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Protein

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

Gene

PLOD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links.

Catalytic activityi

L-lysine-[procollagen] + 2-oxoglutarate + O2 = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO2.

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi656Iron1
Metal bindingi658Iron1
Metal bindingi708Iron1
Active sitei718Sequence analysis1

GO - Molecular functioni

GO - Biological processi

  • cellular protein modification process Source: UniProtKB
  • epidermis development Source: UniProtKB
  • hydroxylysine biosynthetic process Source: UniProtKB
  • oxidation-reduction process Source: UniProtKB
  • response to hypoxia Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding, Vitamin C

Enzyme and pathway databases

BioCyciZFISH:HS01440-MONOMER.
ReactomeiR-HSA-1650814. Collagen biosynthesis and modifying enzymes.

Names & Taxonomyi

Protein namesi
Recommended name:
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (EC:1.14.11.4)
Alternative name(s):
Lysyl hydroxylase 1
Short name:
LH1
Gene namesi
Name:PLOD1
Synonyms:LLH, PLOD
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:9081. PLOD1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Ehlers-Danlos syndrome 6 (EDS6)6 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA connective tissue disorder characterized by generalized joint hypermobility, hyperextensible skin, atrophic cutaneous scars due to tissue fragility, progressive kyphoscoliosis already present at birth, ocular manifestations, arterial rupture, easy bruising, severe neonatal muscle hypotonia and delayed motor development.
See also OMIM:225400
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_009269367 – 371Missing in EDS6. 1 Publication5
Natural variantiVAR_023466446W → G in EDS6. 1 Publication1
Natural variantiVAR_006354532Missing in EDS6. 1 Publication1
Natural variantiVAR_006355612W → C in EDS6. 1 PublicationCorresponds to variant rs121913553dbSNPEnsembl.1
Natural variantiVAR_023467667A → T in EDS6. 1 PublicationCorresponds to variant rs199730384dbSNPEnsembl.1
Natural variantiVAR_006356678G → R in EDS6. 1 PublicationCorresponds to variant rs121913551dbSNPEnsembl.1
Natural variantiVAR_023468706H → R in EDS6. 1 Publication1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi369C → A: Loss of activity. 1 Publication1

Keywords - Diseasei

Disease mutation, Ehlers-Danlos syndrome

Organism-specific databases

DisGeNETi5351.
MalaCardsiPLOD1.
MIMi225400. phenotype.
OpenTargetsiENSG00000083444.
Orphaneti1900. Ehlers-Danlos syndrome, kyphoscoliotic type.
PharmGKBiPA33411.

Chemistry databases

DrugBankiDB00139. Succinic acid.
DB00126. Vitamin C.

Polymorphism and mutation databases

BioMutaiPLOD1.
DMDMi78099790.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 181 PublicationAdd BLAST18
ChainiPRO_000002467819 – 727Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1Add BLAST709

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi163N-linked (GlcNAc...)Sequence analysis1
Glycosylationi197N-linked (GlcNAc...)Curated1
Glycosylationi538N-linked (GlcNAc...)Curated1
Glycosylationi686N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ02809.
MaxQBiQ02809.
PaxDbiQ02809.
PeptideAtlasiQ02809.
PRIDEiQ02809.

PTM databases

iPTMnetiQ02809.
PhosphoSitePlusiQ02809.
SwissPalmiQ02809.

Expressioni

Gene expression databases

BgeeiENSG00000083444.
CleanExiHS_PLOD1.
ExpressionAtlasiQ02809. baseline and differential.
GenevisibleiQ02809. HS.

Organism-specific databases

HPAiHPA049137.
HPA055799.

Interactioni

Subunit structurei

Homodimer.

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi111366. 75 interactors.
IntActiQ02809. 25 interactors.
MINTiMINT-1134973.
STRINGi9606.ENSP00000196061.

Structurei

3D structure databases

ProteinModelPortaliQ02809.
SMRiQ02809.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini636 – 727Fe2OG dioxygenasePROSITE-ProRule annotationAdd BLAST92

Sequence similaritiesi

Contains 1 Fe2OG dioxygenase domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiKOG1971. Eukaryota.
ENOG410Y4QU. LUCA.
GeneTreeiENSGT00550000074427.
HOGENOMiHOG000231099.
HOVERGENiHBG053618.
InParanoidiQ02809.
KOiK00473.
OMAiIRQQDVF.
OrthoDBiEOG091G02DK.
PhylomeDBiQ02809.
TreeFamiTF313826.

Family and domain databases

InterProiIPR029044. Nucleotide-diphossugar_trans.
IPR005123. Oxoglu/Fe-dep_dioxygenase.
IPR006620. Pro_4_hyd_alph.
IPR001006. Procol_lys_dOase.
[Graphical view]
PfamiPF03171. 2OG-FeII_Oxy. 1 hit.
[Graphical view]
SMARTiSM00702. P4Hc. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
PROSITEiPS51471. FE2OG_OXY. 1 hit.
PS01325. LYS_HYDROXYLASE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q02809-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MRPLLLLALL GWLLLAEAKG DAKPEDNLLV LTVATKETEG FRRFKRSAQF
60 70 80 90 100
FNYKIQALGL GEDWNVEKGT SAGGGQKVRL LKKALEKHAD KEDLVILFAD
110 120 130 140 150
SYDVLFASGP RELLKKFRQA RSQVVFSAEE LIYPDRRLET KYPVVSDGKR
160 170 180 190 200
FLGSGGFIGY APNLSKLVAE WEGQDSDSDQ LFYTKIFLDP EKREQINITL
210 220 230 240 250
DHRCRIFQNL DGALDEVVLK FEMGHVRARN LAYDTLPVLI HGNGPTKLQL
260 270 280 290 300
NYLGNYIPRF WTFETGCTVC DEGLRSLKGI GDEALPTVLV GVFIEQPTPF
310 320 330 340 350
VSLFFQRLLR LHYPQKHMRL FIHNHEQHHK AQVEEFLAQH GSEYQSVKLV
360 370 380 390 400
GPEVRMANAD ARNMGADLCR QDRSCTYYFS VDADVALTEP NSLRLLIQQN
410 420 430 440 450
KNVIAPLMTR HGRLWSNFWG ALSADGYYAR SEDYVDIVQG RRVGVWNVPY
460 470 480 490 500
ISNIYLIKGS ALRGELQSSD LFHHSKLDPD MAFCANIRQQ DVFMFLTNRH
510 520 530 540 550
TLGHLLSLDS YRTTHLHNDL WEVFSNPEDW KEKYIHQNYT KALAGKLVET
560 570 580 590 600
PCPDVYWFPI FTEVACDELV EEMEHFGQWS LGNNKDNRIQ GGYENVPTID
610 620 630 640 650
IHMNQIGFER EWHKFLLEYI APMTEKLYPG YYTRAQFDLA FVVRYKPDEQ
660 670 680 690 700
PSLMPHHDAS TFTINIALNR VGVDYEGGGC RFLRYNCSIR APRKGWTLMH
710 720
PGRLTHYHEG LPTTRGTRYI AVSFVDP
Length:727
Mass (Da):83,550
Last modified:October 25, 2005 - v2
Checksum:i6C3E0C11B15D598C
GO
Isoform 2 (identifier: Q02809-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     25-25: E → EAPCCQEGLRAGGSGSLHLGRDFTVLAGARGSPSPSVSSIPRFWIPGS

Note: No experimental confirmation available.
Show »
Length:774
Mass (Da):88,273
Checksum:i27DBE64A45B2A163
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03275467E → D.Corresponds to variant rs7551068dbSNPEnsembl.1
Natural variantiVAR_03275584A → T.Corresponds to variant rs34878020dbSNPEnsembl.1
Natural variantiVAR_01422099A → T.2 PublicationsCorresponds to variant rs7551175dbSNPEnsembl.1
Natural variantiVAR_032756120A → S.1 PublicationCorresponds to variant rs2273285dbSNPEnsembl.1
Natural variantiVAR_035479123Q → H in a breast cancer sample; somatic mutation. 1 Publication1
Natural variantiVAR_009269367 – 371Missing in EDS6. 1 Publication5
Natural variantiVAR_023466446W → G in EDS6. 1 Publication1
Natural variantiVAR_006354532Missing in EDS6. 1 Publication1
Natural variantiVAR_006355612W → C in EDS6. 1 PublicationCorresponds to variant rs121913553dbSNPEnsembl.1
Natural variantiVAR_023467667A → T in EDS6. 1 PublicationCorresponds to variant rs199730384dbSNPEnsembl.1
Natural variantiVAR_006356678G → R in EDS6. 1 PublicationCorresponds to variant rs121913551dbSNPEnsembl.1
Natural variantiVAR_023468706H → R in EDS6. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_05630025E → EAPCCQEGLRAGGSGSLHLG RDFTVLAGARGSPSPSVSSI PRFWIPGS in isoform 2. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L06419 mRNA. Translation: AAA60116.1.
AF490527
, AF490514, AF490515, AF490516, AF490517, AF490518, AF490519, AF490520, AF490521, AF490522, AF490523, AF490524, AF490525, AF490526 Genomic DNA. Translation: AAM12752.1.
AK299150 mRNA. Translation: BAG61199.1.
AK316285 mRNA. Translation: BAH14656.1.
AL096840 Genomic DNA. Translation: CAC19722.1.
BC016657 mRNA. Translation: AAH16657.1.
CCDSiCCDS142.1. [Q02809-1]
PIRiA38206.
RefSeqiNP_000293.2. NM_000302.3. [Q02809-1]
NP_001303249.1. NM_001316320.1. [Q02809-2]
UniGeneiHs.75093.

Genome annotation databases

EnsembliENST00000196061; ENSP00000196061; ENSG00000083444. [Q02809-1]
GeneIDi5351.
KEGGihsa:5351.
UCSCiuc001atm.4. human. [Q02809-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L06419 mRNA. Translation: AAA60116.1.
AF490527
, AF490514, AF490515, AF490516, AF490517, AF490518, AF490519, AF490520, AF490521, AF490522, AF490523, AF490524, AF490525, AF490526 Genomic DNA. Translation: AAM12752.1.
AK299150 mRNA. Translation: BAG61199.1.
AK316285 mRNA. Translation: BAH14656.1.
AL096840 Genomic DNA. Translation: CAC19722.1.
BC016657 mRNA. Translation: AAH16657.1.
CCDSiCCDS142.1. [Q02809-1]
PIRiA38206.
RefSeqiNP_000293.2. NM_000302.3. [Q02809-1]
NP_001303249.1. NM_001316320.1. [Q02809-2]
UniGeneiHs.75093.

3D structure databases

ProteinModelPortaliQ02809.
SMRiQ02809.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111366. 75 interactors.
IntActiQ02809. 25 interactors.
MINTiMINT-1134973.
STRINGi9606.ENSP00000196061.

Chemistry databases

DrugBankiDB00139. Succinic acid.
DB00126. Vitamin C.

PTM databases

iPTMnetiQ02809.
PhosphoSitePlusiQ02809.
SwissPalmiQ02809.

Polymorphism and mutation databases

BioMutaiPLOD1.
DMDMi78099790.

Proteomic databases

EPDiQ02809.
MaxQBiQ02809.
PaxDbiQ02809.
PeptideAtlasiQ02809.
PRIDEiQ02809.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000196061; ENSP00000196061; ENSG00000083444. [Q02809-1]
GeneIDi5351.
KEGGihsa:5351.
UCSCiuc001atm.4. human. [Q02809-1]

Organism-specific databases

CTDi5351.
DisGeNETi5351.
GeneCardsiPLOD1.
GeneReviewsiPLOD1.
HGNCiHGNC:9081. PLOD1.
HPAiHPA049137.
HPA055799.
MalaCardsiPLOD1.
MIMi153454. gene.
225400. phenotype.
neXtProtiNX_Q02809.
OpenTargetsiENSG00000083444.
Orphaneti1900. Ehlers-Danlos syndrome, kyphoscoliotic type.
PharmGKBiPA33411.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1971. Eukaryota.
ENOG410Y4QU. LUCA.
GeneTreeiENSGT00550000074427.
HOGENOMiHOG000231099.
HOVERGENiHBG053618.
InParanoidiQ02809.
KOiK00473.
OMAiIRQQDVF.
OrthoDBiEOG091G02DK.
PhylomeDBiQ02809.
TreeFamiTF313826.

Enzyme and pathway databases

BioCyciZFISH:HS01440-MONOMER.
ReactomeiR-HSA-1650814. Collagen biosynthesis and modifying enzymes.

Miscellaneous databases

ChiTaRSiPLOD1. human.
GenomeRNAii5351.
PROiQ02809.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000083444.
CleanExiHS_PLOD1.
ExpressionAtlasiQ02809. baseline and differential.
GenevisibleiQ02809. HS.

Family and domain databases

InterProiIPR029044. Nucleotide-diphossugar_trans.
IPR005123. Oxoglu/Fe-dep_dioxygenase.
IPR006620. Pro_4_hyd_alph.
IPR001006. Procol_lys_dOase.
[Graphical view]
PfamiPF03171. 2OG-FeII_Oxy. 1 hit.
[Graphical view]
SMARTiSM00702. P4Hc. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
PROSITEiPS51471. FE2OG_OXY. 1 hit.
PS01325. LYS_HYDROXYLASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPLOD1_HUMAN
AccessioniPrimary (citable) accession number: Q02809
Secondary accession number(s): B4DR87, Q96AV9, Q9H132
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: October 25, 2005
Last modified: November 2, 2016
This is version 191 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.