{PDOC50800}
{PS50800; SAP}
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* SAP motif profile *
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The SAP  motif  is  a  35-residue  motif,  which has been named after SAF-A/B,
Acinus and PIAS, three proteins known to contain it. The SAP motif is found in
a variety  of  nuclear  proteins  involved  in  transcription, DNA repair, RNA
processing or  apoptotic  chromatin degradation. As the sap motif of SAF-A has
been shown  to  be  essential  for  specific DNA binding activity, it has been
proposed that it could be a DNA-binding motif [1,2].

A multiple  alignment  of  the  SAP  motif reveals a bipartite distribution of
strongly conserved  hydrophobic,  polar  and  bulky amino acids separated by a
region that  contains  a glycine. Secondary structure predictions suggest that
the SAP motif could form two alpha helices separated by a turn [1].

Some proteins known to contain a SAP motif are listed below:

 - Vertebrate  scaffold  attachment  factors  A  and  B  (SAF-A/B).  These two
   proteins are heterogeneous nuclear ribonucleoproteins (hnRNPs) that bind to
   AT-rich chromosomal  region.  It  has  been  proposed  that they couple RNA
   metabolism to nuclear organization [2,3,4]. The SAF-A protein is cleaved by
   caspase-3 during apoptosis [2,5].
 - Mammalian  Acinus, a protein which induces apoptotic chromatin condensation
   after cleavage  by  caspase-3  [6].  Acinus also contains a RNA-recognition
   motif.
 - Eukaryotic  proteins  of  the  PIAS  (protein  inhibitor of activated STAT)
   family. These proteins interact with phosphorylated STAT dimers and inhibit
   STAT mediated gene activation. Deletion of the first 50 amino acid residues
   containing the  SAP  domain  allows  the  interaction  of  PIAS1 with STAT1
   monomer [7].
 - Plant  poly(ADP-ribose)  polymerase  (PARP). PARP is a nuclear protein that
   catalyzes the   poly(ADP-ribosyl)ation  of  proteins.  It  is  involved  in
   responses to  mild  and  severe oxidative stresses, by mediating DNA repair
   and programmed  cell  death  processes,  respectively  [8]. PARP is tightly
   bound to chromatin or nuclear matrix.
 - Arabidopsis thaliana Arp, an apurinic endonuclease-redox protein.
 - Yeast   THO1   protein.   It   could  be  involved  in  the  regulation  of
   transcriptional elongation by RNA polymerase II [9].
 - Animal  Ku70.  Together with Ku86, it forms a DNA ends binding complex that
   is involved in repairing DNA double-strand breaks.
 - Yeast RAD18, a protein involved in DNA repair.
 - Neurospora crassa UVS-2, the homolog of RAD18.

The profile we developed cover the entire SAP motif.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: February 2003 / First entry.

[ 1] Aravind L., Koonin E.V.
     "SAP - a putative DNA-binding motif involved in chromosomal
     organization."
     Trends Biochem. Sci. 25:112-114(2000).
     PubMed=10694879
[ 2] Goehring F., Schwab B.L., Nicotera P., Leist M., Fackelmayer F.O.
     EMBO J. 16:7361-7371(1997).
[ 3] Weighardt F., Cobianchi F., Cartegni L., Chiodi I., Villa A., Riva S.,
     Biamonti G.
     "A novel hnRNP protein (HAP/SAF-B) enters a subset of hnRNP complexes
     and relocates in nuclear granules in response to heat shock."
     J. Cell Sci. 112:1465-1476(1999).
     PubMed=10212141
[ 4] Nayler O., Stratling W., Bourquin J.P., Stagljar I., Lindemann L.,
     Jasper H., Hartmann A.M., Fackelmayer F.O., Ullrich A., Stamm S.
     "SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR
     elements."
     Nucleic Acids Res. 26:3542-3549(1998).
     PubMed=9671816
[ 5] Kipp M., Schwab B.L., Przybylski M., Nicotera P., Fackelmayer F.O.
     "Apoptotic cleavage of scaffold attachment factor A (SAF-A) by
     caspase-3 occurs at a noncanonical cleavage site."
     J. Biol. Chem. 275:5031-5036(2000).
     PubMed=10671544
[ 6] Sahara S., Aoto M., Eguchi Y., Imamoto N., Yoneda Y., Tsujimoto Y.
     "Acinus is a caspase-3-activated protein required for apoptotic
     chromatin condensation."
     Nature 401:168-173(1999).
     PubMed=10490026; DOI=10.1038/43678
[ 7] Liao J., Fu Y., Shuai K.
     "Distinct roles of the NH2- and COOH-terminal domains of the protein
     inhibitor of activated signal transducer and activator of
     transcription (STAT) 1 (PIAS1) in cytokine-induced PIAS1-Stat1
     interaction."
     Proc. Natl. Acad. Sci. U.S.A. 97:5267-5272(2000).
     PubMed=10805787; DOI=97/10/5267
[ 8] Amor Y., Babiychuk E., Inze D., Levine A.
     "The involvement of poly(ADP-ribose) polymerase in the oxidative
     stress responses in plants."
     FEBS Lett. 440:1-7(1998).
     PubMed=9862413
[ 9] Piruat J.I., Aguilera A.
     "A novel yeast gene, THO2, is involved in RNA pol II transcription and
     provides new evidence for transcriptional elongation-associated
     recombination."
     EMBO J. 17:4859-4872(1998).
     PubMed=9707445; DOI=10.1093/emboj/17.16.4859

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