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    PLOD1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 [ Homo sapiens (human) ]

    Gene ID: 5351, updated on 7-Sep-2023

    Summary

    Official Symbol
    PLOD1provided by HGNC
    Official Full Name
    procollagen-lysine,2-oxoglutarate 5-dioxygenase 1provided by HGNC
    Primary source
    HGNC:HGNC:9081
    See related
    Ensembl:ENSG00000083444 MIM:153454; AllianceGenome:HGNC:9081
    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
    LH; LH1; LLH; EDS6; PLOD; EDSKCL1
    Summary
    Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VI have deficiencies in lysyl hydroxylase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
    Expression
    Ubiquitous expression in placenta (RPKM 47.0), endometrium (RPKM 37.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PLOD1 in Genome Data Viewer
    Location:
    1p36.22
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (11934717..11975537)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (11478837..11519656)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11994774..12035594)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903843 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11985428-11986090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11986091-11986754 Neighboring gene KIAA2013 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11993557-11994482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11994483-11995406 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:11998825-12000024 Neighboring gene Sharpr-MPRA regulatory region 8260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12005168-12005843 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:12026474-12026974 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:12026975-12027475 Neighboring gene mitofusin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12060855-12061784 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12067964-12068629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12068630-12069294 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:12079342-12080212 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12080213-12081083 Neighboring gene migration and invasion inhibitory protein Neighboring gene microRNA 6729

    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 Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 NL4-3 replication is restricted by PLOD1 as enhanced replication was discovered when PLOD1 is deleted through CRISPR/Cas9 genome editing in primary CD4+ T cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with PLOD1; predicted interaction to be within the endoplasmic reticulum PubMed
    Rev rev HIV-1 Rev interacting protein, procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa. The interaction of Rev with PLOD1 is increased by RRE PubMed
    integrase gag-pol HIV-1 IN is identified to have a physical interaction with procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ42041

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-ascorbic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    NOT enables procollagen glucosyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables procollagen-lysine 5-dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables procollagen-lysine 5-dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables procollagen-lysine 5-dioxygenase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables procollagen-lysine 5-dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in epidermis development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in peptidyl-lysine hydroxylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in peptidyl-lysine hydroxylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in peptidyl-lysine hydroxylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    NOT involved_in protein O-linked glycosylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of catalytic complex IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in rough endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
    Names
    lysine hydroxylase
    lysyl hydroxlase 1
    procollagen lysyl hydroxylase 1
    procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1
    NP_000293.2
    NP_001303249.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008159.1 RefSeqGene

      Range
      5029..45849
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000302.4NP_000293.2  procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_000293.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      BQ447373, DC334246, M98252
      Consensus CDS
      CCDS142.1
      UniProtKB/Swiss-Prot
      B4DR87, Q02809, Q96AV9, Q9H132
      UniProtKB/TrEMBL
      A0A024R4H0, B2R5M9
      Related
      ENSP00000196061.4, ENST00000196061.5
      Conserved Domains (1) summary
      smart00702
      Location:562725
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
    2. NM_001316320.2NP_001303249.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AI347587, AK299150, BM991136, DC334246
      UniProtKB/Swiss-Prot
      Q02809
      UniProtKB/TrEMBL
      B2R5M9
      Conserved Domains (1) summary
      smart00702
      Location:609772
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      11934717..11975537
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      11478837..11519656
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)