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: 115.72   (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: 115.72   (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

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Expression Data (0 Tissues)

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No expression data found

Related Tools

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:

10

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 ()

No disease associations found

GWAS Traits (25)

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1 – 5 of 25

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
platelet count	EFO_0004309	4	4	3	2.2	97.7
NT-proBNP measurement	EFO_0004745	2	3	3		95.2
platelet crit	EFO_0007985	2	2	2		95
BNP measurement	EFO_0006920	2	2	2		88.1
blood protein measurement	EFO_0007937	1	2	2		81.4

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 25

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
platelet count	EFO_0004309	3	2.2	97.7
NT-proBNP measurement	EFO_0004745	3		95.2
platelet crit	EFO_0007985	2		95
BNP measurement	EFO_0006920	2		88.1
blood protein measurement	EFO_0007937	2		81.4

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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
eosinophil count
eosinophil percentage of granulocytes
eosinophil percentage of leukocytes
folic acid measurement
hip circumference
homocysteine measurement

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 115.72

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