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    ppk-3 1-phosphatidylinositol-3-phosphate 5-kinase [ Caenorhabditis elegans ]

    Gene ID: 181428, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ppk-3
    Official Full Name
    1-phosphatidylinositol-3-phosphate 5-kinase
    Primary source
    WormBase:WBGene00004089
    Locus tag
    CELE_VF11C1L.1
    See related
    AllianceGenome:WB:WBGene00004089
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Caenorhabditis elegans (strain: Bristol N2)
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
    Summary
    Predicted to enable 1-phosphatidylinositol-3-phosphate 5-kinase activity and phosphatidylinositol-3-phosphate binding activity. Predicted to be involved in phosphatidylinositol phosphate biosynthetic process and vacuole organization. Located in axon; cytoplasm; and neuronal cell body. Is expressed in several structures, including intestine; nervous system; non-striated muscle; pharynx; and rectal gland cell. Human ortholog(s) of this gene implicated in Fleck corneal dystrophy. Orthologous to human PIKFYVE (phosphoinositide kinase, FYVE-type zinc finger containing). [provided by Alliance of Genome Resources, Nov 2024]
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    Genomic context

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    See ppk-3 in Genome Data Viewer
    Location:
    chromosome: X
    Exon count:
    14
    Sequence:
    Chromosome: X; NC_003284.9 (12968910..12975645, complement)

    Chromosome X - NC_003284.9Genomic Context describing neighboring genes Neighboring gene tRNA-Leu Neighboring gene GM2 Activator Protein family member Neighboring gene Neuropeptide-Like Protein Neighboring gene G-protein coupled receptors family 1 profile domain-containing protein Neighboring gene Photosystem reaction center subunit H Neighboring gene Lipid droplet-associated hydrolase Neighboring gene Uncharacterized protein Neighboring gene SCAVenger receptor (CD36 family) related Neighboring gene Mitochondrial fission factor

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003284.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The amino acid transporter SLC-36.1 cooperates with PtdIns3P 5-kinase to control phagocytic lysosome reformation. Gan Q, et al. J Cell Biol, 2019 Aug 5. PMID 31235480, Free PMC Article
    2. The phosphoinositide kinase PIKfyve/Fab1p regulates terminal lysosome maturation in Caenorhabditis elegans. Nicot AS, et al. Mol Biol Cell, 2006 Jul. PMID 16801682, Free PMC Article
    3. PIKfyve Regulates Vacuole Maturation and Nutrient Recovery following Engulfment. Krishna S, et al. Dev Cell, 2016 Sep 12. PMID 27623384, Free PMC Article
    4. Role of phosphatidylinositol-4-phosphate 5' kinase (ppk-1) in ovulation of Caenorhabditis elegans. Xu X, et al. Exp Cell Res, 2007 Jul 1. PMID 17475243, Free PMC Article
    5. Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells. Yu X, et al. PLoS Biol, 2008 Mar 18. PMID 18351800, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. This work strongly suggests that the main function of PPK-3 is to mediate membrane retrieval from matured lysosomes through regulation of PtdIns(3,5)P2.
      Title: The phosphoinositide kinase PIKfyve/Fab1p regulates terminal lysosome maturation in Caenorhabditis elegans.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by WormBase

    Function Evidence Code Pubs
    enables 1-phosphatidylinositol-3-phosphate 5-kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 1-phosphatidylinositol-3-phosphate 5-kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in phosphatidylinositol metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol phosphate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vacuole organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in axon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in neuronal cell body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    1-phosphatidylinositol-3-phosphate 5-kinase
    NP_001391085.1
    • Confirmed by transcript evidence
    NP_510155.3
    • Confirmed by transcript evidence

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003284.9 Reference assembly

      Range
      12968910..12975645 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_077754.11 → NP_510155.3  1-phosphatidylinositol-3-phosphate 5-kinase [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_510155.3

      Status: REVIEWED

      UniProtKB/TrEMBL
      G5ED98
      Conserved Domains (3) summary
      cd00139
      Location:1164 → 1482
      PIPKc; Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II ...
      cd03334
      Location:378 → 642
      Fab1_TCP; TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this ...
      cd15725
      Location:106 → 167
      FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins

    2. NM_001404212.1 → NP_001391085.1  1-phosphatidylinositol-3-phosphate 5-kinase [Caenorhabditis elegans]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A8D9I628
    Nucleotide Protein
    Heading Accession and Version

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