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PLOD1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 [ Homo sapiens (human) ]

Gene ID: 5351, updated on 11-Sep-2019

Summary

Official Symbol
PLOD1provided by HGNC
Official Full Name
procollagen-lysine,2-oxoglutarate 5-dioxygenase 1provided by HGNC
Primary source
HGNC:HGNC:9081
See related
Ensembl:ENSG00000083444 MIM:153454
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
LH; LH1; LLH; EDS6; PLOD; EDSKCL1
Summary
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]
Expression
Ubiquitous expression in placenta (RPKM 47.0), endometrium (RPKM 37.3) and 25 other tissues See more
Orthologs

Genomic context

See PLOD1 in Genome Data Viewer
Location:
1p36.22
Exon count:
20
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (11934717..11975537)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11994724..12035599)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U5E small nuclear 4, pseudogene Neighboring gene KIAA2013 Neighboring gene Sharpr-MPRA regulatory region 3946 Neighboring gene Sharpr-MPRA regulatory region 8260 Neighboring gene mitofusin 2 Neighboring gene migration and invasion inhibitory protein Neighboring gene microRNA 6729

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 NL4-3 replication is restricted by PLOD1 as enhanced replication was discovered when PLOD1 is deleted through CRISPR/Cas9 genome editing in primary CD4+ T cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with PLOD1; predicted interaction to be within the endoplasmic reticulum PubMed
Rev rev HIV-1 Rev interacting protein, procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa. The interaction of Rev with PLOD1 is increased by RRE PubMed
integrase gag-pol HIV-1 IN is identified to have a physical interaction with procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1) 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

Clone Names

  • FLJ42041

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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
procollagen-lysine 5-dioxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
protein homodimerization activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cellular protein modification process NAS
Non-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 
epidermis development IMP
Inferred from Mutant Phenotype
more info
PubMed 
epidermis development TAS
Traceable Author Statement
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 
hydroxylysine biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
hydroxylysine biosynthetic process TAS
Traceable Author Statement
more info
PubMed 
oxidation-reduction process TAS
Traceable Author Statement
more info
PubMed 
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
catalytic complex IEA
Inferred from Electronic Annotation
more info
 
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 1
Names
lysine hydroxylase
lysyl hydroxlase 1
procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1
NP_000293.2
NP_001303249.1

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_008159.1 RefSeqGene

    Range
    5029..45849
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000302.4NP_000293.2  procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_000293.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    BQ447373, DC334246, M98252
    Consensus CDS
    CCDS142.1
    UniProtKB/Swiss-Prot
    Q02809
    UniProtKB/TrEMBL
    A0A024R4H0
    Related
    ENSP00000196061.4, ENST00000196061.5
    Conserved Domains (1) summary
    smart00702
    Location:562725
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues
  2. NM_001316320.2NP_001303249.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AI347587, AK299150, BM991136, DC334246
    UniProtKB/Swiss-Prot
    Q02809
    Conserved Domains (1) summary
    smart00702
    Location:609772
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    11934717..11975537
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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