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31  structures 174  species 2  interactions 1396  sequences 105  architectures

Family: SapB_1 (PF05184)

Summary: Saposin-like type B, region 1

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This is the Wikipedia entry entitled "Saposin protein domain". More...

Saposin protein domain Edit Wikipedia article

Identifiers
Symbol SapA
Pfam PF02199
InterPro IPR003119
PROSITE PDOC51110
Saposin-like type B, region 1
Saposin C 2qyp.png
Crystal structure of human saposin C dimer in an open conformation.[1]
Identifiers
Symbol SapB_1
Pfam PF05184
InterPro IPR007856
PROSITE PDOC50015
Identifiers
Symbol SapB_2
Pfam PF03489
InterPro IPR008138
PROSITE PDOC50015
SCOP 1nkl
SUPERFAMILY 1nkl
OPM superfamily 83
OPM protein 1sn6

In molecular biology a saposin protein domain is a region of the saposin protein that has a certain conserved sequence or structure that defines a domain. Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes.[2] They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes.[3][4]

Domain organization[edit]

Below is a schematic diagram of the primary structure of the prosaposin protein depicting the N- and C-terminal SapA domains and the four SapB1 and four SapB2 domains. Proteolytic cleavage of the proprotein occurs in the grey regions. Adjacent pairs of SapB1 and SapB2 domains remain connected after proteolytic processing of prosaposin and each pair comprises one of the mature saponin A-D proteins.

Prosaposin schematic.png

Human proteins containing this domain[edit]

References[edit]

  1. ^ PDB 2qyp, Rossmann M, Schultz-Heienbrok R, Behlke J, Remmel N, Alings C, Sandhoff K, Saenger W, Maier T (May 2008). "Crystal structures of human saposins C and D: implications for lipid recognition and membrane interactions". Structure 16 (5): 809–17. doi:10.1016/j.str.2008.02.016. PMID 18462685. 
  2. ^ Munford RS, Sheppard PO, O Hara PJ (1995). "Saposin-like proteins (SAPLIP) carry out diverse functions on a common backbone structure". J. Lipid Res. 36 (8): 1653–1663. PMID 7595087. 
  3. ^ Ponting CP (1994). "Acid sphingomyelinase possesses a domain homologous to its activator proteins: saposins B and D". Protein Sci. 3 (2): 359–361. doi:10.1002/pro.5560030219. PMC 2142785. PMID 8003971. 
  4. ^ Hofmann K, Tschopp J (1996). "Cytotoxic T cells: more weapons for new targets?". Trends Microbiol. 4 (3): 91–94. doi:10.1016/0966-842X(96)81522-8. PMID 8868085. 

Further reading[edit]

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR008138

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

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Saposin-like type B, region 1 Provide feedback

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Literature references

  1. Ponting CP, Russell RB; , Trends Biochem Sci 1995;20:179-180.: Swaposins: circular permutations within genes encoding saposin homologues. PUBMED:7610480 EPMC:7610480


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007856

Synonym(s):cerebroside sulphate activator, CSAct

Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [PUBMED:12518053].

Gene Ontology

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Domain organisation

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

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Alignments

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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.

  Seed
(161)
Full
(1396)
Representative proteomes NCBI
(1402)
Meta
(4)
RP15
(247)
RP35
(355)
RP55
(514)
RP75
(654)
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  Seed
(161)
Full
(1396)
Representative proteomes NCBI
(1402)
Meta
(4)
RP15
(247)
RP35
(355)
RP55
(514)
RP75
(654)
Alignment:
Format:
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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.

  Seed
(161)
Full
(1396)
Representative proteomes NCBI
(1402)
Meta
(4)
RP15
(247)
RP35
(355)
RP55
(514)
RP75
(654)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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Trees

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: Manual
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 161
Number in full: 1396
Average length of the domain: 38.80 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 19.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 20.7
Trusted cut-off 20.8 20.7
Noise cut-off 20.6 20.6
Model length: 39
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

SapB_2 SapB_1

Structures

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 SapB_1 domain has been found. There are 31 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 seqence.

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