Protein:PSAP |
Protein Summary |
 Gene summary |
| Gene name: PSAP | ASpdb.0 ID: 5660 | Gene | Gene symbol | PSAP | Gene ID | 5660 |
| Gene name | prosaposin |
| Synonyms | GLBA|PARK24|PSAPD|SAP1|SAP2 |
| Cytomap | 10q22.1 |
| Type of gene | protein-coding |
| Description | prosaposinprecursor of saposinsproactivator polypeptidesaposin-Asaposin-Bsaposin-Csaposin-Dsphingolipid activator protein-1sphingolipid activator protein-2 |
| Modification date | 20240407 |
| UniProtAcc | P07602 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | PSAP | GO:0005543 | phospholipid binding | 14674747 |
| Gene | PSAP | GO:0005615 | extracellular space | 1454804 |
| Gene | PSAP | GO:0005764 | lysosome | 22431521|26370502|28541286 |
| Gene | PSAP | GO:0005770 | late endosome | 26370502 |
| Gene | PSAP | GO:0007041 | lysosomal transport | 26370502 |
| Gene | PSAP | GO:0042803 | protein homodimerization activity | 18462685 |
| Gene | PSAP | GO:0043231 | intracellular membrane-bounded organelle | - |
| Gene | PSAP | GO:1903771 | positive regulation of beta-galactosidase activity | 1454804 |
| Gene | PSAP | GO:1905572 | ganglioside GM1 transport to membrane | 1454804 |
| Gene | PSAP | GO:1905573 | ganglioside GM1 binding | 1454804 |
| Gene | PSAP | GO:1905574 | ganglioside GM2 binding | 1454804 |
| Gene | PSAP | GO:1905575 | ganglioside GM3 binding | 1454804 |
| Gene | PSAP | GO:1905576 | ganglioside GT1b binding | 1454804 |
| Gene | PSAP | GO:1905577 | ganglioside GP1c binding | 1454804 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| P07602-1 | P07602-1_2dob_A.pdb | 2DOB | X-ray | 2.0 | A | 60 | 140 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| P07602 | PSAP | P07602-1 | P07602-2 | 524 | 526 | 259 | 259 | Substitution | M | MDQ | 259 | 261 |
| P07602 | PSAP | P07602-1 | P07602-3 | 524 | 527 | 260 | 260 | Substitution | Q | QDQQ | 260 | 263 |
| Multiple sequence alignment of our canonical and alternatively spliced PSAP |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PSAP |
| UniProt-id | ENSG | ENST | ENSP |
| P07602-1 | ENSG00000197746.15 | ENST00000394936.8 | ENSP00000378394.3 |
| UniProt-id | NM ID | NP ID |
| P07602-1 | NM_002778.3 | NP_002769.1 |
| P07602-2 | NM_001042466.2 | NP_001035931.1 |
| P07602-3 | NM_001042465.2 | NP_001035930.1 |
| Amino acid sequences of our canonical and alternatively spliced PSAP |
| accession_id | Protein sequence |
| P07602-1 | MYALFLLASLLGAALAGPVLGLKECTRGSAVWCQNVKTASDCGAVKHCLQTVWNKPTVKSLPCDICKDVVTAAGDMLKDNATEEEILVYL EKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNLCESLQKHLAELNHQKQLESNKIPELDMTEVVAPFMANIPLLLY PQDGPRSKPQPKDNGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGF CDEVKEMPMQTLVPAKVASKNVIPALELVEPIKKHEVPAKSDVYCEVCEFLVKEVTKLIDNNKTEKEILDAFDKMCSKLPKSLSEECQEV VDTYGSSILSILLEEVSPELVCSMLHLCSGTRLPALTVHVTQPKDGGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQ |
| P07602-2 | MYALFLLASLLGAALAGPVLGLKECTRGSAVWCQNVKTASDCGAVKHCLQTVWNKPTVKSLPCDICKDVVTAAGDMLKDNATEEEILVYL EKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNLCESLQKHLAELNHQKQLESNKIPELDMTEVVAPFMANIPLLLY PQDGPRSKPQPKDNGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMDQQPKEICALV GFCDEVKEMPMQTLVPAKVASKNVIPALELVEPIKKHEVPAKSDVYCEVCEFLVKEVTKLIDNNKTEKEILDAFDKMCSKLPKSLSEECQ EVVDTYGSSILSILLEEVSPELVCSMLHLCSGTRLPALTVHVTQPKDGGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQ |
| P07602-3 | MYALFLLASLLGAALAGPVLGLKECTRGSAVWCQNVKTASDCGAVKHCLQTVWNKPTVKSLPCDICKDVVTAAGDMLKDNATEEEILVYL EKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNLCESLQKHLAELNHQKQLESNKIPELDMTEVVAPFMANIPLLLY PQDGPRSKPQPKDNGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQDQQPKEICAL VGFCDEVKEMPMQTLVPAKVASKNVIPALELVEPIKKHEVPAKSDVYCEVCEFLVKEVTKLIDNNKTEKEILDAFDKMCSKLPKSLSEEC QEVVDTYGSSILSILLEEVSPELVCSMLHLCSGTRLPALTVHVTQPKDGGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPY |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| PSAP (go to UniProt):P07602 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P07602 | Domain | 194 | 275 | Note=Saposin B-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00415 | Type=Substitution;Start=259;End=259 |
| P07602 | Domain | 194 | 275 | Note=Saposin B-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00415 | Type=Substitution;Start=260;End=260 |
Gene Isoform Structures and Expression Levels for PSAP |
| Gene structures of our canonical and alternative spliced genes of PSAP * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of P07602-1 |
| 3D view using mol* of P07602-2 |
| 3D view using mol* of P07602-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of P07602-1 |
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| pLDDT distribution across the protein length of P07602-2 |
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| pLDDT distribution across the protein length of P07602-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of P07602-1 |
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| Ramachandran plot of P07602-2 |
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| Ramachandran plot of P07602-3 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| P07602-1 | 1.113 | 159 | 1.214 | 348.488 | 0.566 | 0.693 | 0.88 | 2.126 | 0.435 | 4.89 | 1.842 | 35,36,37,62,65,66,68,69,70,73,86,89,90,92,93,94,95 ,96,97,98,102,105,106,109,110,117,118,121,131,135, 136,137,446,447,450 |
| P07602-2 | 1.191 | 139 | 1.309 | 264.453 | 0.453 | 0.762 | 0.927 | 2.776 | 0.271 | 10.249 | 2.504 | 62,65,66,68,69,70,90,93,96,97,102,105,106,109,110, 117,121,131,135,137 |
| P07602-3 | 1.187 | 132 | 1.296 | 264.796 | 0.429 | 0.774 | 0.991 | 2.875 | 0.334 | 8.617 | 5.273 | 62,65,66,69,70,73,90,93,94,96,97,102,105,106,109,1 10,117,121,131,135,137 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of P07602-1_P07602-1_2dob_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P07602-1_2dob_A_P07602-2.pdb |
| 3D view using mol* of P07602-1_2dob_A_P07602-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P07602-1_P07602-2.pdb |
| 3D view using mol* of P07602-1_P07602-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P07602-1_vs_P07602-2.png |
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| ./stats/secondary_structure/figure/P07602-1_vs_P07602-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P07602-1_vs_P07602-2.png |
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| ./stats/relative_asa/P07602-1_vs_P07602-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to PSAP |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
| P07602 | PSAP | DB01966 | Di-Stearoyl-3-Sn-Phosphatidylethanolamine | experimental |
Related Diseases to PSAP |
| Previous studies relating to the alternative splicing of PSAP and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| PSAP | 2066109 | The mechanism for a 33-nucleotide insertion in mRNA causing sphingolipid activator protein (SAP-1)-deficient metachromatic leukodystrophy. | Metachromatic leukodystrophy is a severe autosomal recessive disorder caused by accumulation of sulfatide resulting from deficient lysosomal degradation. While most patients have mutations in the lysosomal enzyme arylsulfatase A, some patients have mutations in a required heat stable sphingolipid activator protein, we call SAP-1. One patient with SAP-1 deficiency was previously demonstrated to have a 33-nucleotide insertion in her mRNA. This resulted in the production of mature SAP-1 with 11 extra amino acids, which was unstable during intracellular processing. In this manuscript we demonstrate that the 33 nucleotides are present near the middle of a 4-kb intron, and that a single base change, c to a, in the second position preceding the 33-nucleotide insertion, coupled with the presence of a string of pyrimidines immediately upstream from this change, creates a new 3' splice junction. The presence of a string of pyrimidines within the 33-nucleotide insertion, which has three cag trinucleotides near the 3' end, leads to alternative splicing in normal people as found in this laboratory and by others. The insertion region is followed by a gt dinucleotide that is spliced to a typical 3' consensus sequence. The single nucleotide change, c to a, was confirmed by identifying normal and mutant sequence in the consanguineous parents and a sister, previously identified as a carrier of this disorder. | D007966 | Leukodystrophy, Metachromatic |
Clinically important variants in PSAP |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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