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HLCS holocarboxylase synthetase [ Homo sapiens (human) ]

Gene ID: 3141, updated on 13-Feb-2019

Summary

Official Symbol
HLCSprovided by HGNC
Official Full Name
holocarboxylase synthetaseprovided by HGNC
Primary source
HGNC:HGNC:4976
See related
Ensembl:ENSG00000159267 MIM:609018
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HCS
Summary
This gene encodes an enzyme that catalyzes the binding of biotin to carboxylases and histones. The protein plays an important role in gluconeogenesis, fatty acid synthesis and branched chain amino acid catabolism. Defects in this gene are the cause of holocarboxylase synthetase deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Jun 2011]
Expression
Ubiquitous expression in thyroid (RPKM 4.3), prostate (RPKM 3.3) and 25 other tissues See more
Orthologs

Genomic context

See HLCS in Genome Data Viewer
Location:
21q22.13
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 21 NC_000021.9 (36748625..36990394, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38123189..38362545, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369308 Neighboring gene uncharacterized LOC107985492 Neighboring gene SIM bHLH transcription factor 2 Neighboring gene uncharacterized LOC105369305 Neighboring gene HLCS intron CAGE-defined mid-level expression enhancer Neighboring gene RNA, 5S ribosomal pseudogene 491 Neighboring gene divergent-paired related homeobox pseudogene 5 Neighboring gene mitochondrial ribosomal protein L20 pseudogene 1 Neighboring gene ripply transcriptional repressor 3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Biotin metabolism, organism-specific biosystem (from KEGG)
    Biotin metabolism, organism-specific biosystemBiotin (vitamin H or vitamin B7) is the essential cofactor of biotin-dependent carboxylases, such as pyruvate carboxylase and acetyl-CoA carboxylase. Mammals cannot synthesize biotin, while in bacter...
  • Biotin metabolism, conserved biosystem (from KEGG)
    Biotin metabolism, conserved biosystemBiotin (vitamin H or vitamin B7) is the essential cofactor of biotin-dependent carboxylases, such as pyruvate carboxylase and acetyl-CoA carboxylase. Mammals cannot synthesize biotin, while in bacter...
  • Biotin transport and metabolism, organism-specific biosystem (from REACTOME)
    Biotin transport and metabolism, organism-specific biosystemBiotin (Btn) is an essential cofactor in a variety of carboxylation reactions (Zempleni et al. 2009). Humans cannot synthesize Btn but it is abundant in the human diet and can be taken up from the in...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, classified according to their solubility, either fat-soluble or water-soluble, that are either not synthesized or synthesized only in limited amount...
  • Metabolism of water-soluble vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of water-soluble vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only ...
  • biotin-carboxyl carrier protein assembly, organism-specific biosystem (from BIOCYC)
    biotin-carboxyl carrier protein assembly, organism-specific biosystem
    biotin-carboxyl carrier protein assembly

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
biotin binding IDA
Inferred from Direct Assay
more info
PubMed 
biotin-[acetyl-CoA-carboxylase] ligase activity IEA
Inferred from Electronic Annotation
more info
 
biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity IEA
Inferred from Electronic Annotation
more info
 
biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity IEA
Inferred from Electronic Annotation
more info
 
biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
biotin-protein ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
biotin-protein ligase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
biotin-protein ligase activity TAS
Traceable Author Statement
more info
 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
biotin metabolic process TAS
Traceable Author Statement
more info
 
cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone biotinylation IDA
Inferred from Direct Assay
more info
PubMed 
histone modification IDA
Inferred from Direct Assay
more info
PubMed 
protein biotinylation IDA
Inferred from Direct Assay
more info
PubMed 
response to biotin IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
chromatin IDA
Inferred from Direct Assay
more info
PubMed 
cytosol HDA PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
nuclear lamina IDA
Inferred from Direct Assay
more info
PubMed 
nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
biotin--protein ligase
Names
biotin apo-protein ligase
biotin--[acetyl-CoA-carboxylase] ligase
biotin--[methylcrotonoyl-CoA-carboxylase] ligase
biotin--[methylmalonyl-CoA-carboxytransferase] ligase
holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)
holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)
NP_000402.3
NP_001229713.1
NP_001229714.1
NP_001339443.1
NP_001339444.1
NP_001339445.1
NP_001339446.1
NP_001339447.1
XP_006724058.1
XP_011527840.1
XP_011527841.1
XP_011527842.1
XP_016883819.1
XP_024307833.1
XP_024307834.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_016193.2 RefSeqGene

    Range
    5001..246770
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000411.7NP_000402.3  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_000402.3

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000704, D23672, D87328, DA334377
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    P50747
    Related
    ENSP00000338387.3, ENST00000336648.8
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  2. NM_001242784.2NP_001229713.1  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_001229713.1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000704, D87328, DB290499
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    P50747
    Related
    ENSP00000382071.1, ENST00000399120.5
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  3. NM_001242785.2NP_001229714.1  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_001229714.1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    P50747
    Related
    ENSP00000479939.1, ENST00000612277.4
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  4. NM_001352514.1NP_001339443.1  biotin--protein ligase isoform 2

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Conserved Domains (3) summary
    pfam02237
    Location:816863
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:614794
    BPL; biotin protein ligase
    cl00020
    Location:349607
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  5. NM_001352515.1NP_001339444.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  6. NM_001352516.1NP_001339445.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  7. NM_001352517.1NP_001339446.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  8. NM_001352518.1NP_001339447.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

RNA

  1. NR_148020.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
  2. NR_148021.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p12 Primary Assembly

    Range
    36748625..36990394 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028330.1XP_016883819.1  biotin--protein ligase isoform X1

    UniProtKB/Swiss-Prot
    P50747
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  2. XM_024452065.1XP_024307833.1  biotin--protein ligase isoform X2

    Conserved Domains (3) summary
    pfam02237
    Location:612659
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:410590
    BPL; biotin protein ligase
    cl00020
    Location:145403
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  3. XM_011529539.3XP_011527841.1  biotin--protein ligase isoform X1

    See identical proteins and their annotated locations for XP_011527841.1

    UniProtKB/Swiss-Prot
    P50747
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  4. XM_011529538.1XP_011527840.1  biotin--protein ligase isoform X1

    See identical proteins and their annotated locations for XP_011527840.1

    UniProtKB/Swiss-Prot
    P50747
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  5. XM_024452066.1XP_024307834.1  biotin--protein ligase isoform X2

    Conserved Domains (3) summary
    pfam02237
    Location:612659
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:410590
    BPL; biotin protein ligase
    cl00020
    Location:145403
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  6. XM_006723995.1XP_006724058.1  biotin--protein ligase isoform X1

    See identical proteins and their annotated locations for XP_006724058.1

    UniProtKB/Swiss-Prot
    P50747
    Conserved Domains (3) summary
    pfam02237
    Location:669716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467647
    BPL; biotin protein ligase
    cl00020
    Location:202460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain
  7. XM_011529540.2XP_011527842.1  biotin--protein ligase isoform X3

    Conserved Domains (1) summary
    cl00020
    Location:349607
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

RNA

  1. XR_001754836.1 RNA Sequence

  2. XR_001754835.1 RNA Sequence

  3. XR_001754840.1 RNA Sequence

  4. XR_001754837.2 RNA Sequence

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