB code:
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Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain.
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Hum Mol Genet,
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PDB code:
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The C-terminal region of Ge-1 presents conserved structural features required for P-body localization.
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RNA,
14,
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PDB code:
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Q.Li,
N.Zhang,
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Classical nuclear localization signals: definition, function, and interaction with importin alpha.
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282,
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and
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(2007).
Structure and nuclear import function of the C-terminal domain of influenza virus polymerase PB2 subunit.
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Nat Struct Mol Biol,
14,
229-233.
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PDB codes:
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M.Stewart
(2007).
Molecular mechanism of the nuclear protein import cycle.
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Nat Rev Mol Cell Biol,
8,
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L.Vinther,
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K.Kooi,
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Nuclear localization of human DNA mismatch repair protein exonuclease 1 (hEXO1).
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Nucleic Acids Res,
35,
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W.Gillon,
and
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(2007).
Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties.
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Protein Sci,
16,
176-188.
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PDB code:
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R.J.Bick,
B.J.Poindexter,
L.M.Buja,
C.H.Lawyer,
S.M.Milner,
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Nuclear Localization of HBD-1 in Human Keratinocytes.
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J Burns Wounds,
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W.Albig,
D.Doenecke,
and
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(2007).
Sequence elements in both subunits of the DNA fragmentation factor are essential for its nuclear transport.
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J Biol Chem,
282,
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A novel conserved nuclear localization signal is recognized by a group of yeast importins.
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Alternative splicing controls nuclear translocation of the cell cycle-regulated Nek2 kinase.
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282,
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N.Jura,
P.A.Cole,
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(2007).
Inhibition of the EGF receptor by binding of MIG6 to an activating kinase domain interface.
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Nature,
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PDB codes:
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A.S.Madrid,
and
K.Weis
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Nuclear transport is becoming crystal clear.
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Chromosoma,
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T.Sommer,
E.Hartmann,
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(2006).
Nuclear localization signal and protein context both mediate importin alpha specificity of nuclear import substrates.
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Mol Cell Biol,
26,
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J.S.Hontz,
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Differences in crystal and solution structures of the cytolethal distending toxin B subunit: Relevance to nuclear translocation and functional activation.
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J Biol Chem,
281,
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PDB code:
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K.Tschöp,
G.A.Müller,
J.Grosche,
and
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(2006).
Human cyclin B3. mRNA expression during the cell cycle and identification of three novel nonclassical nuclear localization signals.
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FEBS J,
273,
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Nuclear import of Epstein-Barr virus nuclear antigen 1 mediated by NPI-1 (Importin alpha5) is up- and down-regulated by phosphorylation of the nuclear localization signal for which Lys379 and Arg380 are essential.
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J Virol,
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The monopartite nuclear localization signal of autoimmune regulator mediates its nuclear import and interaction with multiple importin alpha molecules.
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Traffic,
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N.Walker-Kopp,
P.J.Sims,
and
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(2005).
Phospholipid scramblase 1 contains a nonclassical nuclear localization signal with unique binding site in importin alpha.
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| |
J Biol Chem,
280,
10599-10606.
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PDB code:
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M.Umeda,
S.Izaddoost,
I.Cushman,
M.S.Moore,
and
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(2005).
The fission yeast Schizosaccharomyces pombe has two importin-alpha proteins, Imp1p and Cut15p, which have common and unique functions in nucleocytoplasmic transport and cell cycle progression.
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Genetics,
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M.Vujanac,
A.Fenaroli,
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(2005).
Constitutive nuclear import and stress-regulated nucleocytoplasmic shuttling of mammalian heat-shock factor 1.
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| |
Traffic,
6,
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D.S.Goldfarb,
A.H.Corbett,
D.A.Mason,
M.T.Harreman,
and
S.A.Adam
(2004).
Importin alpha: a multipurpose nuclear-transport receptor.
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| |
Trends Cell Biol,
14,
505-514.
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E.S.Shih,
and
M.J.Hwang
(2004).
Alternative alignments from comparison of protein structures.
|
| |
Proteins,
56,
519-527.
|
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K.Ray,
C.S.Hines,
J.Coll-Rodriguez,
and
D.W.Rodgers
(2004).
Crystal structure of human thimet oligopeptidase provides insight into substrate recognition, regulation, and localization.
|
| |
J Biol Chem,
279,
20480-20489.
|
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PDB code:
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L.L.Videau,
W.B.Arendall,
and
J.S.Richardson
(2004).
The cis-Pro touch-turn: a rare motif preferred at functional sites.
|
| |
Proteins,
56,
298-309.
|
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M.Jínek,
J.Rehwinkel,
B.D.Lazarus,
E.Izaurralde,
J.A.Hanover,
and
E.Conti
(2004).
The superhelical TPR-repeat domain of O-linked GlcNAc transferase exhibits structural similarities to importin alpha.
|
| |
Nat Struct Mol Biol,
11,
1001-1007.
|
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PDB code:
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M.Luo,
C.W.Pang,
A.E.Gerken,
and
T.G.Brock
(2004).
Multiple nuclear localization sequences allow modulation of 5-lipoxygenase nuclear import.
|
| |
Traffic,
5,
847-854.
|
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M.T.Harreman,
T.M.Kline,
H.G.Milford,
M.B.Harben,
A.E.Hodel,
and
A.H.Corbett
(2004).
Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals.
|
| |
J Biol Chem,
279,
20613-20621.
|
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Importin-alpha mediates the regulated nuclear targeting of serum- and glucocorticoid-inducible protein kinase (Sgk) by recognition of a nuclear localization signal in the kinase central domain.
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Synergy of silent and hot spot mutations in importin beta reveals a dynamic mechanism for recognition of a nuclear localization signal.
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EMBO J,
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PDB code:
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K.Melen,
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Importin alpha nuclear localization signal binding sites for STAT1, STAT2, and influenza A virus nucleoprotein.
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CRM1/Ran-mediated nuclear export of p27(Kip1) involves a nuclear export signal and links p27 export and proteolysis.
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Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha.
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PDB codes:
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PDB code:
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Structural and functional criteria reveal a new nuclear import sequence on the 5-lipoxygenase protein.
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PDB code:
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PDB codes:
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Where a reference describes a PDB structure, the PDB
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