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    PPCDC phosphopantothenoylcysteine decarboxylase [ Homo sapiens (human) ]

    Gene ID: 60490, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PPCDCprovided by HGNC
    Official Full Name
    phosphopantothenoylcysteine decarboxylaseprovided by HGNC
    Primary source
    HGNC:HGNC:28107
    See related
    Ensembl:ENSG00000138621 MIM:609854; AllianceGenome:HGNC:28107
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    coaC; MDS018; PPC-DC
    Summary
    Biosynthesis of coenzyme A (CoA) from pantothenic acid (vitamin B5) is an essential universal pathway in prokaryotes and eukaryotes. PPCDC (EC 4.1.1.36), one of the last enzymes in this pathway, converts phosphopantothenoylcysteine to 4-prime-phosphopantetheine (Daugherty et al., 2002 [PubMed 11923312]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 1.6), appendix (RPKM 1.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PPCDC in Genome Data Viewer
    Location:
    15q24.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (75023590..75050726)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72893580..72920712)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (75315931..75343067)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75246929-75247862 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75247863-75248796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75248797-75249730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75250725-75251281 Neighboring gene ribonuclease P and MRP subunit p25 Neighboring gene secretory carrier membrane protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75323765-75324265 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:75326220-75326413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75328766-75329266 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:75329616-75329854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9821 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:75335422-75336621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6663 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:75343839-75344340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:75344341-75344840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9830 Neighboring gene uncharacterized LOC124903529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9834 Neighboring gene stromal cell derived factor 2 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Unusual space-group pseudosymmetry in crystals of human phosphopantothenoylcysteine decarboxylase. Manoj N, et al. Acta Crystallogr D Biol Crystallogr, 2003 Oct. PMID 14501115
    2. Mechanistic studies on phosphopantothenoylcysteine decarboxylase: trapping of an enethiolate intermediate with a mechanism-based inactivating agent. Strauss E, et al. Biochemistry, 2004 Dec 14. PMID 15581364
    3. Complex stability and dynamic subunit interchange modulates the disparate activities of the yeast moonlighting proteins Hal3 and Vhs3. Abrie JA, et al. Sci Rep, 2015 Oct 30. PMID 26514574, Free PMC Article
    4. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. Daugherty M, et al. J Biol Chem, 2002 Jun 14. PMID 11923312
    5. Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption. Cornelis MC, et al. PLoS Genet, 2011 Apr. PMID 21490707, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14585

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables FMN binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables FMN binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables phosphopantothenoylcysteine decarboxylase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables phosphopantothenoylcysteine decarboxylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphopantothenoylcysteine decarboxylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in coenzyme A biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in coenzyme A biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in coenzyme A biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in coenzyme A biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of phosphopantothenoylcysteine decarboxylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    phosphopantothenoylcysteine decarboxylase
    NP_001288030.1
    NP_001288031.1
    NP_001288032.1
    NP_001288033.1
    NP_001288034.1
    NP_068595.3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001301101.2 → NP_001288030.1  phosphopantothenoylcysteine decarboxylase isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AY358848, BC005877, BF243417, BM555704
      Consensus CDS
      CCDS73759.1
      UniProtKB/TrEMBL
      H3BQB0
      Related
      ENSP00000455691.1, ENST00000568649.5
      Conserved Domains (1) summary
      cl19190
      Location:16 → 161
      Flavoprotein; Flavoprotein

    2. NM_001301102.2 → NP_001288031.1  phosphopantothenoylcysteine decarboxylase isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.
      Source sequence(s)
      AY358848, BC005877, BF243417, BU500301, DW437029
      Consensus CDS
      CCDS73760.1
      UniProtKB/TrEMBL
      H3BRQ0
      Related
      ENSP00000456353.1, ENST00000567336.1
      Conserved Domains (1) summary
      cl19190
      Location:16 → 172
      Flavoprotein; Flavoprotein

    3. NM_001301103.2 → NP_001288032.1  phosphopantothenoylcysteine decarboxylase isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons in the central coding region, compared to variant 1, resulting in an isoform (d) that is shorter than isoform a.
      Source sequence(s)
      AY358848, BC005877, BF243417, BI833814
      Consensus CDS
      CCDS73761.1
      UniProtKB/TrEMBL
      H3BSE3
      Related
      ENSP00000456665.1, ENST00000564923.5
      Conserved Domains (1) summary
      cl19190
      Location:34 → 129
      Flavoprotein; Flavoprotein

    4. NM_001301104.2 → NP_001288033.1  phosphopantothenoylcysteine decarboxylase isoform e

      See identical proteins and their annotated locations for NP_001288033.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains alternate 5' exon structure, and it thus differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (e) is shorter at the N-terminus, compared to isoform a. Both variants 5 and 6 encode isoform e.
      Source sequence(s)
      AF182419, BC005877, DW437029
      Consensus CDS
      CCDS76781.1
      UniProtKB/TrEMBL
      H3BU63
      Related
      ENSP00000457490.1, ENST00000563393.1
      Conserved Domains (1) summary
      cl19190
      Location:9 → 72
      Flavoprotein; Flavoprotein

    5. NM_001301105.2 → NP_001288034.1  phosphopantothenoylcysteine decarboxylase isoform e

      See identical proteins and their annotated locations for NP_001288034.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) contains alternate 5' exon structure, and it thus differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (e) is shorter at the N-terminus, compared to isoform a. Both variants 5 and 6 encode isoform e.
      Source sequence(s)
      AY358848, BC005877, BG744258, BI907452, DW437029
      Consensus CDS
      CCDS76781.1
      UniProtKB/TrEMBL
      H3BU63
      Conserved Domains (1) summary
      cl19190
      Location:9 → 72
      Flavoprotein; Flavoprotein

    6. NM_021823.5 → NP_068595.3  phosphopantothenoylcysteine decarboxylase isoform a

      See identical proteins and their annotated locations for NP_068595.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AY358848, BC005877, BF243417, DW437029
      Consensus CDS
      CCDS10275.1
      UniProtKB/Swiss-Prot
      Q96CD2, Q96SX0, Q9HC17
      Related
      ENSP00000343190.3, ENST00000342932.8
      Conserved Domains (1) summary
      cl19190
      Location:16 → 204
      Flavoprotein; Flavoprotein

    RNA

    1. NR_125369.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks an alternate exon in the 5' region, compared to variant 1. This variant is represented as non-coding because it does not contain an ORF that meets RefSeq quality criteria
      Source sequence(s)
      AY358848, BC005877, BF243417, DB488540, DW437029

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      75023590..75050726
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      72893580..72920712
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96CD2.2 GenPept UniProtKB/Swiss-Prot:Q96CD2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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