Tbio PLOD1 Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

Protein Summary

Description

Part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils (By similarity). Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens (PubMed:8621606, PubMed:10686424, PubMed:15854030). These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links (Probable). Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the 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 VI have deficiencies in lysyl hydroxylase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

Uniprot Accession IDs

• Q02809
• B4DR87
• Q96AV9
• Q9H132

Gene Name

• PLOD1

Ensembl ID

• ENST00000196061
• ENSP00000196061
• ENSG00000083444

Symbol

• LLH
• PLOD
• LH
• LH1
• LLH
• EDS6
• PLOD
• EDSKCL1

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
interacting protein	0.95
protein complex	0.88
molecular function	0.86
PubMedID	0.78
histone modification site profile	0.75

Protein Classes

PANTHER Classes

Protein / Oxidoreductase / Oxygenase / Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

DTO Classes

Protein / Enzyme / Oxidoreductase / Oxygenase / Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 150.18   (req: < 5)

Gene RIFs: 13   (req: <= 3)

Antibodies: 124   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 150.18   (req: >= 5)

Gene RIFs: 13   (req: > 3)

Antibodies: 124   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 12

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (143)

Explore Interacting Targets

1 – 10 of 143

• See Interactions on String-DB

COL4A6

Tbio

Novelty:  0.02524039

p_int:  0.999999981

p_ni:  1.6e-8

p_wrong:  4e-9

Score:  0.932

Data Source:  BioPlex,STRINGDB

COL4A5

Tbio

Novelty:  0.00283701

p_int:  0.999999977

p_ni:  1.5e-8

p_wrong:  8e-9

Score:  0.929

Data Source:  BioPlex,STRINGDB

COL4A1

Tbio

Novelty:  0.00358049

p_int:  0.999999975

p_ni:  2.2e-8

p_wrong:  3e-9

Score:  0.948

Data Source:  BioPlex,STRINGDB

COL5A1

Tbio

Novelty:  0.00506815

p_int:  0.99999971

p_ni:  2.9e-7

Score:  0.971

Data Source:  BioPlex,STRINGDB

COL2A1

Tbio

Novelty:  0.0011102

p_int:  0.999999588

p_ni:  4.12e-7

Score:  0.936

Data Source:  BioPlex,STRINGDB

MEX3D

Tdark

Novelty:  0.02245732

p_int:  0.999999479

p_ni:  5.18e-7

p_wrong:  4e-9

Score:  0.17

Data Source:  BioPlex,STRINGDB

COL4A2

Tbio

Novelty:  0.00782053

p_int:  0.999998756

p_ni:  0.000001244

Score:  0.937

Data Source:  BioPlex,STRINGDB

FOXA1

Tbio

Family:  TF

Novelty:  0.00235269

p_int:  0.99999362

p_ni:  1.4e-8

p_wrong:  0.000006366

Score:  0.199

Data Source:  BioPlex,STRINGDB

ODF2

Tbio

Novelty:  0.03203587

p_int:  0.999991298

p_ni:  8.33e-7

p_wrong:  0.000007869

Score:  0.173

Data Source:  BioPlex,STRINGDB

FAM122B

Tdark

Novelty:  1.90668674

p_int:  0.999987249

p_ni:  0.000012722

p_wrong:  2.8e-8

Data Source:  BioPlex

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (4)

Reactome (3)

KEGG (1)

Collagen biosynthesis and modifying enzymes (R-HSA-1650814)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Collagen biosynthesis and modifying enzymes	67 targets	R-HSA-1650814
Reactome	Collagen formation	90 targets	R-HSA-1474290
Reactome	Extracellular matrix organization	297 targets	R-HSA-1474244

Name	Explore in Pharos	Explore in Source
Collagen biosynthesis and modifying enzymes	67 targets	R-HSA-1650814
Collagen formation	90 targets	R-HSA-1474290
Extracellular matrix organization	297 targets	R-HSA-1474244

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (16)

Functions (4)

Components (4)

Processes (8)

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Items per page:

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1 – 4 of 4

GO Term	Evidence	Assigned by
procollagen-lysine 5-dioxygenase activity	Inferred from Direct Assay (IDA)	CAFA
protein homodimerization activity	Traceable Author Statement (TAS)	UniProtKB
iron ion binding	Inferred from Electronic Annotation (IEA)	InterPro
L-ascorbic acid binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

Disease Associations (null)

No disease associations found

GWAS Traits (27)

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1 – 5 of 27

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
NT-proBNP measurement	EFO_0004745	2	3	3		98.6
platelet count	EFO_0004309	6	6	5	2.2	97.6
BNP measurement	EFO_0006920	2	2	2		96.1
blood protein measurement	EFO_0007937	3	4	4		94.3
mitochondrial DNA measurement	EFO_0006312	2	2	2		89.2

• Explore on Target Illumination GWAS Analytics (TIGA)

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1 – 5 of 27

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
NT-proBNP measurement	EFO_0004745	3		98.6
platelet count	EFO_0004309	5	2.2	97.6
BNP measurement	EFO_0006920	2		96.1
blood protein measurement	EFO_0007937	4		94.3
mitochondrial DNA measurement	EFO_0006312	2		89.2

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UniProt Keyword Find Similar Targets

No Header	No Header
Alternative splicing
Complete proteome
Dioxygenase
Direct protein sequencing
Disease mutation
Ehlers-Danlos syndrome
Endoplasmic reticulum
Glycoprotein
Iron
Membrane

GWAS Trait Find Similar Targets

No Header	No Header
blood protein measurement
BMI-adjusted hip circumference
BNP measurement
cardiovascular disease biomarker measurement
educational attainment
eosinophil count
eosinophil percentage of granulocytes
eosinophil percentage of leukocytes
folic acid measurement
free cholesterol:total lipids ratio

MGI Phenotype Find Similar Targets

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behavior/neurological phenotype
cardiovascular system phenotype
integument phenotype
mortality/aging
muscle phenotype
skeleton phenotype

IDG Resources

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Orthologs (13)

1 – 5 of 13

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	procollagen-lysine,2-oxoglutarate 5-dioxygenase 1	VGNC:10032	457956
Mouse	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	MGI:99907	18822
Rat	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	RGD:621382	116552
Dog	procollagen-lysine,2-oxoglutarate 5-dioxygenase 1	VGNC:44701	487440
Horse	procollagen-lysine,2-oxoglutarate 5-dioxygenase 1	VGNC:21585	100050902

Species	Name	OMA	EggNOG	Inparanoid
Chimp	procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
Mouse	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1
Rat	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1
Dog	procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
Horse	procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

Publication Statistics

PubMed Score 150.18

PubMed score by year

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PubTator Score 140.06

PubTator score by year

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Related Publications

Text Mined References (42)

GeneRif Annotations (13)

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PMID	Year	Title