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; 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; BCARD
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
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (101205984..101217581, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (102529447..102541882, complement)
RS_2024_09	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?

PLOD3 facilitated T cell activation in the colorectal tumor microenvironment and liver metastasis by the TNF-alpha/ NF-kappaB pathway.
Title: PLOD3 facilitated T cell activation in the colorectal tumor microenvironment and liver metastasis by the TNF-α/ NF-κB pathway.
Lysyl hydroxylase 3-mediated post-translational modifications are required for proper biosynthesis of collagen alpha1alpha1alpha2(IV).
Title: Lysyl hydroxylase 3-mediated post-translational modifications are required for proper biosynthesis of collagen α1α1α2(IV).
PLOD3 regulates the expression of YAP1 to affect the progression of non-small cell lung cancer via the PKCdelta/CDK1/LIMD1 signaling pathway.
Title: PLOD3 regulates the expression of YAP1 to affect the progression of non-small cell lung cancer via the PKCδ/CDK1/LIMD1 signaling pathway.
Polypeptide N-acetylgalactosaminyltransferase 18 retains in endoplasmic reticulum depending on its luminal regions interacting with ER resident UGGT1, PLOD3 and LPCAT1.
Title: Polypeptide N-acetylgalactosaminyltransferase 18 retains in endoplasmic reticulum depending on its luminal regions interacting with ER resident UGGT1, PLOD3 and LPCAT1.
COLGALT2 is overexpressed in ovarian cancer and interacts with PLOD3.
Title: COLGALT2 is overexpressed in ovarian cancer and interacts with PLOD3.
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.
Integrated Profiling Identifies PLOD3 as a Potential Prognostic and Immunotherapy Relevant Biomarker in Colorectal Cancer.
Title: Integrated Profiling Identifies PLOD3 as a Potential Prognostic and Immunotherapy Relevant Biomarker in Colorectal Cancer.
A Human Pan-Cancer System Analysis of Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3 (PLOD3).
Title: A Human Pan-Cancer System Analysis of Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3 (PLOD3).
PLOD3 Is Associated with Immune Cell Infiltration and Genomic Instability in Colon Adenocarcinoma.
Title: PLOD3 Is Associated with Immune Cell Infiltration and Genomic Instability in Colon Adenocarcinoma.
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.

Submit: New GeneRIF Correction See all GeneRIFs (29)

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

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	IBA Inferred from Biological aspect of Ancestor 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	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
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
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	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
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
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

XP_054215277.1

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

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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

B2R6W6, O60568, Q540C3

UniProtKB/TrEMBL

B3KQQ3

Related

ENSP00000223127.3, ENST00000223127.8

Conserved Domains (1) summary

smart00702
Location:573 → 736

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

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

101205984..101217581 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

102529447..102541882 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B2R6W6, O60568, Q540C3

UniProtKB/TrEMBL

B3KQQ3