PLOD2 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLOD2provided by HGNC
Official Full Name: procollagen-lysine,2-oxoglutarate 5-dioxygenase 2provided by HGNC
Primary source: HGNC:HGNC:9082
See related: Ensembl:ENSG00000152952 MIM:601865; AllianceGenome:HGNC:9082
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LH2; TLH; BRKS2
Summary: 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]
Expression: Broad expression in thyroid (RPKM 48.4), fat (RPKM 35.4) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q24

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (146069440..146161184, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (148824992..148916735, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (145787227..145878971, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 promotes collagen cross-linking and ECM stiffening to induce liver fibrosis.
Title: Procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 promotes collagen cross-linking and ECM stiffening to induce liver fibrosis.
METTL3 facilitates renal cell carcinoma progression by PLOD2 m[6]A-methylation under prolonged hypoxia.
Title: METTL3 facilitates renal cell carcinoma progression by PLOD2 m(6)A-methylation under prolonged hypoxia.
Hypoxia-induced PLOD2 promotes clear cell renal cell carcinoma progression via modulating EGFR-dependent AKT pathway activation.
Title: Hypoxia-induced PLOD2 promotes clear cell renal cell carcinoma progression via modulating EGFR-dependent AKT pathway activation.
Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4.
Title: Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4.
The PLOD2/succinate axis regulates the epithelial-mesenchymal plasticity and cancer cell stemness.
Title: The PLOD2/succinate axis regulates the epithelial-mesenchymal plasticity and cancer cell stemness.
Apelin promotes osteosarcoma metastasis by upregulating PLOD2 expression via the Hippo signaling pathway and hsa_circ_0000004/miR-1303 axis.
Title: Apelin promotes osteosarcoma metastasis by upregulating PLOD2 expression via the Hippo signaling pathway and hsa_circ_0000004/miR-1303 axis.
circRNA PLOD2 promotes tumorigenesis and Warburg effect in colon cancer by the miR-513a-5p/SIX1/LDHA axis.
Title: circRNA PLOD2 promotes tumorigenesis and Warburg effect in colon cancer by the miR-513a-5p/SIX1/LDHA axis.
Clinicopathological significances of PLOD2, epithelial-mesenchymal transition markers, and cancer stem cells in patients with esophageal squamous cell carcinoma.
Title: Clinicopathological significances of PLOD2, epithelial-mesenchymal transition markers, and cancer stem cells in patients with esophageal squamous cell carcinoma.
PLOD2 Is a Prognostic Marker in Glioblastoma That Modulates the Immune Microenvironment and Tumor Progression.
Title: PLOD2 Is a Prognostic Marker in Glioblastoma That Modulates the Immune Microenvironment and Tumor Progression.
Bruck syndrome in 13 new patients: Identification of five novel FKBP10 and PLOD2 variants and further expansion of the phenotypic spectrum.
Title: Bruck syndrome in 13 new patients: Identification of five novel FKBP10 and PLOD2 variants and further expansion of the phenotypic spectrum.

Submit: New GeneRIF Correction See all GeneRIFs (63)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Bruck syndrome 2 MedGen: C1836602 OMIM: 609220 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
integrase	gag-pol	HIV-1 IN is identified to have a physical interaction with procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S3410 (e-PCR)
- UniSTS:81282

STS-N98463 (e-PCR)
- UniSTS:137

G29915 (e-PCR)
- UniSTS:17034

G16641 (e-PCR)
- UniSTS:921

RH78870 (e-PCR)
- UniSTS:35268

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-ascorbic acid binding	IEA Inferred from Electronic Annotation more info
enables iron ion binding	IEA Inferred from Electronic Annotation more info
NOT enables procollagen glucosyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables procollagen-lysine 5-dioxygenase activity	IBA Inferred from Biological aspect of Ancestor more info
enables procollagen-lysine 5-dioxygenase activity	IDA Inferred from Direct Assay more info	PubMed
enables procollagen-lysine 5-dioxygenase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Process	Evidence Code	Pubs
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in hydroxylysine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-lysine hydroxylation	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-lysine hydroxylation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
NOT involved_in protein O-linked glycosylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein modification process	TAS Traceable Author Statement more info	PubMed
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
is_active_in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in rough endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: procollagen-lysine,2-oxoglutarate 5-dioxygenase 2

Names: lysine hydroxylase 2; lysyl hydroxlase 2; lysyl hydroxylase 2; procollagen lysyl hydroxylase 2; procollagen-lysine 5-dioxygenase; telopeptide lysyl hydroxylase; telopeptidyl lysyl hydroxylase

NP_000926.2

EC 1.14.11.4

NP_891988.1

EC 1.14.11.4

XP_016862114.1

EC 1.14.11.4

XP_047304275.1

EC 1.14.11.4

XP_047304276.1

EC 1.14.11.4

XP_054202843.1

EC 1.14.11.4

XP_054202844.1

EC 1.14.11.4

XP_054202845.1

EC 1.14.11.4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_009251.1 RefSeqGene

Range

5001..97056

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000935.3 → NP_000926.2 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform 2 precursor

See identical proteins and their annotated locations for NP_000926.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal in-frame coding exon compared to transcript variant 1, resulting in a shorter isoform (2, also known as LH2a) missing a 21 aa protein segment compared to isoform 1.

Source sequence(s)

AB209879, AC107021, BC037169, BM724669

Consensus CDS

CCDS3131.1

UniProtKB/Swiss-Prot

B3KWS3, O00469, Q59ED2, Q8N170

UniProtKB/TrEMBL

A0A9L9PX47

Related

ENSP00000353170.3, ENST00000360060.7

Conserved Domains (2) summary

smart00702
Location:572 → 735

P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

COG0463
Location:349 → 574

WcaA; Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]
NM_182943.3 → NP_891988.1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_891988.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1, also known as LH2b).

Source sequence(s)

AC107021, BC037169, BM724669

Consensus CDS

CCDS3132.1

UniProtKB/TrEMBL

E7ETU9

Related

ENSP00000282903.5, ENST00000282903.10

Conserved Domains (1) summary

smart00702
Location:593 → 756

P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

146069440..146161184 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047448319.1 → XP_047304275.1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1
XM_017006625.3 → XP_016862114.1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1

UniProtKB/TrEMBL

E7ETU9

Related

ENST00000703519.1

Conserved Domains (1) summary

smart00702
Location:501 → 664

P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
XM_047448320.1 → XP_047304276.1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X2

UniProtKB/TrEMBL

A0A994J6S5

Related

ENSP00000515351.1, ENST00000703520.1

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

148824992..148916735 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054346869.1 → XP_054202844.1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1
XM_054346868.1 → XP_054202843.1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1
XM_054346870.1 → XP_054202845.1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X2

UniProtKB/TrEMBL

A0A994J6S5