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PPCDC phosphopantothenoylcysteine decarboxylase [ Homo sapiens (human) ]

Gene ID: 60490, updated on 5-Mar-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
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Genomic context

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Location:
15q24.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (75023590..75050726)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72893580..72920712)
105.20220307 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
  • 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. 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
  2. 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
  3. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. Daugherty M, et al. J Biol Chem, 2002 Jun 14. PMID 11923312
  4. 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
  5. Unusual space-group pseudosymmetry in crystals of human phosphopantothenoylcysteine decarboxylase. Manoj N, et al. Acta Crystallogr D Biol Crystallogr, 2003 Oct. PMID 14501115

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_2023_10

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

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