U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 5351, updated on 27-Nov-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Ehlers Danlos syndrome, kyphoscoliotic type due to Lysyl Hydroxylase 1 deficiency in two children without congenital or early onset kyphoscoliosis. van Dijk FS, et al. Eur J Med Genet, 2017 Oct. PMID 28757364
  2. Characterization of a partial cDNA for lysyl hydroxylase from human skin fibroblasts; lysyl hydroxylase mRNAs are regulated differently by minoxidil derivatives and hydralazine. Yeowell HN, et al. J Invest Dermatol, 1992 Dec. PMID 1335016
  3. A homozygous stop codon in the lysyl hydroxylase gene in two siblings with Ehlers-Danlos syndrome type VI. Hyland J, et al. Nat Genet, 1992 Nov. PMID 1345174
  4. PLOD1 promotes cell growth and aerobic glycolysis by regulating the SOX9/PI3K/Akt/mTOR signaling pathway in gastric cancer. Zhang Y, et al. Front Biosci (Landmark Ed), 2021 Aug 30. PMID 34455762
  5. New mechanistic insights to PLOD1-mediated human vascular disease. Koenig SN, et al. Transl Res, 2022 Jan. PMID 34400365, Free PMC Article

See all (165) 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

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

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

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

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_000302.4 → 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.

Chemical Information
Medical
Molecular Biology Databases
Research Materials
Tools
Miscellaneous