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

    Gene ID: 5351, updated on 28-Oct-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See PLOD1 in Genome Data Viewer
    Location:
    1p36.22
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (11934717..11975537)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (11478837..11519656)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 181 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:11977020-11977175 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 ReSE screen-validated silencer GRCh37_chr1:12023296-12023497 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:12026474-12026974 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:12026975-12027475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 183 Neighboring gene mitofusin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12060855-12061784 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:12065587-12065864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 185 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12067964-12068629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12068630-12069294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 186 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

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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. Intracellular enzymes of collagen biosynthesis in human platelets. Anttinen H, et al. Blood, 1977 Jul. PMID 194639
    2. Retrieval-independent localization of lysyl hydroxylase in the endoplasmic reticulum via a peptide fold in its iron-binding domain. Suokas M, et al. Biochem J, 2003 Mar 15. PMID 12452796, Free PMC Article
    3. PLOD1 Is a Prognostic Biomarker and Mediator of Proliferation and Invasion in Osteosarcoma. Jiang H, et al. Biomed Res Int, 2020. PMID 33134376, Free PMC Article
    4. A novel mutation in the lysyl hydroxylase 1 gene causes decreased lysyl hydroxylase activity in an Ehlers-Danlos VIA patient. Walker LC, et al. J Invest Dermatol, 2005 May. PMID 15854030
    5. Mutation analysis of the PLOD1 gene: an efficient multistep approach to the molecular diagnosis of the kyphoscoliotic type of Ehlers-Danlos syndrome (EDS VIA). Giunta C, et al. Mol Genet Metab, 2005 Sep-Oct. PMID 15979919

    See all (164) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. miR-449a ameliorates acute rejection after liver transplantation via targeting procollagen-lysine1,2-oxoglutarate5-dioxygenase 1 in macrophages.
      Title: miR-449a ameliorates acute rejection after liver transplantation via targeting procollagen-lysine1,2-oxoglutarate5-dioxygenase 1 in macrophages.
    2. P3H4 and PLOD1 expression associates with poor prognosis in bladder cancer.
      Title: P3H4 and PLOD1 expression associates with poor prognosis in bladder cancer.
    3. PLOD1 acts as a tumor promoter in glioma via activation of the HSF1 signaling pathway.
      Title: PLOD1 acts as a tumor promoter in glioma via activation of the HSF1 signaling pathway.
    4. PLOD1 promotes cell growth and aerobic glycolysis by regulating the SOX9/PI3K/Akt/mTOR signaling pathway in gastric cancer.
      Title: PLOD1 promotes cell growth and aerobic glycolysis by regulating the SOX9/PI3K/Akt/mTOR signaling pathway in gastric cancer.
    5. Characterization of a cancer-associated Epstein-Barr virus EBNA1 variant reveals a novel interaction with PLOD1 and PLOD3.
      Title: Characterization of a cancer-associated Epstein-Barr virus EBNA1 variant reveals a novel interaction with PLOD1 and PLOD3.
    6. New mechanistic insights to PLOD1-mediated human vascular disease.
      Title: New mechanistic insights to PLOD1-mediated human vascular disease.
    7. A floppy infant without lingual frenulum and kyphoscoliosis: Ehlers Danlos syndrome case report.
      Title: A floppy infant without lingual frenulum and kyphoscoliosis: Ehlers Danlos syndrome case report.
    8. PLODs are overexpressed in ovarian cancer and are associated with gap junctions via connexin 43.
      Title: PLODs are overexpressed in ovarian cancer and are associated with gap junctions via connexin 43.
    9. Hypoxia-induced PLOD1 overexpression contributes to the malignant phenotype of glioblastoma via NF-kappaB signaling.
      Title: Hypoxia-induced PLOD1 overexpression contributes to the malignant phenotype of glioblastoma via NF-κB signaling.
    10. PLOD1 Is a Prognostic Biomarker and Mediator of Proliferation and Invasion in Osteosarcoma.
      Title: PLOD1 Is a Prognostic Biomarker and Mediator of Proliferation and Invasion in Osteosarcoma.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    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

    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

    HIV-1 interactions

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    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

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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

    • 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
    		  
    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 collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in epidermis development IMP
    Inferred from Mutant Phenotype
    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
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in rough endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    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)

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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_008159.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_000302.4 → NP_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
      B2R5M9
      Related
      ENSP00000196061.4, ENST00000196061.5
      Conserved Domains (1) summary
      smart00702
      Location:562 → 725
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    2. NM_001316320.2 → NP_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/TrEMBL
      B2R5M9
      Conserved Domains (1) summary
      smart00702
      Location:609 → 772
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    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_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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q02809.2 GenPept UniProtKB/Swiss-Prot:Q02809

    Gene LinkOut

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

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