Format

Send to:

Choose Destination

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

Gene ID: 5352, updated on 10-Dec-2019

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
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

Genomic context

See PLOD2 in Genome Data Viewer
Location:
3q24
Exon count:
23
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (146069437..146161495, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (145787225..145879282, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986138 Neighboring gene lncRNA sorafenib resistance in renal cell carcinoma associated Neighboring gene uncharacterized LOC105374145 Neighboring gene phospholipid scramblase 4

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

NHGRI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

HIV-1 interactions

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

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-ascorbic acid binding IEA
Inferred from Electronic Annotation
more info
 
iron ion binding IEA
Inferred from Electronic Annotation
more info
 
NOT procollagen glucosyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
procollagen-lysine 5-dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
procollagen-lysine 5-dioxygenase activity IDA
Inferred from Direct Assay
more info
PubMed 
procollagen-lysine 5-dioxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Process Evidence Code Pubs
cellular protein modification process TAS
Traceable Author Statement
more info
PubMed 
collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
hydroxylysine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
hydroxylysine biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
peptidyl-lysine hydroxylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
peptidyl-lysine hydroxylation IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-lysine hydroxylation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
NOT protein O-linked glycosylation IDA
Inferred from Direct Assay
more info
PubMed 
response to hypoxia IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum TAS
Traceable Author Statement
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
rough endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
Names
lysine hydroxylase 2
lysyl hydroxlase 2
lysyl hydroxylase 2
procollagen-lysine 5-dioxygenase
telopeptide lysyl hydroxylase
NP_000926.2
NP_891988.1
XP_005247592.1
XP_016862114.1
XP_024309367.1

NCBI Reference Sequences (RefSeq)

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

  1. NG_009251.1 RefSeqGene

    Range
    5001..97056
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000935.2NP_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
    O00469
    Related
    ENSP00000353170.3, ENST00000360060.7
    Conserved Domains (2) summary
    smart00702
    Location:572735
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
    COG0463
    Location:349574
    WcaA; Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]
  2. NM_182943.3NP_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/Swiss-Prot
    O00469
    Related
    ENSP00000282903.5, ENST00000282903.10
    Conserved Domains (1) summary
    smart00702
    Location:593756
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    146069437..146161495 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453599.1XP_024309367.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X2

    Conserved Domains (1) summary
    smart00702
    Location:480643
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
  2. XM_005247535.4XP_005247592.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1

    Conserved Domains (1) summary
    smart00702
    Location:501664
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
  3. XM_017006625.2XP_016862114.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform X1

    Conserved Domains (1) summary
    smart00702
    Location:501664
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

RNA

  1. XR_001740176.2 RNA Sequence

Support Center