Protein:XPNPEP3 |
Protein Summary |
 Gene summary |
| Gene name: XPNPEP3 | ASpdb.0 ID: 63929 | Gene | Gene symbol | XPNPEP3 | Gene ID | 63929 |
| Gene name | X-prolyl aminopeptidase 3 |
| Synonyms | APP3|ICP55|NPHPL1 |
| Cytomap | 22q13.2 |
| Type of gene | protein-coding |
| Description | xaa-Pro aminopeptidase 3Intermediate Cleaving Peptidase 55X-Pro aminopeptidase 3X-prolyl aminopeptidase 3, mitochondrialprobable Xaa-Pro aminopeptidase 3 |
| Modification date | 20240305 |
| UniProtAcc | Q9NQH7 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | XPNPEP3 | GO:0005737 | cytoplasm | 25609706 |
| Gene | XPNPEP3 | GO:0005739 | mitochondrion | 20179356|25609706 |
| Gene | XPNPEP3 | GO:0005829 | cytosol | - |
| Gene | XPNPEP3 | GO:0006508 | proteolysis | 28476889 |
| Gene | XPNPEP3 | GO:0030145 | manganese ion binding | 28476889 |
| Gene | XPNPEP3 | GO:0070006 | metalloaminopeptidase activity | 25609706|28476889 |
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 |
| Q9NQH7-1 | Q9NQH7-1_5x49_A.pdb | 5X49 | X-ray | 1.65 | A | 57 | 503 |
| 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 |
| Q9NQH7 | XPNPEP3 | Q9NQH7-1 | Q9NQH7-2 | 507 | 428 | 1 | 79 | Deletion | none | none | 0 | 0 |
| Q9NQH7 | XPNPEP3 | Q9NQH7-1 | Q9NQH7-3 | 507 | 278 | 265 | 278 | Substitution | AFIETMFTSKAPVE | RQGFSVLSRLVSNS | 265 | 278 |
| Q9NQH7 | XPNPEP3 | Q9NQH7-1 | Q9NQH7-3 | 507 | 278 | 279 | 507 | Deletion | none | none | 278 | 278 |
| Q9NQH7 | XPNPEP3 | Q9NQH7-1 | Q9NQH7-4 | 507 | 484 | 1 | 23 | Deletion | none | none | 0 | 0 |
| Q9NQH7 | XPNPEP3 | Q9NQH7-1 | Q9NQH7-5 | 507 | 288 | 265 | 288 | Substitution | AFIETMFTSKAPVEEAFLYAKFEF | KSVLLARHGGSRLYSHHFGRPRLS | 265 | 288 |
| Q9NQH7 | XPNPEP3 | Q9NQH7-1 | Q9NQH7-5 | 507 | 288 | 289 | 507 | Deletion | none | none | 288 | 288 |
| Multiple sequence alignment of our canonical and alternatively spliced XPNPEP3 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of XPNPEP3 |
| UniProt-id | ENSG | ENST | ENSP |
| Q9NQH7-1 | ENSG00000196236.13 | ENST00000357137.9 | ENSP00000349658.4 |
| UniProt-id | NM ID | NP ID |
| Q9NQH7-1 | NM_022098.3 | NP_071381.1 |
| Amino acid sequences of our canonical and alternatively spliced XPNPEP3 |
| accession_id | Protein sequence |
| Q9NQH7-1 | MPWLLSAPKLVPAVANVRGLSGCMLCSQRRYSLQPVPERRIPNRYLGQPSPFTHPHLLRPGEVTPGLSQVEYALRRHKLMSLIQKEAQGQ SGTDQTVVVLSNPTYYMSNDIPYTFHQDNNFLYLCGFQEPDSILVLQSLPGKQLPSHKAILFVPRRDPSRELWDGPRSGTDGAIALTGVD EAYTLEEFQHLLPKMKAETNMVWYDWMRPSHAQLHSDYMQPLTEAKAKSKNKVRGVQQLIQRLRLIKSPAEIERMQIAGKLTSQAFIETM FTSKAPVEEAFLYAKFEFECRARGADILAYPPVVAGGNRSNTLHYVKNNQLIKDGEMVLLDGGCESSCYVSDITRTWPVNGRFTAPQAEL YEAVLEIQRDCLALCFPGTSLENIYSMMLTLIGQKLKDLGIMKNIKENNAFKAARKYCPHHVGHYLGMDVHDTPDMPRSLPLQPGMVITI |
| Q9NQH7-2 | MSLIQKEAQGQSGTDQTVVVLSNPTYYMSNDIPYTFHQDNNFLYLCGFQEPDSILVLQSLPGKQLPSHKAILFVPRRDPSRELWDGPRSG TDGAIALTGVDEAYTLEEFQHLLPKMKAETNMVWYDWMRPSHAQLHSDYMQPLTEAKAKSKNKVRGVQQLIQRLRLIKSPAEIERMQIAG KLTSQAFIETMFTSKAPVEEAFLYAKFEFECRARGADILAYPPVVAGGNRSNTLHYVKNNQLIKDGEMVLLDGGCESSCYVSDITRTWPV NGRFTAPQAELYEAVLEIQRDCLALCFPGTSLENIYSMMLTLIGQKLKDLGIMKNIKENNAFKAARKYCPHHVGHYLGMDVHDTPDMPRS |
| Q9NQH7-3 | MPWLLSAPKLVPAVANVRGLSGCMLCSQRRYSLQPVPERRIPNRYLGQPSPFTHPHLLRPGEVTPGLSQVEYALRRHKLMSLIQKEAQGQ SGTDQTVVVLSNPTYYMSNDIPYTFHQDNNFLYLCGFQEPDSILVLQSLPGKQLPSHKAILFVPRRDPSRELWDGPRSGTDGAIALTGVD EAYTLEEFQHLLPKMKAETNMVWYDWMRPSHAQLHSDYMQPLTEAKAKSKNKVRGVQQLIQRLRLIKSPAEIERMQIAGKLTSQRQGFSV |
| Q9NQH7-4 | MLCSQRRYSLQPVPERRIPNRYLGQPSPFTHPHLLRPGEVTPGLSQVEYALRRHKLMSLIQKEAQGQSGTDQTVVVLSNPTYYMSNDIPY TFHQDNNFLYLCGFQEPDSILVLQSLPGKQLPSHKAILFVPRRDPSRELWDGPRSGTDGAIALTGVDEAYTLEEFQHLLPKMKAETNMVW YDWMRPSHAQLHSDYMQPLTEAKAKSKNKVRGVQQLIQRLRLIKSPAEIERMQIAGKLTSQAFIETMFTSKAPVEEAFLYAKFEFECRAR GADILAYPPVVAGGNRSNTLHYVKNNQLIKDGEMVLLDGGCESSCYVSDITRTWPVNGRFTAPQAELYEAVLEIQRDCLALCFPGTSLEN IYSMMLTLIGQKLKDLGIMKNIKENNAFKAARKYCPHHVGHYLGMDVHDTPDMPRSLPLQPGMVITIEPGIYIPEDDKDAPEKFRGLGVR |
| Q9NQH7-5 | MPWLLSAPKLVPAVANVRGLSGCMLCSQRRYSLQPVPERRIPNRYLGQPSPFTHPHLLRPGEVTPGLSQVEYALRRHKLMSLIQKEAQGQ SGTDQTVVVLSNPTYYMSNDIPYTFHQDNNFLYLCGFQEPDSILVLQSLPGKQLPSHKAILFVPRRDPSRELWDGPRSGTDGAIALTGVD EAYTLEEFQHLLPKMKAETNMVWYDWMRPSHAQLHSDYMQPLTEAKAKSKNKVRGVQQLIQRLRLIKSPAEIERMQIAGKLTSQKSVLLA |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| XPNPEP3 (go to UniProt):Q9NQH7 |
| 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 |
| Q9NQH7 | Region | 54 | 79 | Note=Interaction with TNFRSF1B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25609706;Dbxref=PMID:25609706 | Type=Deletion;Start=1;End=79 |
Gene Isoform Structures and Expression Levels for XPNPEP3 |
| Gene structures of our canonical and alternative spliced genes of XPNPEP3 * 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 Q9NQH7-1 |
| 3D view using mol* of Q9NQH7-2 |
| 3D view using mol* of Q9NQH7-3 |
| 3D view using mol* of Q9NQH7-4 |
| 3D view using mol* of Q9NQH7-5 |
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 Q9NQH7-1 |
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| pLDDT distribution across the protein length of Q9NQH7-2 |
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| pLDDT distribution across the protein length of Q9NQH7-3 |
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| pLDDT distribution across the protein length of Q9NQH7-4 |
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| pLDDT distribution across the protein length of Q9NQH7-5 |
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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 Q9NQH7-1 |
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| Ramachandran plot of Q9NQH7-3 |
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| Ramachandran plot of Q9NQH7-4 |
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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 |
| Q9NQH7-1 | 1.009 | 101 | 0.876 | 245.931 | 0.528 | 0.712 | 0.927 | 0.047 | 1.506 | 0.031 | 1.731 | 300,301,303,313,314,316,331,342,381,420,421,423,42 4,425,430,431,432,433,434,436,437,438,451,473,475 |
| Q9NQH7-2 | 1 | 100 | 0.867 | 254.849 | 0.545 | 0.697 | 0.92 | 0.056 | 1.506 | 0.037 | 1.401 | 221,222,224,234,235,237,252,263,341,342,344,345,34 6,351,352,353,355,356,357,358,359,372,394,396 |
| Q9NQH7-3 | 1.005 | 109 | 1.018 | 387.247 | 0.648 | 0.705 | 0.864 | 0.437 | 1.057 | 0.414 | 0.624 | 29,31,36,37,38,39,41,51,52,60,61,62,63,69,70,73,74 ,76,77,139,145,146,147,149,175,176,178,179,180 |
| Q9NQH7-4 | 1 | 103 | 0.864 | 271.999 | 0.532 | 0.698 | 0.921 | 0.083 | 1.517 | 0.054 | 1.728 | 277,278,280,287,289,290,291,293,306,308,319,397,39 8,400,401,402,407,408,409,411,413,414,415,428,450, 452 |
| Q9NQH7-5 | 1.023 | 142 | 1.065 | 649.642 | 0.63 | 0.686 | 0.87 | 0.772 | 0.881 | 0.877 | 0.496 | 29,30,31,32,33,34,36,37,38,39,40,41,51,60,61,68,69 ,70,73,74,76,77,143,144,145,146,147,148,149,175,17 8,179,180 |
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 Q9NQH7-1_Q9NQH7-1_5x49_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 Q9NQH7-1_5x49_A_Q9NQH7-2.pdb |
| 3D view using mol* of Q9NQH7-1_5x49_A_Q9NQH7-3.pdb |
| 3D view using mol* of Q9NQH7-1_5x49_A_Q9NQH7-4.pdb |
| 3D view using mol* of Q9NQH7-1_5x49_A_Q9NQH7-5.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9NQH7-1_Q9NQH7-2.pdb |
| 3D view using mol* of Q9NQH7-1_Q9NQH7-3.pdb |
| 3D view using mol* of Q9NQH7-1_Q9NQH7-4.pdb |
| 3D view using mol* of Q9NQH7-1_Q9NQH7-5.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q9NQH7-1_vs_Q9NQH7-2.png |
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| ./stats/secondary_structure/figure/Q9NQH7-1_vs_Q9NQH7-3.png |
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| ./stats/secondary_structure/figure/Q9NQH7-1_vs_Q9NQH7-4.png |
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| ./stats/secondary_structure/figure/Q9NQH7-1_vs_Q9NQH7-5.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q9NQH7-1_vs_Q9NQH7-2.png |
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| ./stats/relative_asa/Q9NQH7-1_vs_Q9NQH7-3.png |
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| ./stats/relative_asa/Q9NQH7-1_vs_Q9NQH7-4.png |
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| ./stats/relative_asa/Q9NQH7-1_vs_Q9NQH7-5.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Q9NQH7 | Region | 54 | 79 | Note=Interaction with TNFRSF1B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25609706;Dbxref=PMID:25609706 | Type=Deletion;Start=1;End=79 |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to XPNPEP3 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to XPNPEP3 |
| Previous studies relating to the alternative splicing of XPNPEP3 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| XPNPEP3 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D004392 | Dwarfism |
| XPNPEP3 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D006130 | Growth Disorders |
| XPNPEP3 | 24711643 | Identifying biological pathways that underlie primordial short stature using network analysis. | Mutations in CUL7, OBSL1 and CCDC8, leading to disordered ubiquitination, cause one of the commonest primordial growth disorders, 3-M syndrome. This condition is associated with i) abnormal p53 function, ii) GH and/or IGF1 resistance, which may relate to failure to recycle signalling molecules, and iii) cellular IGF2 deficiency. However the exact molecular mechanisms that may link these abnormalities generating growth restriction remain undefined. In this study, we have used immunoprecipitation/mass spectrometry and transcriptomic studies to generate a 3-M 'interactome', to define key cellular pathways and biological functions associated with growth failure seen in 3-M. We identified 189 proteins which interacted with CUL7, OBSL1 and CCDC8, from which a network including 176 of these proteins was generated. To strengthen the association to 3-M syndrome, these proteins were compared with an inferred network generated from the genes that were differentially expressed in 3-M fibroblasts compared with controls. This resulted in a final 3-M network of 131 proteins, with the most significant biological pathway within the network being mRNA splicing/processing. We have shown using an exogenous insulin receptor (INSR) minigene system that alternative splicing of exon 11 is significantly changed in HEK293 cells with altered expression of CUL7, OBSL1 and CCDC8 and in 3-M fibroblasts. The net result is a reduction in the expression of the mitogenic INSR isoform in 3-M syndrome. From these preliminary data, we hypothesise that disordered ubiquitination could result in aberrant mRNA splicing in 3-M; however, further investigation is required to determine whether this contributes to growth failure. | D009123 | Muscle Hypotonia |
Clinically important variants in XPNPEP3 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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