Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
3  structures 1474  species 0  interactions 9281  sequences 149  architectures

Family: Syja_N (PF02383)

Summary: SacI homology domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "SacI homology domain". More...

SacI homology domain Edit Wikipedia article

SacI homology domain
Symbol Syja_N
Pfam PF02383
InterPro IPR002013

SacI homology domain is a family of evolutionarily related proteins.[1]

This Pfam family represents a protein domain which shows homology to the yeast protein SacI P32368. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.

Synaptic vesicles are recycled with remarkable speed and precision in nerve terminals. A major recycling pathway involves clathrin-mediated endocytosis at endocytic zones located around sites of release. Different 'accessory' proteins linked to this pathway have been shown to alter the shape and composition of lipid membranes, to modify membrane-coat protein interactions, and to influence actin polymerization. These include the GTPase dynamin, the lysophosphatidic acid acyl transferase endophilin, and the phosphoinositide phosphatase synaptojanin.[2]

The recessive suppressor of secretory defect in yeast Golgi and yeast actin function belongs to this family. This protein may be involved in the coordination of the activities of the secretory pathway and the actin cytoskeleton.

Human synaptojanin which may be localised on coated endocytic intermediates in nerve terminals also belongs to this family.


Human genes encoding proteins containing this domain include:



  1. ^ Nemoto Y, Arribas M, Haffner C, DeCamilli P (December 1997). "Synaptojanin 2, a novel synaptojanin isoform with a distinct targeting domain and expression pattern". The Journal of Biological Chemistry. 272 (49): 30817–21. doi:10.1074/jbc.272.49.30817. PMID 9388224. 
  2. ^ Cox DN, Chao A, Baker J, Chang L, Qiao D, Lin H (December 1998). "A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal". Genes & Development. 12 (23): 3715–27. doi:10.1101/gad.12.23.3715. PMC 317255Freely accessible. PMID 9851978. 

This article incorporates text from the public domain Pfam and InterPro IPR002013

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

SacI homology domain Provide feedback

This Pfam family represents a protein domain which shows homology to the yeast protein SacI P32368. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin.

Literature references

  1. Nemoto Y, Arribas M, Haffner C, DeCamilli P; , J Biol Chem 1997;272:30817-30821.: Synaptojanin 2, a novel synaptojanin isoform with a distinct targeting domain and expression pattern. PUBMED:9388224 EPMC:9388224

This tab holds annotation information from the InterPro database.

InterPro entry IPR002013

The Sac domain is a region of homology between the N terminus of synaptojanin and the otherwise unrelated yeast protein Sac1p. The Sac domain is approximately 400 residues in length, and proteins containing this domain show approximately 35% identity with other Sac domains throughout this region. The Sac domain exhibits phosphatidylinositol polyphosphate phosphatase activity and can hydrolyse phosphate from any of the three positions of inositol that may be phosphorylated (3-, 4- and 5). However, adjacent phosphates are resistant to hydrolysis. Sac domains cannot hydrolyse phosphate from phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2), or PtdIns(3,4)P2, or PtdIns(3,4,5)P3, but can hydrolyse PtdIns(3,5)P2 [ PUBMED:11413010 ].

The Sac domain consists of seven highly conserved motifs which appear to define the catalytic and regulatory regions of the phosphatase. The sixth conserved region contains a highly conserved C-x(5)-R-[TS] motif, thought to be the catalytic motif of many metal-independent protein and inositide polyphosphate phosphatases. Interestingly, the Inp51p Sac domain in which the cysteine, arginine and threonine/serine residues within the C-x(5)-R-[TS] motif are absent, does not exhibit any phosphatase activity [ PUBMED:11413010 ].

Two classes of Sac domain proteins have been identified in mammals as well as lower eukaryotes [ PUBMED:11413010 ]. The first comprises proteins, which, in addition to an N-terminal phosphatase Sac domain, have all the domains associated with type II phosphatidylinositol phosphate 5-phosphatases:

  • Mammalian synaptojanins, type II phosphatidylinositol phosphate 5- phosphatases.
  • Yeast INP51, a 108kDa membrane protein. It is involved in endocytosis and regulation of the actin cytoskeleton under conditions of normal vegetative growth. Although the Sac phosphatase domain of INP51 may be catalytically inactive, the domain may retain other functions.
  • Yeast INP52, a 133kDa membrane protein. It is involved in endocytosis and regulation of the actin cytoskeleton under conditions of normal vegetative growth.
  • Yeast INP53, a 124kDa membrane protein. It appears to have a role in intra-Golgi and Golgi-to-endosomal trafficking.

The other class of Sac-containing phosphatases consists of proteins with an N-terminal Sac phosphatase domain and no other recognizable domains:

  • Yeast Sac1p, a 67kDa membrane protein found in the endoplasmic reticulum (ER) and Golgi. It regulates the actin cytoskeleton and phospholipid metabolism.
  • Yeast FIG4, a 101kDa protein encoded by a pheromone regulated or induced gene. FIG4 might function to regulate effector molecules of the actin cytoskeleton during mating.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan Phosphatase (CL0031), which has the following description:

This family includes tyrosine and dual specificity phosphatase enzymes.

The clan contains the following 16 members:

CDKN3 DSPc DSPn DUF442 Init_tRNA_PT LMWPc Myotub-related NleF_casp_inhib PTPlike_phytase PTS_IIB Rhodanese Ssu72 Syja_N Y_phosphatase Y_phosphatase2 Y_phosphatase3


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...

View options

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.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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

HMM logo

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.

Note: You can also download the data file for the tree.

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: Pfam-B_1090 (release 5.2)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 454
Number in full: 9281
Average length of the domain: 295.90 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 34.02 %

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 20.9 20.9
Trusted cut-off 21.4 20.9
Noise cut-off 20.8 20.7
Model length: 322
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

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


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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 Syja_N domain has been found. There are 3 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.

Loading structure mapping...