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Aliases for PLOD3 Gene

Aliases for PLOD3 Gene

  • Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3 2 3
  • LH3 3 4 6
  • Lysyl Hydroxylase 3 3 4
  • Lysyl Hydroxlase 3 2 3
  • EC 1.14.11.4 4 64
  • Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 3
  • Lysine Hydroxylase 3 3

External Ids for PLOD3 Gene

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 iron ion binding and procollagen-lysine 5-dioxygenase activity. 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

Genomic Location for PLOD3 Gene

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

Regulatory Elements 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

  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn63 and Asn548

Other Protein References for PLOD3 Gene

Domains for PLOD3 Gene

UniProtKB/Swiss-Prot:

PLOD3_HUMAN
Domain:
  • Contains 1 Fe2OG dioxygenase domain.:
    • O60568
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:

miRNA for PLOD3 Gene

miRTarBase miRNAs that target PLOD3

No data available for Transcription Factor Targeting 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 2
cytosol 1
golgi apparatus 1
lysosome 1
mitochondrion 1
nucleus 1
peroxisome 1
plasma membrane 1

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 for PLOD3 Gene

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

Pathways by source for PLOD3 Gene

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

Compounds for PLOD3 Gene

(9) HMDB Compounds for PLOD3 Gene

Compound Synonyms Cas Number PubMed IDs
5-Hydroxylysine
  • (2S,5R)-2,6-diamino-5-hydroxyhexanoic acid
1190-94-9
Ascorbic acid
  • (+)-ascorbate
50-81-7
Carbon dioxide
  • Carbon oxide
124-38-9
Iron
  • Armco iron
7439-89-6
L-Lysine
  • (+)-S-Lysine
56-87-1

(2) Drugbank Compounds for PLOD3 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Succinic acid
  • 1,2-Ethanedicarboxylic acid
110-15-6 target
Vitamin C
  • Ascorbate
50-81-7 target

(2) Novoseek inferred chemical compound relationships for PLOD3 Gene

Compound -log(P) Hits PubMed IDs
pyridinoline 59.9 1
lysine 58.8 3
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

Integrated Proteomics: protein expression 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 expressions with PLOD3: view

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
  • 99.55 (n)
  • 99.59 (a)
PLOD3 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PLOD3 36
  • 89.86 (n)
  • 94.67 (a)
PLOD3 37
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PLOD3 36
  • 89.51 (n)
  • 95.13 (a)
PLOD3 37
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Plod3 36
  • 85.77 (n)
  • 91.6 (a)
Plod3 16
Plod3 37
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PLOD3 37
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PLOD3 37
  • 77 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Plod3 36
  • 85.55 (n)
  • 91.33 (a)
lizard
(Anolis carolinensis)
Reptilia PLOD3 37
  • 73 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia plod-prov 36
tropical clawed frog
(Silurana tropicalis)
Amphibia plod3 36
  • 69.04 (n)
  • 69.6 (a)
Str.1520 36
zebrafish
(Danio rerio)
Actinopterygii plod3 37
  • 65 (a)
OneToMany
PLOD3 (2 of 2) 37
  • 65 (a)
OneToMany
wu:fb72h05 36
  • 67.28 (n)
  • 66.34 (a)
wufa10a05 36
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001507 36
  • 57.83 (n)
  • 47.58 (a)
fruit fly
(Drosophila melanogaster)
Insecta Plod 36
  • 55.14 (n)
  • 47.03 (a)
Plod 37
  • 45 (a)
OneToMany
CG6199 38
  • 46 (a)
worm
(Caenorhabditis elegans)
Secernentea let-268 36
  • 51.63 (n)
  • 47.69 (a)
let-268 37
  • 46 (a)
OneToMany
let-268 38
  • 46 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 37
  • 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

Selected 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/T)CTGCA reference, 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

Relevant External Links for PLOD3 Gene

HapMap Linkage Disequilibrium report
PLOD3
Human Gene Mutation Database (HGMD)
PLOD3
Locus Specific Mutation Databases (LSDB)
PLOD3

Disorders for PLOD3 Gene

(1) OMIM Diseases for PLOD3 Gene (603066)

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.

(2) University of Copenhagen DISEASES for PLOD3 Gene

(1) Novoseek inferred disease relationships for PLOD3 Gene

Disease -log(P) Hits PubMed IDs
ehlers-danlos syndrome 70.4 1

Relevant External Links for PLOD3

Genetic Association Database (GAD)
PLOD3
Human Genome Epidemiology (HuGE) Navigator
PLOD3
genes like me logo Genes that share disorders with PLOD3: view

Publications for PLOD3 Gene

  1. 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 3 4 23
  2. 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 3 4 23
  3. Complete exon-intron organization of the gene for human lysyl hydroxylase 3 (LH3). (PMID: 10686427) Rautavuoma K. … Kivirikko K.I. (Matrix Biol. 2000) 3 4 23
  4. A connective tissue disorder caused by mutations of the lysyl hydroxylase 3 gene. (PMID: 18834968) Salo A.M. … Myllylae R. (Am. J. Hum. Genet. 2008) 3 4 23
  5. The third activity for lysyl hydroxylase 3: galactosylation of hydroxylysyl residues in collagens in vitro. (PMID: 12475640) Wang C. … MyllylAo R. (Matrix Biol. 2002) 3 23

Products for PLOD3 Gene

Sources for PLOD3 Gene

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