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    PLOD2 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 [ Homo sapiens (human) ]

    Gene ID: 5352, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PLOD2provided by HGNC
    Official Full Name
    procollagen-lysine,2-oxoglutarate 5-dioxygenase 2provided by HGNC
    Primary source
    HGNC:HGNC:9082
    See related
    Ensembl:ENSG00000152952 MIM:601865; AllianceGenome:HGNC:9082
    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
    LH2; TLH; BRKS2
    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. Mutations in the coding region of this gene are associated with Bruck syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in thyroid (RPKM 48.4), fat (RPKM 35.4) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PLOD2 in Genome Data Viewer
    Location:
    3q24
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (146069440..146161184, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (148824992..148916735, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (145787227..145878971, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986138 Neighboring gene lncRNA sorafenib resistance in renal cell carcinoma associated Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:145815129-145815678 Neighboring gene MPRA-validated peak4856 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:145852057-145852829 Neighboring gene uncharacterized LOC105374145 Neighboring gene phospholipid scramblase 4

    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. Phenotypic and molecular characterization of Bruck syndrome (osteogenesis imperfecta with contractures of the large joints) caused by a recessive mutation in PLOD2. Ha-Vinh R, et al. Am J Med Genet A, 2004 Dec 1. PMID 15523624
    2. Procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 promotes hypoxia-induced glioma migration and invasion. Xu Y, et al. Oncotarget, 2017 Apr 4. PMID 28423580, Free PMC Article
    3. Novel Mutations in PLOD2 Cause Rare Bruck Syndrome. Lv F, et al. Calcif Tissue Int, 2018 Mar. PMID 29177700
    4. Identification and Validation of PLOD2 as an Adverse Prognostic Biomarker for Oral Squamous Cell Carcinoma. Sun Y, et al. Biomolecules, 2021 Dec 7. PMID 34944486, Free PMC Article
    5. Identification of PLOD2 as telopeptide lysyl hydroxylase, an important enzyme in fibrosis. van der Slot AJ, et al. J Biol Chem, 2003 Oct 17. PMID 12881513

    See all (141) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 promotes collagen cross-linking and ECM stiffening to induce liver fibrosis.
      Title: Procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 promotes collagen cross-linking and ECM stiffening to induce liver fibrosis.
    2. METTL3 facilitates renal cell carcinoma progression by PLOD2 m[6]A-methylation under prolonged hypoxia.
      Title: METTL3 facilitates renal cell carcinoma progression by PLOD2 m(6)A-methylation under prolonged hypoxia.
    3. Hypoxia-induced PLOD2 promotes clear cell renal cell carcinoma progression via modulating EGFR-dependent AKT pathway activation.
      Title: Hypoxia-induced PLOD2 promotes clear cell renal cell carcinoma progression via modulating EGFR-dependent AKT pathway activation.
    4. Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4.
      Title: Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4.
    5. The PLOD2/succinate axis regulates the epithelial-mesenchymal plasticity and cancer cell stemness.
      Title: The PLOD2/succinate axis regulates the epithelial-mesenchymal plasticity and cancer cell stemness.
    6. Apelin promotes osteosarcoma metastasis by upregulating PLOD2 expression via the Hippo signaling pathway and hsa_circ_0000004/miR-1303 axis.
      Title: Apelin promotes osteosarcoma metastasis by upregulating PLOD2 expression via the Hippo signaling pathway and hsa_circ_0000004/miR-1303 axis.
    7. circRNA PLOD2 promotes tumorigenesis and Warburg effect in colon cancer by the miR-513a-5p/SIX1/LDHA axis.
      Title: circRNA PLOD2 promotes tumorigenesis and Warburg effect in colon cancer by the miR-513a-5p/SIX1/LDHA axis.
    8. Clinicopathological significances of PLOD2, epithelial-mesenchymal transition markers, and cancer stem cells in patients with esophageal squamous cell carcinoma.
      Title: Clinicopathological significances of PLOD2, epithelial-mesenchymal transition markers, and cancer stem cells in patients with esophageal squamous cell carcinoma.
    9. PLOD2 Is a Prognostic Marker in Glioblastoma That Modulates the Immune Microenvironment and Tumor Progression.
      Title: PLOD2 Is a Prognostic Marker in Glioblastoma That Modulates the Immune Microenvironment and Tumor Progression.
    10. Bruck syndrome in 13 new patients: Identification of five novel FKBP10 and PLOD2 variants and further expansion of the phenotypic spectrum.
      Title: Bruck syndrome in 13 new patients: Identification of five novel FKBP10 and PLOD2 variants and further expansion of the phenotypic spectrum.
    Submit: New GeneRIF Correction See all GeneRIFs (63)

    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
    Bruck syndrome 2
    MedGen: C1836602 OMIM: 609220 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    integrase gag-pol HIV-1 IN is identified to have a physical interaction with procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2) 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

    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in hydroxylysine biosynthetic process IDA
    Inferred from Direct Assay
    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 protein modification process TAS
    Traceable Author Statement
    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
    		  
    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 2
    Names
    lysine hydroxylase 2
    lysyl hydroxlase 2
    lysyl hydroxylase 2
    procollagen lysyl hydroxylase 2
    procollagen-lysine 5-dioxygenase
    telopeptide lysyl hydroxylase
    telopeptidyl lysyl hydroxylase
    NP_000926.2
    NP_891988.1
    XP_016862114.1
    XP_047304275.1
    XP_047304276.1
    XP_054202843.1
    XP_054202844.1
    XP_054202845.1

    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_009251.1 RefSeqGene

      Range
      5001..97056
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000935.3 → NP_000926.2  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform 2 precursor

      See identical proteins and their annotated locations for NP_000926.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal in-frame coding exon compared to transcript variant 1, resulting in a shorter isoform (2, also known as LH2a) missing a 21 aa protein segment compared to isoform 1.
      Source sequence(s)
      AB209879, AC107021, BC037169, BM724669
      Consensus CDS
      CCDS3131.1
      UniProtKB/Swiss-Prot
      B3KWS3, O00469, Q59ED2, Q8N170
      UniProtKB/TrEMBL
      A0A9L9PX47
      Related
      ENSP00000353170.3, ENST00000360060.7
      Conserved Domains (2) summary
      smart00702
      Location:572 → 735
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
      COG0463
      Location:349 → 574
      WcaA; Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]

    2. NM_182943.3 → NP_891988.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_891988.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1, also known as LH2b).
      Source sequence(s)
      AC107021, BC037169, BM724669
      Consensus CDS
      CCDS3132.1
      UniProtKB/TrEMBL
      E7ETU9
      Related
      ENSP00000282903.5, ENST00000282903.10
      Conserved Domains (1) summary
      smart00702
      Location:593 → 756
      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      146069440..146161184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448319.1 → XP_047304275.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1

    2. XM_017006625.3 → XP_016862114.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1

      UniProtKB/TrEMBL
      E7ETU9
      Related
      ENST00000703519.1
      Conserved Domains (1) summary
      smart00702
      Location:501 → 664
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    3. XM_047448320.1 → XP_047304276.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X2

      UniProtKB/TrEMBL
      A0A994J6S5
      Related
      ENSP00000515351.1, ENST00000703520.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      148824992..148916735 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346869.1 → XP_054202844.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1

    2. XM_054346868.1 → XP_054202843.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1

    3. XM_054346870.1 → XP_054202845.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X2

      UniProtKB/TrEMBL
      A0A994J6S5
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O00469.2 GenPept UniProtKB/Swiss-Prot:O00469

    Gene LinkOut

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