{PDOC51214}
{PS51214; IBB}
{BEGIN}
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* IBB domain profile *
**********************

Cytosolic proteins  bearing a classical nuclear localization signal (NLS) (see
<PDOC00015>) enter  the  nucleus  bound to a heterodimer of importin-alpha and
importin-beta (also   called   karyopherin-alpha  and  -beta).  Importin-alpha
contains the NLS-binding site and importin-beta is responsible for the docking
of the importin-substrate complex to the filaments of the nuclear pore complex
(NPC) and  its  translocation through the pore. Importin-alpha consists of two
functional domains,  a highly basic amino-terminal region of roughly 40 amino-
acid residues  (the  IBB domain) responsible for importin-beta binding, and an
NLS-binding domain  built of armadillo (ARM) repeats (see <PDOC50176>). Appart
from the  classical  protein-import pathway, importin-beta is also involved in
the nuclear  import  of spliceosomal small nuclear ribonucleoprotein particles
(snRNPs), which  is  mediated by the 45K protein snurportin-1. Snurportin-1 is
functionally analogous    to    importin-alpha,    as    it   recognizes   the
trimethylguanosine (m3G)  cap  structure  of the small nuclear RNAs U1, U2, U4
and U5,  and  binds  to  importin-beta  through  an  IBB-domain.  Snurportin-1
contains an N-terminal IBB domain and a C-terminal m3G-cap-binding region with
no structural similarity to the arm repeat domain of importin-alpha [1-3].

The IBB domain is an L-shapped molecule with an N-terminal extended moiety and
a C-terminal   helix   running   in  mutually  perpendicular  directions  (see
<PDB:1QGK>). The  IBB  domain  is  intimately  bound  on  the inner surface of
importin-beta that  contains many acidic residues and is thus complementary to
the highly positively charged IBB domain [1,2].

The profile we developed covers the entire IBB domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: June 2006 / First entry.

[ 1] Kobe B.
     "Autoinhibition by an internal nuclear localization signal revealed by
     the crystal structure of mammalian importin alpha."
     Nat. Struct. Biol. 6:388-397(1999).
     PubMed=10201409; DOI=10.1038/7625
[ 2] Cingolani G., Petosa C., Weis K., Mueller C.W.
     "Structure of importin-beta bound to the IBB domain of
     importin-alpha."
     Nature 399:221-229(1999).
     PubMed=10353244; DOI=10.1038/20367
[ 3] Huber J., Cronshagen U., Kadokura M., Marshallsay C., Wada T.,
     Sekine M., Luehrmann R.
     "Snurportin1, an m3G-cap-specific nuclear import receptor with a novel
     domain structure."
     EMBO J. 17:4114-4126(1998).
     PubMed=9670026; DOI=10.1093/emboj/17.14.4114

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{END}