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18  structures 1533  species 0  interactions 11761  sequences 477  architectures

Family: SAP (PF02037)

Summary: SAP domain

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SAP domain Provide feedback

The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.

Literature references

  1. Aravind L, Koonin EV; , Trends Biochem Sci 2000;25:112-114.: SAP - a putative DNA-binding motif involved in chromosomal organization. PUBMED:10694879 EPMC:10694879

  2. Iida T, Kawaguchi R, Nakayama J; , Curr Biol. 2006;16:1459-1464.: Conserved ribonuclease, Eri1, negatively regulates heterochromatin assembly in fission yeast. PUBMED:16797182 EPMC:16797182

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003034

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 [ PUBMED:10694879 ].

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 [ PUBMED:10694879 ].

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 organisation [ PUBMED:10212141 , PUBMED:9671816 ]. The SAF-A protein is cleaved by caspase-3 during apoptosis [ PUBMED:10671544 ].
  • Mammalian Acinus, a protein which induces apoptotic chromatin condensation after cleavage by caspase-3 [ PUBMED:10490026 ]. 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 [ PUBMED:10805787 ].
  • 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 [ PUBMED:9862413 ]. 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 [ PUBMED:9707445 ].
  • 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 homologue of RAD18.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HeH (CL0306), which has the following description:

This superfamily includes protein domains with the helix-extended loop-helix (HeH) structure.

The clan contains the following 11 members:

ARMET_C Endonuc-dimeris FANC_SAP HeH LEM Lsr2 PADR1 Rho_N SAP SAP_new25 Thymopoietin


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 145
Number in full: 11761
Average length of the domain: 34.60 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 5.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.7 27.7
Trusted cut-off 27.7 27.7
Noise cut-off 27.6 27.6
Model length: 35
Family (HMM) version: 29
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SAP domain has been found. There are 18 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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