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

Gene ID: 5352, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (146069440..146161184, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (148824992..148916735, complement)
105.20220307 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
  • 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. The PLOD2/succinate axis regulates the epithelial-mesenchymal plasticity and cancer cell stemness. Tong Y, et al. Proc Natl Acad Sci U S A, 2023 May 16. PMID 37155842, Free PMC Article
  2. circRNA PLOD2 promotes tumorigenesis and Warburg effect in colon cancer by the miR-513a-5p/SIX1/LDHA axis. Li Y, et al. Cell Cycle, 2022 Dec. PMID 36071678, Free PMC Article
  3. Clinicopathological significances of PLOD2, epithelial-mesenchymal transition markers, and cancer stem cells in patients with esophageal squamous cell carcinoma. Gong X, et al. Medicine (Baltimore), 2022 Aug 26. PMID 36042592, Free PMC Article
  4. PLOD2 Is a Prognostic Marker in Glioblastoma That Modulates the Immune Microenvironment and Tumor Progression. Kreße N, et al. Int J Mol Sci, 2022 May 27. PMID 35682709, Free PMC Article
  5. 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

See all (132) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Identification and Validation of PLOD2 as an Adverse Prognostic Biomarker for Oral Squamous Cell Carcinoma.
    Title: Identification and Validation of PLOD2 as an Adverse Prognostic Biomarker for Oral Squamous Cell Carcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (62)

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
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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 hydroxylysine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
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 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 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 
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_2023_10

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

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