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Protein

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

Gene

PLOD1

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

Functioni

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).By similarityCurated3 Publications

Catalytic activityi

L-lysine-[procollagen] + 2-oxoglutarate + O2 = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO2.3 Publications

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi656Iron1 Publication1
Metal bindingi658Iron1 Publication1
Metal bindingi708Iron1 Publication1
Active sitei718Sequence analysis1

GO - Molecular functioni

  • iron ion binding Source: InterPro
  • L-ascorbic acid binding Source: UniProtKB-KW
  • procollagen-lysine 5-dioxygenase activity Source: CAFA
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

  • cellular protein modification process Source: UniProtKB
  • epidermis development Source: UniProtKB
  • hydroxylysine biosynthetic process Source: CAFA
  • oxidation-reduction process Source: UniProtKB
  • peptidyl-lysine hydroxylation Source: UniProtKB
  • response to hypoxia Source: UniProtKB

Keywordsi

Molecular functionDioxygenase, Oxidoreductase
LigandIron, Metal-binding, Vitamin C

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (EC:1.14.11.43 Publications)
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

EuPathDBiHostDB:ENSG00000083444.16
HGNCiHGNC:9081 PLOD1
MIMi153454 gene
neXtProtiNX_Q02809

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Ehlers-Danlos syndrome, kyphoscoliotic type, 1 (EDSKSCL1)6 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. EDSKSCL1 is an autosomal recessive form characterized by severe muscle hypotonia at birth, generalized joint laxity, scoliosis at birth, and scleral fragility and rupture of the ocular globe.
See also OMIM:225400
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_009269367 – 371Missing in EDSKSCL1. 1 Publication5
Natural variantiVAR_023466446W → G in EDSKSCL1; loss of enzyme activity. 1 Publication1
Natural variantiVAR_006354532Missing in EDSKSCL1. 1 Publication1
Natural variantiVAR_006355612W → C in EDSKSCL1. 1 PublicationCorresponds to variant dbSNP:rs121913553EnsemblClinVar.1
Natural variantiVAR_023467667A → T in EDSKSCL1. 1 PublicationCorresponds to variant dbSNP:rs199730384Ensembl.1
Natural variantiVAR_006356678G → R in EDSKSCL1. 1 PublicationCorresponds to variant dbSNP:rs121913551EnsemblClinVar.1
Natural variantiVAR_023468706H → R in EDSKSCL1. 1 Publication1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi369C → A: Loss of activity. 1 Publication1
Mutagenesisi656H → S: Loss of enzyme activity. 1 Publication1
Mutagenesisi658D → A: Loss of enzyme activity. 1 Publication1
Mutagenesisi706H → S: Loss of enzyme activity. 1 Publication1
Mutagenesisi708H → S: Loss of enzyme activity. 1 Publication1

Keywords - Diseasei

Disease mutation, Ehlers-Danlos syndrome

Organism-specific databases

DisGeNETi5351
GeneReviewsiPLOD1
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...) asparagineSequence analysis1
Glycosylationi197N-linked (GlcNAc...) asparagineCurated1
Glycosylationi538N-linked (GlcNAc...) asparagineCurated1
Glycosylationi686N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ02809
MaxQBiQ02809
PaxDbiQ02809
PeptideAtlasiQ02809
PRIDEiQ02809
ProteomicsDBi58126

PTM databases

GlyConnecti1633
iPTMnetiQ02809
PhosphoSitePlusiQ02809
SwissPalmiQ02809

Expressioni

Gene expression databases

BgeeiENSG00000083444 Expressed in 224 organ(s), highest expression level in heart left ventricle
CleanExiHS_PLOD1
ExpressionAtlasiQ02809 baseline and differential
GenevisibleiQ02809 HS

Organism-specific databases

HPAiHPA049137
HPA055799

Interactioni

Subunit structurei

Homodimer (By similarity). Identified in a complex with P3H3 and P3H4 (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111366, 120 interactors
IntActiQ02809, 26 interactors
MINTiQ02809
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

Keywords - Domaini

Signal

Phylogenomic databases

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

Family and domain databases

InterProiView protein in InterPro
IPR029044 Nucleotide-diphossugar_trans
IPR005123 Oxoglu/Fe-dep_dioxygenase
IPR006620 Pro_4_hyd_alph
IPR001006 Procol_lys_dOase
PfamiView protein in Pfam
PF03171 2OG-FeII_Oxy, 1 hit
SMARTiView protein in SMART
SM00702 P4Hc, 1 hit
SUPFAMiSSF53448 SSF53448, 1 hit
PROSITEiView protein in PROSITE
PS51471 FE2OG_OXY, 1 hit
PS01325 LYS_HYDROXYLASE, 1 hit

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

This entry has 2 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q5JXB7Q5JXB7_HUMAN
Procollagen-lysine,2-oxoglutarate 5...
PLOD1
283Annotation score:
Q5JXB8Q5JXB8_HUMAN
Procollagen-lysine,2-oxoglutarate 5...
PLOD1
225Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03275467E → D. Corresponds to variant dbSNP:rs7551068Ensembl.1
Natural variantiVAR_03275584A → T. Corresponds to variant dbSNP:rs34878020EnsemblClinVar.1
Natural variantiVAR_01422099A → T2 PublicationsCorresponds to variant dbSNP:rs7551175EnsemblClinVar.1
Natural variantiVAR_032756120A → S1 PublicationCorresponds to variant dbSNP:rs2273285EnsemblClinVar.1
Natural variantiVAR_035479123Q → H in a breast cancer sample; somatic mutation. 1 Publication1
Natural variantiVAR_009269367 – 371Missing in EDSKSCL1. 1 Publication5
Natural variantiVAR_023466446W → G in EDSKSCL1; loss of enzyme activity. 1 Publication1
Natural variantiVAR_006354532Missing in EDSKSCL1. 1 Publication1
Natural variantiVAR_006355612W → C in EDSKSCL1. 1 PublicationCorresponds to variant dbSNP:rs121913553EnsemblClinVar.1
Natural variantiVAR_023467667A → T in EDSKSCL1. 1 PublicationCorresponds to variant dbSNP:rs199730384Ensembl.1
Natural variantiVAR_006356678G → R in EDSKSCL1. 1 PublicationCorresponds to variant dbSNP:rs121913551EnsemblClinVar.1
Natural variantiVAR_023468706H → R in EDSKSCL1. 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 No translation available.
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

Similar proteinsi

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 No translation available.
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, 120 interactors
IntActiQ02809, 26 interactors
MINTiQ02809
STRINGi9606.ENSP00000196061

Chemistry databases

DrugBankiDB00139 Succinic acid
DB00126 Vitamin C

PTM databases

GlyConnecti1633
iPTMnetiQ02809
PhosphoSitePlusiQ02809
SwissPalmiQ02809

Polymorphism and mutation databases

BioMutaiPLOD1
DMDMi78099790

Proteomic databases

EPDiQ02809
MaxQBiQ02809
PaxDbiQ02809
PeptideAtlasiQ02809
PRIDEiQ02809
ProteomicsDBi58126

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
EuPathDBiHostDB:ENSG00000083444.16
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
OMAiKFEMGHV
OrthoDBiEOG091G02DK
PhylomeDBiQ02809
TreeFamiTF313826

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiPLOD1 human
GenomeRNAii5351
PROiPR:Q02809
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000083444 Expressed in 224 organ(s), highest expression level in heart left ventricle
CleanExiHS_PLOD1
ExpressionAtlasiQ02809 baseline and differential
GenevisibleiQ02809 HS

Family and domain databases

InterProiView protein in InterPro
IPR029044 Nucleotide-diphossugar_trans
IPR005123 Oxoglu/Fe-dep_dioxygenase
IPR006620 Pro_4_hyd_alph
IPR001006 Procol_lys_dOase
PfamiView protein in Pfam
PF03171 2OG-FeII_Oxy, 1 hit
SMARTiView protein in SMART
SM00702 P4Hc, 1 hit
SUPFAMiSSF53448 SSF53448, 1 hit
PROSITEiView protein in PROSITE
PS51471 FE2OG_OXY, 1 hit
PS01325 LYS_HYDROXYLASE, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPLOD1_HUMAN
AccessioniPrimary (citable) accession number: Q02809
Secondary accession number(s): B4DR87, Q96AV9, Q9H132
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: October 25, 2005
Last modified: October 10, 2018
This is version 207 of the entry and version 2 of the sequence. See 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
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