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Aliases for PLOD2 Gene

Aliases for PLOD2 Gene

  • Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 2 2 3
  • Lysyl Hydroxylase 2 3 4
  • Lysyl Hydroxlase 2 2 3
  • EC 1.14.11.4 4 63
  • LH2 3 4
  • Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase (Lysine Hydroxylase) 2 2
  • Telopeptide Lysyl Hydroxylase 3
  • Lysine Hydroxylase 2 3
  • BRKS2 3
  • TLH 3

External Ids for PLOD2 Gene

Previous GeneCards Identifiers for PLOD2 Gene

  • GC03M142579
  • GC03M146646
  • GC03M147068
  • GC03M147109
  • GC03M147110
  • GC03M147269
  • GC03M145787
  • GC03M143165

Summaries for PLOD2 Gene

Entrez Gene Summary for PLOD2 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. 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]

GeneCards Summary for PLOD2 Gene

PLOD2 (Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 2) is a Protein Coding gene. Diseases associated with PLOD2 include bruck syndrome and bruck syndrome 2. Among its related pathways are Degradation of the extracellular matrix and Collagen biosynthesis and modifying enzymes. 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 PLOD2 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

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLOD2 Gene

Genomics for PLOD2 Gene

Regulatory Elements for PLOD2 Gene

Epigenetics Products

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

Genomic Location for PLOD2 Gene

Chromosome:
3
Start:
146,069,436 bp from pter
End:
146,163,653 bp from pter
Size:
94,218 bases
Orientation:
Minus strand

Genomic View for PLOD2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PLOD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLOD2 Gene

Proteins for PLOD2 Gene

  • Protein details for PLOD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00469-PLOD2_HUMAN
    Recommended name:
    Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
    Protein Accession:
    O00469
    Secondary Accessions:
    • B3KWS3
    • Q59ED2
    • Q8N170

    Protein attributes for PLOD2 Gene

    Size:
    737 amino acids
    Molecular mass:
    84686 Da
    Cofactor:
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Homodimer.
    SequenceCaution:
    • Sequence=BAD93116.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for PLOD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PLOD2 Gene

Proteomics data for PLOD2 Gene at MOPED

Post-translational modifications for PLOD2 Gene

  • Ubiquitination at Lys 344
  • Glycosylation at Asn 63, Asn 209, Asn 297, Asn 365, Asn 522, Asn 696, and Asn 725
  • Modification sites at PhosphoSitePlus

Other Protein References for PLOD2 Gene

Antibody Products

  • R&D Systems Antibodies for PLOD2 (Lysine Hydroxylase 2/PLOD2)

Domains & Families for PLOD2 Gene

Graphical View of Domain Structure for InterPro Entry

O00469

UniProtKB/Swiss-Prot:

PLOD2_HUMAN :
  • Contains 1 Fe2OG dioxygenase domain.
Domain:
  • Contains 1 Fe2OG dioxygenase domain.
genes like me logo Genes that share domains with PLOD2: view

No data available for Gene Families for PLOD2 Gene

Function for PLOD2 Gene

Molecular function for PLOD2 Gene

GENATLAS Biochemistry:
procollagen-lysine,2-oxoglutarate 5 dioxygenase 2
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 PLOD2 Gene

Gene Ontology (GO) - Molecular Function for PLOD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
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 --
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors --
genes like me logo Genes that share ontologies with PLOD2: view
genes like me logo Genes that share phenotypes with PLOD2: view

Animal Model Products

CRISPR Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PLOD2 Gene

Localization for PLOD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLOD2 Gene

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

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PLOD2 Gene COMPARTMENTS Subcellular localization image for PLOD2 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5

Gene Ontology (GO) - Cellular Components for PLOD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum TAS 9054364
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0030867 rough endoplasmic reticulum membrane IEA --
GO:0070062 extracellular exosome IDA 19199708
genes like me logo Genes that share ontologies with PLOD2: view

Pathways & Interactions for PLOD2 Gene

genes like me logo Genes that share pathways with PLOD2: view

Pathways by source for PLOD2 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for PLOD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEP 15174142
GO:0006464 cellular protein modification process TAS 9054364
GO:0030198 extracellular matrix organization TAS --
GO:0032870 cellular response to hormone stimulus IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with PLOD2: view

No data available for SIGNOR curated interactions for PLOD2 Gene

Drugs & Compounds for PLOD2 Gene

(4) Drugs for PLOD2 Gene - From: HMDB, NovoSeek, and DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin C Approved Nutra Target 398,398
L-Lysine Approved Nutra Full agonist, Agonist 0
Succinic acid Approved Nutra Full agonist, Agonist 0
lysine Nutra 70

(8) Additional Compounds for PLOD2 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 PLOD2: view

Transcripts for PLOD2 Gene

Unigene Clusters for PLOD2 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PLOD2

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLOD2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1: -
SP2: - -
SP3:

Relevant External Links for PLOD2 Gene

GeneLoc Exon Structure for
PLOD2
ECgene alternative splicing isoforms for
PLOD2

Expression for PLOD2 Gene

mRNA expression in normal human tissues for PLOD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLOD2 Gene

This gene is overexpressed in Bone marrow stromal cell (32.4), Amniocyte (10.9), and Islet of Langerhans (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PLOD2 Gene



SOURCE GeneReport for Unigene cluster for PLOD2 Gene Hs.477866

mRNA Expression by UniProt/SwissProt for PLOD2 Gene

O00469-PLOD2_HUMAN
Tissue specificity: Highly expressed in pancreas and muscle. Isoform 1 and isoform 2 are expressed in the majority of the examined cell types. Isoform 2 is specifically expressed in skin, lung, dura and aorta.
genes like me logo Genes that share expression patterns with PLOD2: view

Protein tissue co-expression partners for PLOD2 Gene

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for PLOD2 Gene

Orthologs for PLOD2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLOD2 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PLOD2 35
  • 93.05 (n)
  • 94.59 (a)
PLOD2 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PLOD2 35
  • 93.9 (n)
  • 95.93 (a)
PLOD2 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Plod2 35
  • 87.51 (n)
  • 90.5 (a)
Plod2 16
Plod2 36
  • 91 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PLOD2 35
  • 99.73 (n)
  • 99.73 (a)
PLOD2 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Plod2 35
  • 87.28 (n)
  • 92.02 (a)
oppossum
(Monodelphis domestica)
Mammalia PLOD2 36
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 94 (a)
OneToMany
-- 36
  • 85 (a)
OneToMany
chicken
(Gallus gallus)
Aves PLOD2 35
  • 78.94 (n)
  • 83.29 (a)
PLOD2 36
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLOD2 36
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plod2 35
  • 74.78 (n)
  • 76.48 (a)
zebrafish
(Danio rerio)
Actinopterygii plod2 35
  • 68.67 (n)
  • 71.21 (a)
plod2 36
  • 69 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG6199 37
  • 44 (a)
Plod 36
  • 44 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea let-268 37
  • 43 (a)
let-268 36
  • 42 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.15539 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 36
  • 49 (a)
OneToMany
Species with no ortholog for PLOD2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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 PLOD2 Gene

ENSEMBL:
Gene Tree for PLOD2 (if available)
TreeFam:
Gene Tree for PLOD2 (if available)

Paralogs for PLOD2 Gene

Paralogs for PLOD2 Gene

(3) SIMAP similar genes for PLOD2 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with PLOD2: view

Variants for PLOD2 Gene

Sequence variations from dbSNP and Humsavar for PLOD2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs6710 -- 146,070,680(-) TTTGG(A/G)TGAAT utr-variant-3-prime
rs764755 -- 146,083,331(+) AGAAG(C/G)TAGAA intron-variant
rs895928 -- 146,126,452(+) GAAAA(C/T)GTAAC intron-variant
rs895929 -- 146,126,623(+) AGACA(C/G)AAAAG intron-variant
rs895930 -- 146,126,686(+) GTCAC(A/G)GACCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PLOD2 Gene

Variant ID Type Subtype PubMed ID
nsv877584 CNV Gain 21882294
nsv877606 CNV Gain 21882294
nsv525829 CNV Loss 19592680
nsv4046 CNV Loss 18451855
nsv877613 CNV Gain 21882294

Variation tolerance for PLOD2 Gene

Residual Variation Intolerance Score: 37.97% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.55; 44.43% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PLOD2 Gene

HapMap Linkage Disequilibrium report
PLOD2
Human Gene Mutation Database (HGMD)
PLOD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLOD2 Gene

Disorders for PLOD2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PLOD2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
bruck syndrome
  • bruck syndrome 2
bruck syndrome 2
  • osteogenesis imperfecta with congenital joint contractures
ehlers-danlos syndrome, kyphoscoliotic form
  • lysyl-hydroxylase deficiency
diverticulitis
  • diverticulitis nos
systemic scleroderma
  • diffuse scleroderma
- elite association
Search PLOD2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PLOD2_HUMAN
  • Bruck syndrome 2 (BRKS2) [MIM:609220]: An autosomal recessive disease characterized by generalized osteopenia, congenital joint contractures, fragile bones with onset of fractures in infancy or early childhood, short stature, severe limb deformity, progressive scoliosis, and pterygia. It is distinguished from osteogenesis imperfecta by the absence of hearing loss and dentinogenesis imperfecta, and by the presence of clubfoot and congenital joint limitations. {ECO:0000269 PubMed:12881513, ECO:0000269 PubMed:15523624}. Note=The disease is caused by mutations affecting the gene represented in this entry. The molecular defect leading to Bruck syndrome is an aberrant cross-linking of bone collagen, due to underhydroxylation of lysine residues within the telopeptides of type I collagen, whereas the lysine residues in the triple helix are normal.
  • Note=PLOD2 mutations give rise to a broad variety of phenotypes with variable degrees of severity of bone fragility and joint contractures. Disease-associated mutations have been found in patients with autosomal recessive osteogenesis imperfecta (AR-OI) (PubMed:22689593). {ECO:0000269 PubMed:22689593}.

Relevant External Links for PLOD2

Genetic Association Database (GAD)
PLOD2
Human Genome Epidemiology (HuGE) Navigator
PLOD2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PLOD2
genes like me logo Genes that share disorders with PLOD2: view

No data available for Genatlas for PLOD2 Gene

Publications for PLOD2 Gene

  1. Cloning and characterization of a novel human lysyl hydroxylase isoform highly expressed in pancreas and muscle. (PMID: 9054364) Valtavaara M. … Myllylae R. (J. Biol. Chem. 1997) 2 23 67
  2. Differential effects of homocysteine and beta aminopropionitrile on preosteoblastic MC3T3-E1 cells. (PMID: 19895920) Thaler R. … Varga F. (Bone 2010) 23 67
  3. Fox-2 protein regulates the alternative splicing of scleroderma-associated lysyl hydroxylase 2 messenger RNA. (PMID: 20131247) Seth P. … Yeowell H.N. (Arthritis Rheum. 2010) 23 67
  4. Missense mutations that cause Bruck syndrome affect enzymatic activity, folding, and oligomerization of lysyl hydroxylase 2. (PMID: 19762917) Hyry M. … Myllyharju J. (J. Biol. Chem. 2009) 23 67
  5. Bruck syndrome: osteogenesis imperfecta and arthrogryposis multiplex congenita. (PMID: 19460271) YapicioA9lu H. … Ozbek M.H. (Ann Trop Paediatr 2009) 23 67

Products for PLOD2 Gene

Sources for PLOD2 Gene

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