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Aliases for PLOD3 Gene

Aliases for PLOD3 Gene

  • Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3 2 3
  • Lysyl Hydroxylase 3 3 4
  • Lysyl Hydroxlase 3 2 3
  • EC 1.14.11.4 4 63
  • LH3 3 4
  • Lysine Hydroxylase 3 3

External Ids for PLOD3 Gene

Previous GeneCards Identifiers for PLOD3 Gene

  • GC07M099332
  • GC07M100395
  • GC07M100409
  • GC07M100442
  • GC07M100635
  • GC07M100849
  • GC07M095442

Summaries for PLOD3 Gene

Entrez Gene Summary for PLOD3 Gene

  • 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]

GeneCards Summary for PLOD3 Gene

PLOD3 (Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3) is a Protein Coding gene. Diseases associated with PLOD3 include lysyl hydroxylase 3 deficiency and connective tissue disorder due to lysyl hydroxylase-3 deficiency. Among its related pathways are Degradation of the extracellular matrix and Other types of O-glycan biosynthesis. GO annotations related to this gene include oxidoreductase activity and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen. An important paralog of this gene is COLGALT1.

UniProtKB/Swiss-Prot for PLOD3 Gene

  • Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links

Gene Wiki entry for PLOD3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLOD3 Gene

Genomics for PLOD3 Gene

Regulatory Elements for PLOD3 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for PLOD3 Gene

Chromosome:
7
Start:
101,205,977 bp from pter
End:
101,218,420 bp from pter
Size:
12,444 bases
Orientation:
Minus strand

Genomic View for PLOD3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PLOD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLOD3 Gene

Proteins for PLOD3 Gene

  • Protein details for PLOD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60568-PLOD3_HUMAN
    Recommended name:
    Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
    Protein Accession:
    O60568
    Secondary Accessions:
    • B2R6W6
    • Q540C3

    Protein attributes for PLOD3 Gene

    Size:
    738 amino acids
    Molecular mass:
    84785 Da
    Cofactor:
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Homodimer

neXtProt entry for PLOD3 Gene

Proteomics data for PLOD3 Gene at MOPED

Post-translational modifications for PLOD3 Gene

  • Glycosylation at Asn 63 and Asn 548
  • Modification sites at PhosphoSitePlus

Other Protein References for PLOD3 Gene

Domains & Families for PLOD3 Gene

Suggested Antigen Peptide Sequences for PLOD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O60568

UniProtKB/Swiss-Prot:

PLOD3_HUMAN :
  • Contains 1 Fe2OG dioxygenase domain.
Domain:
  • Contains 1 Fe2OG dioxygenase domain.
genes like me logo Genes that share domains with PLOD3: view

No data available for Gene Families for PLOD3 Gene

Function for PLOD3 Gene

Molecular function for PLOD3 Gene

GENATLAS Biochemistry:
procollagen-lysine,2-oxoglutarate 5 dioxygenase 3,highly expressed in heart,placenta,pancreas
UniProtKB/Swiss-Prot CatalyticActivity:
L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO(2)
UniProtKB/Swiss-Prot Function:
Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links

Enzyme Numbers (IUBMB) for PLOD3 Gene

Gene Ontology (GO) - Molecular Function for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0008475 procollagen-lysine 5-dioxygenase activity IEA --
GO:0016491 oxidoreductase activity --
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen --
genes like me logo Genes that share ontologies with PLOD3: view
genes like me logo Genes that share phenotypes with PLOD3: view

Animal Models for PLOD3 Gene

MGI Knock Outs for PLOD3:

Animal Model Products

CRISPR Products

miRNA for PLOD3 Gene

miRTarBase miRNAs that target PLOD3

No data available for Transcription Factor Targets and HOMER Transcription for PLOD3 Gene

Localization for PLOD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLOD3 Gene

Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PLOD3 Gene COMPARTMENTS Subcellular localization image for PLOD3 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5

Gene Ontology (GO) - Cellular Components for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum TAS 9724729
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0030867 rough endoplasmic reticulum membrane IEA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PLOD3: view

Pathways & Interactions for PLOD3 Gene

genes like me logo Genes that share pathways with PLOD3: view

Pathways by source for PLOD3 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0001886 endothelial cell morphogenesis IEA --
GO:0006464 cellular protein modification process TAS 9724729
GO:0008104 protein localization IEA --
GO:0021915 neural tube development IEA --
genes like me logo Genes that share ontologies with PLOD3: view

No data available for SIGNOR curated interactions for PLOD3 Gene

Drugs & Compounds for PLOD3 Gene

(6) Drugs for PLOD3 Gene - From: HMDB, DrugBank, and NovoSeek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Succinic acid Approved Nutra Full agonist, Agonist, Target 0
Vitamin C Approved Nutra Target 398,398
L-Lysine Approved Nutra Full agonist, Agonist 0
Uridine 5'-diphosphate Experimental Pharma 0
Uridine diphosphategalactose Experimental Pharma 0

(8) Additional Compounds for PLOD3 Gene - From: HMDB and NovoSeek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-Hydroxylysine
  • (2S,5R)-2,6-diamino-5-hydroxyhexanoate
  • (2S,5R)-2,6-diamino-5-hydroxyhexanoic acid
  • (2S,5R)-5-hydroxylysine
  • (5R)-5-hydroxy-L-lysine
  • 5-Hydroxy-L-lysine
1190-94-9
carbon dioxide
  • Carbon oxide
  • Carbon-12 dioxide
  • Carbonic acid anhydride
  • Carbonic acid gas
  • Carbonic anhydride
124-38-9
Fe2+
  • Armco iron
  • Carbonyl iron
  • FE
  • Ferrovac e
  • Hematite
15438-31-0
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
oxygen
  • Dioxygen
  • Molecular oxygen
  • O2
  • Oxygen
  • Oxygen molecule
7782-44-7
genes like me logo Genes that share compounds with PLOD3: view

Transcripts for PLOD3 Gene

Unigene Clusters for PLOD3 Gene

Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PLOD3 Gene

No ASD Table

Relevant External Links for PLOD3 Gene

GeneLoc Exon Structure for
PLOD3
ECgene alternative splicing isoforms for
PLOD3

Expression for PLOD3 Gene

mRNA expression in normal human tissues for PLOD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLOD3 Gene

This gene is overexpressed in Bone marrow stromal cell (32.2) and Testis (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PLOD3 Gene



SOURCE GeneReport for Unigene cluster for PLOD3 Gene Hs.153357

genes like me logo Genes that share expression patterns with PLOD3: view

Protein tissue co-expression partners for PLOD3 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PLOD3 Gene

Orthologs for PLOD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLOD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLOD3 36
  • 100 (a)
OneToOne
PLOD3 35
  • 99.55 (n)
  • 99.59 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia PLOD3 36
  • 77 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Plod3 36
  • 91 (a)
OneToOne
Plod3 16
Plod3 35
  • 85.77 (n)
  • 91.6 (a)
oppossum
(Monodelphis domestica)
Mammalia PLOD3 36
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PLOD3 36
  • 94 (a)
OneToOne
PLOD3 35
  • 89.51 (n)
  • 95.13 (a)
cow
(Bos Taurus)
Mammalia PLOD3 36
  • 92 (a)
OneToOne
PLOD3 35
  • 89.86 (n)
  • 94.67 (a)
rat
(Rattus norvegicus)
Mammalia Plod3 35
  • 85.55 (n)
  • 91.33 (a)
lizard
(Anolis carolinensis)
Reptilia PLOD3 36
  • 73 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia plod-prov 35
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.1520 35
plod3 35
  • 69.04 (n)
  • 69.6 (a)
zebrafish
(Danio rerio)
Actinopterygii PLOD3 (2 of 2) 36
  • 65 (a)
OneToMany
plod3 36
  • 65 (a)
OneToMany
wufa10a05 35
wu:fb72h05 35
  • 67.28 (n)
  • 66.34 (a)
fruit fly
(Drosophila melanogaster)
Insecta Plod 36
  • 45 (a)
OneToMany
Plod 35
  • 55.14 (n)
  • 47.03 (a)
CG6199 37
  • 46 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001507 35
  • 57.83 (n)
  • 47.58 (a)
worm
(Caenorhabditis elegans)
Secernentea let-268 36
  • 46 (a)
OneToMany
let-268 35
  • 51.63 (n)
  • 47.69 (a)
let-268 37
  • 46 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 36
  • 50 (a)
OneToMany
Species with no ortholog for PLOD3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PLOD3 Gene

ENSEMBL:
Gene Tree for PLOD3 (if available)
TreeFam:
Gene Tree for PLOD3 (if available)

Paralogs for PLOD3 Gene

Paralogs for PLOD3 Gene

(5) SIMAP similar genes for PLOD3 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with PLOD3: view

Variants for PLOD3 Gene

Sequence variations from dbSNP and Humsavar for PLOD3 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type MAF
rs917112 -- 101,213,710(+) TTTTT(C/T)ATGCT intron-variant
rs1134907 - 101,212,865(-) AGGAC(C/T)GGAGG reference, missense
rs1468358 -- 101,209,892(+) CAATA(C/T)ACAGG intron-variant
rs1546840 -- 101,212,596(-) CCCCG(C/T)TTCCT reference, synonymous-codon
rs1546841 -- 101,212,542(-) CTTTT(C/G/T)CTGCA reference, missense, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for PLOD3 Gene

Variant ID Type Subtype PubMed ID
esv2734888 CNV Deletion 23290073
nsv831075 CNV Loss 17160897
esv2422376 CNV Duplication 17116639
dgv7409n71 CNV Loss 21882294
esv2752134 CNV Gain 17911159
nsv831076 CNV Loss 17160897
dgv7410n71 CNV Loss 21882294
esv2422326 CNV Duplication 17116639

Variation tolerance for PLOD3 Gene

Residual Variation Intolerance Score: 90.52% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.90; 67.67% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PLOD3 Gene

HapMap Linkage Disequilibrium report
PLOD3
Human Gene Mutation Database (HGMD)
PLOD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLOD3 Gene

Disorders for PLOD3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PLOD3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
lysyl hydroxylase 3 deficiency
  • bone fragility with contractures, arterial rupture, and deafness
connective tissue disorder due to lysyl hydroxylase-3 deficiency
  • bone fragility-contractures-arterial rupture-deafness syndrome
ullrich congenital muscular dystrophy 1
  • ullrich congenital muscular dystrophy
- elite association
Search PLOD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PLOD3_HUMAN
  • Lysyl hydroxylase 3 deficiency (LH3 deficiency) [MIM:612394]: Connective tissue disorder. The syndrome is characterized by congenital malformations severely affecting many tissues and organs and revealing features of several collagen disorders, most of them involving COL2A1 (type II collagen). The findings suggest that the failure of lysyl hydroxylation and hydroxylysyl carbohydrate addition, which affects many collagens, is the molecular basis of this syndrome. {ECO:0000269 PubMed:18834968}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PLOD3

Genetic Association Database (GAD)
PLOD3
Human Genome Epidemiology (HuGE) Navigator
PLOD3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PLOD3
genes like me logo Genes that share disorders with PLOD3: view

No data available for Genatlas for PLOD3 Gene

Publications for PLOD3 Gene

  1. Cloning and characterization of a third human lysyl hydroxylase isoform. (PMID: 9724729) Passoja K. … Kivirikko K.I. (Proc. Natl. Acad. Sci. U.S.A. 1998) 2 23 67
  2. Primary structure, tissue distribution, and chromosomal localization of a novel isoform of lysyl hydroxylase (lysyl hydroxylase 3). (PMID: 9582318) Valtavaara M. … Myllylae R. (J. Biol. Chem. 1998) 2 23 67
  3. The human collagen beta(1-O)galactosyltransferase, GLT25D1, is a soluble endoplasmic reticulum localized protein. (PMID: 20470363) Liefhebber J.M. … van Leeuwen H.C. (BMC Cell Biol. 2010) 23 67
  4. Differential effects of bone morphogenetic protein-2 and transforming growth factor-beta1 on gene expression of collagen-modifying enzymes in human adipose tissue-derived mesenchymal stem cells. (PMID: 19231972) Knippenberg M. … Klein-Nulend J. (Tissue Eng Part A 2009) 23 67
  5. The glycosyltransferase activities of lysyl hydroxylase 3 (LH3) in the extracellular space are important for cell growth and viability. (PMID: 18298658) Wang C. … MyllylAo R. (J. Cell. Mol. Med. 2009) 23 67

Products for PLOD3 Gene

Sources for PLOD3 Gene

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