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

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
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: mouse all
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Genomic context

Location:: 7q22.1

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
109.20210514	current	GRCh38.p13 (GCF_000001405.39)	7	NC_000007.14 (101205984..101217581, complement)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (100849265..100860862, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Involvement of LH3 and GLT25D1 for glucosyl-galactosyl-hydroxylation on non-collagen-like domain of FGL1.
Title: Involvement of LH3 and GLT25D1 for glucosyl-galactosyl-hydroxylation on non-collagen-like domain of FGL1.
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.
Knockdown of PLOD3 suppresses the malignant progression of renal cell carcinoma via reducing TWIST1 expression.
Title: Knockdown of PLOD3 suppresses the malignant progression of renal cell carcinoma via reducing TWIST1 expression.
Procollagen-lysine, 2-oxoglutarate 5-dioxygenases 1, 2, and 3 are potential prognostic indicators in patients with clear cell renal cell carcinoma.
Title: Procollagen-lysine, 2-oxoglutarate 5-dioxygenases 1, 2, and 3 are potential prognostic indicators in patients with clear cell renal cell carcinoma.
These data are consistent with pathogenic variants in PLOD3 resulting in a clinically distinct Stickler-like syndrome with vascular complications and variable features of EDS and EB. Early identification of PLOD3 variants would improve monitoring for comorbidities and may avoid serious adverse ocular and vascular outcomes.
Title: Pathogenic variants in <i>PLOD3</i> result in a Stickler syndrome-like connective tissue disorder with vascular complications.
PLOD3 siRNA suppresses radioresistance and chemoresistance by inducing apoptosis and renders PLOD3 as a candidate lung cancer biomarker.
Title: PLOD3 suppression exerts an anti-tumor effect on human lung cancer cells by modulating the PKC-delta signaling pathway.
our results demonstrate the novel function of the collagen-like glycosylation of CCN1 and suggest that lysyl hydroxylase3-mediated glycosylation is important for CCN1 secretion.
Title: Identification and characterization of collagen-like glycosylation and hydroxylation of CCN1.
These results indicate that PLOD3 promotes lung cancer metastasis in a RAS-MAP kinase pathway-independent manner. Therefore, secreted PLOD3 serves as a potent inducer of lung cancer metastasis and a potential therapeutic target to enhance survival in lung cancer.
Title: PLOD3 promotes lung metastasis via regulation of STAT3.
Results indicate that procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD3) may promote the progression of gastric cancer (GC).
Title: PLOD3 is Upregulated in Gastric Cancer and Correlated with Clinicopathologic Characteristics.
VIPAR, with its partner proteins, regulate sorting of lysyl hydroxylase 3 (LH3, also known as PLOD3) into newly identified post-Golgi collagen IV carriers
Title: Regulation of post-Golgi LH3 trafficking is essential for collagen homeostasis.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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
Bone fragility with contractures, arterial rupture, and deafness MedGen: C2676285 OMIM: 612394 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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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

PLOD3_8880 (e-PCR)
- UniSTS:468607

WI-8602 (e-PCR)
- UniSTS:10126

A002S06 (e-PCR)
- UniSTS:57286

Homology

Homologs of the PLOD3 gene: The PLOD3 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, zebrafish, fruit fly, mosquito, C.elegans, and frog.
Orthologs from Annotation Pipeline: 285 organisms have orthologs with human gene PLOD3
Orthologs

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
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	PubMed
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	PubMed
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

Process	Evidence Code	Pubs
involved_in basement membrane assembly	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hormone stimulus	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	PubMed
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	PubMed
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 more info	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

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Preferred Names: multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

Names: lysine hydroxylase 3; lysyl hydroxlase 3; lysyl hydroxylase 3

NP_001075.1

EC 1.14.11.4

EC 2.4.1.50

EC 2.4.1.66

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

NG_012148.1 RefSeqGene

Range

5150..16747

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001084.5 → NP_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

O60568

UniProtKB/TrEMBL

Q9UG85

Related

ENSP00000223127.3, ENST00000223127.8

Conserved Domains (1) summary

smart00702
Location:573 → 736

P4Hc; Prolyl 4-hydroxylase alpha subunit homologues