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PLPBP pyridoxal phosphate binding protein [ Homo sapiens (human) ]

Gene ID: 11212, updated on 5-Mar-2024

Summary

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Official Symbol
PLPBPprovided by HGNC
Official Full Name
pyridoxal phosphate binding proteinprovided by HGNC
Primary source
HGNC:HGNC:9457
See related
Ensembl:ENSG00000147471 MIM:604436; AllianceGenome:HGNC:9457
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
EPEO1; PROSC; EPVB6D
Summary
This gene encodes a pyridoxal 5'-phosphate binding protein involved in the homeostatic regulation of intracellular pyridoxal 5'-phosphate. This gene has a tumor suppressive effect on hepatocellular carcinoma and other solid tumors of epithelial origin. Naturally occurring mutations in this gene are associated with a pyridoxine-dependent epilepsy. [provided by RefSeq, Mar 2017]
Expression
Ubiquitous expression in kidney (RPKM 12.8), colon (RPKM 10.6) and 25 other tissues See more
Orthologs
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Genomic context

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See PLPBP in Genome Data Viewer
Location:
8p11.23
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (37762546..37779768)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38038942..38056164)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (37620064..37637286)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27228 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:37594714-37595506 Neighboring gene ER lipid raft associated 2 Neighboring gene STING1 ER exit protein 1 pseudogene Neighboring gene uncharacterized LOC124901934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27229 Neighboring gene Sharpr-MPRA regulatory region 13802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27231 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:37638448-37639647 Neighboring gene uncharacterized LOC105379381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37645266-37645774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37652831-37653396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37653397-37653962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19109 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27233 Neighboring gene adhesion G protein-coupled receptor A2 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37667034-37667256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37671601-37672366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37672367-37673132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37673133-37673898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37679325-37679898 Neighboring gene VISTA enhancer hs1665 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37685664-37686632 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37696873-37697010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37699228-37699928 Neighboring gene BRF2 RNA polymerase III transcription initiation factor subunit

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. PLPBP Deficiency. Adam MP, et al. , 1993. PMID 36795901
  2. Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B(6) -dependent epilepsy. Tremiño L, et al. FEBS Lett, 2017 Oct. PMID 28914444
  3. Confirmation of mutations in PROSC as a novel cause of vitamin B ((6)) -dependent epilepsy. Plecko B, et al. J Med Genet, 2017 Dec. PMID 28391250
  4. Mutations in PROSC Disrupt Cellular Pyridoxal Phosphate Homeostasis and Cause Vitamin-B(6)-Dependent Epilepsy. Darin N, et al. Am J Hum Genet, 2016 Dec 1. PMID 27912044, Free PMC Article
  5. Integrative genomic identification of genes on 8p associated with hepatocellular carcinoma progression and patient survival. Roessler S, et al. Gastroenterology, 2012 Apr. PMID 22202459, Free PMC Article

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Maintenance of cellular vitamin B6 levels and mitochondrial oxidative function depend on pyridoxal 5'-phosphate homeostasis protein.
    Title: Maintenance of cellular vitamin B(6) levels and mitochondrial oxidative function depend on pyridoxal 5'-phosphate homeostasis protein.
  2. We therefore confirm PROSC as a novel gene for vitamin-B6-dependent epilepsy and delineate a non-specific plasma vitamin B6 profile under pyridoxine treatment.
    Title: Confirmation of mutations in PROSC as a novel cause of vitamin B ((6)) -dependent epilepsy.
  3. Exploiting the universality of the Synechococcus elongatus COG0325 (PiPY) functions, it has been used in site-directed mutagenesis studies to shed light on disease causation by epilepsy-associated mutations in the human COG0325 gene PROSC.
    Title: Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B(6) -dependent epilepsy.
  4. studies suggest that PROSC is involved in intracellular homeostatic regulation of pyridoxal 5'-phosphate, supplying this cofactor to apoenzymes while minimizing any toxic side reactions
    Title: Mutations in PROSC Disrupt Cellular Pyridoxal Phosphate Homeostasis and Cause Vitamin-B(6)-Dependent Epilepsy.
Submit: New GeneRIF Correction

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

Associated conditions

Description Tests
Epilepsy, early-onset, vitamin B6-dependent
MedGen: C4310632 OMIM: 617290 GeneReviews: PLPBP Deficiency
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EBI GWAS Catalog

Description
Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11861

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables pyridoxal phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
located_in cytoplasm NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in intracellular anatomical structure IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
pyridoxal phosphate homeostasis protein
Names
PLP homeostasis protein
proline synthase co-transcribed bacterial homolog protein
proline synthetase co-transcribed bacterial homolog protein

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.

Genomic

  1. NG_053030.1 RefSeqGene

    Range
    5893..23016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001349346.2 → NP_001336275.1  pyridoxal phosphate homeostasis protein isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC138356, AL136616, BC012334, BM984988
    UniProtKB/TrEMBL
    A8K520
    Conserved Domains (1) summary
    cd06822
    Location:17 → 258
    PLPDE_III_YBL036c_euk; Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins

  2. NM_001349347.2 → NP_001336276.1  pyridoxal phosphate homeostasis protein isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC138356, BM984988
    UniProtKB/TrEMBL
    A8K520
    Conserved Domains (1) summary
    cd06822
    Location:17 → 246
    PLPDE_III_YBL036c_euk; Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins

  3. NM_001349348.2 → NP_001336277.1  pyridoxal phosphate homeostasis protein isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses a downstream start codon compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to variant 1.
    Source sequence(s)
    AC138356, BM984988
    UniProtKB/TrEMBL
    B3KMP6
    Conserved Domains (1) summary
    cd06822
    Location:1 → 196
    PLPDE_III_YBL036c_euk; Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins

  4. NM_001349349.1 → NP_001336278.1  pyridoxal phosphate homeostasis protein isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks a portion of the 3' coding region and differs in the 3' UTR compared to variant 1. The encoded protein has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AA463397, AC138356
    Conserved Domains (1) summary
    cl00261
    Location:52 → 142
    PLPDE_III; Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes

  5. NM_007198.4 → NP_009129.1  pyridoxal phosphate homeostasis protein isoform 2

    See identical proteins and their annotated locations for NP_009129.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AL136616, BC012334, BM984988
    Consensus CDS
    CCDS6096.1
    UniProtKB/Swiss-Prot
    O94903, Q6FI94
    UniProtKB/TrEMBL
    A8K520
    Related
    ENSP00000333551.3, ENST00000328195.8
    Conserved Domains (1) summary
    cd06822
    Location:17 → 248
    PLPDE_III_YBL036c_euk; Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    37762546..37779768
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    38038942..38056164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O94903.1 GenPept UniProtKB/Swiss-Prot:O94903

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