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    PLOD3 procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 [ Homo sapiens (human) ]

    Gene ID: 8985, updated on 7-Apr-2024

    Summary

    Official Symbol
    PLOD3provided by HGNC
    Official Full Name
    procollagen-lysine,2-oxoglutarate 5-dioxygenase 3provided by HGNC
    Primary source
    HGNC:HGNC:9083
    See related
    Ensembl:ENSG00000106397 MIM:603066; AllianceGenome:HGNC:9083
    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
    LH3
    Summary
    The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough 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 VIB have deficiencies in lysyl hydroxylase activity. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in placenta (RPKM 21.7), endometrium (RPKM 12.9) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PLOD3 in Genome Data Viewer
    Location:
    7q22.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (101205984..101217581, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102529447..102541882, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100849265..100860862, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100845469-100846276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100846277-100847083 Neighboring gene diacylglycerol O-acyltransferase 2 like 7, pseudogene Neighboring gene ribosomal protein SA pseudogene 46 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100859968-100860490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100861252-100861793 Neighboring gene zinc finger HIT-type containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:100870334-100870510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100874831-100875752 Neighboring gene claudin 15

    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
    Knockdown of procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 (PLOD3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells 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

    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 EXP
    Inferred from Experiment
    more info
    PubMed 
    enables metal ion binding EXP
    Inferred from Experiment
    more info
    PubMed 
    enables procollagen galactosyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables procollagen galactosyltransferase activity TAS
    Traceable Author Statement
    more info
     
    enables procollagen glucosyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables procollagen glucosyltransferase activity IMP
    Inferred from Mutant Phenotype
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables small molecule binding EXP
    Inferred from Experiment
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in basement membrane assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in collagen fibril organization TAS
    Traceable Author Statement
    more info
     
    involved_in collagen metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endothelial cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epidermis morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hydroxylysine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lung morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural tube development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in peptidyl-lysine hydroxylation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in peptidyl-lysine hydroxylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in peptidyl-lysine hydroxylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein O-linked glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in vasodilation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in collagen-containing extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in endoplasmic reticulum lumen IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular space ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in rough endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     
    located_in trans-Golgi network IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
    Names
    lysine hydroxylase 3
    lysyl hydroxlase 3
    lysyl hydroxylase 3
    NP_001075.1
    XP_054215277.1

    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_012148.1 RefSeqGene

      Range
      5150..16747
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001084.5NP_001075.1  multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 precursor

      See identical proteins and their annotated locations for NP_001075.1

      Status: REVIEWED

      Source sequence(s)
      AC004876, AL049952, BC011674
      Consensus CDS
      CCDS5715.1
      UniProtKB/Swiss-Prot
      B2R6W6, O60568, Q540C3
      UniProtKB/TrEMBL
      B3KQQ3
      Related
      ENSP00000223127.3, ENST00000223127.8
      Conserved Domains (1) summary
      smart00702
      Location:573736
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      101205984..101217581 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      102529447..102541882 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359302.1XP_054215277.1  multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 isoform X1

      UniProtKB/Swiss-Prot
      B2R6W6, O60568, Q540C3