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Q02809

- PLOD1_HUMAN

UniProt

Q02809 - PLOD1_HUMAN

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Protein

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1

Gene
PLOD1, LLH, PLOD
Organism
Homo sapiens (Human)
Status
Reviewed - 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

Iron.
Ascorbate.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi656 – 6561Iron
Metal bindingi658 – 6581Iron
Metal bindingi708 – 7081Iron
Active sitei718 – 7181 Reviewed prediction

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. L-ascorbic acid binding Source: UniProtKB-KW
  3. procollagen-lysine 5-dioxygenase activity Source: UniProtKB-EC
  4. protein homodimerization activity Source: UniProtKB

GO - Biological processi

  1. cellular protein modification process Source: UniProtKB
  2. epidermis development Source: UniProtKB
  3. extracellular matrix organization Source: Reactome
  4. hydroxylysine biosynthetic process Source: UniProtKB
  5. oxidation-reduction process Source: UniProtKB
  6. response to hypoxia Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding, Vitamin C

Enzyme and pathway databases

ReactomeiREACT_121139. 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
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:9081. PLOD1.

Subcellular locationi

GO - Cellular componenti

  1. endoplasmic reticulum membrane Source: Reactome
  2. extracellular vesicular exosome Source: UniProt
  3. rough endoplasmic reticulum membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Ehlers-Danlos syndrome 6 (EDS6) [MIM:225400]: A 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.
Note: The disease is caused by mutations affecting the gene represented in this entry.6 Publications
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti367 – 3715Missing in EDS6.
VAR_009269
Natural varianti446 – 4461W → G in EDS6. 1 Publication
VAR_023466
Natural varianti532 – 5321Missing in EDS6. 1 Publication
VAR_006354
Natural varianti612 – 6121W → C in EDS6. 1 Publication
VAR_006355
Natural varianti667 – 6671A → T in EDS6. 1 Publication
Corresponds to variant rs199730384 [ dbSNP | Ensembl ].
VAR_023467
Natural varianti678 – 6781G → R in EDS6. 1 Publication
VAR_006356
Natural varianti706 – 7061H → R in EDS6. 1 Publication
VAR_023468

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi369 – 3691C → A: Loss of activity. 1 Publication

Keywords - Diseasei

Disease mutation, Ehlers-Danlos syndrome

Organism-specific databases

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 18181 PublicationAdd
BLAST
Chaini19 – 727709Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1PRO_0000024678Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi163 – 1631N-linked (GlcNAc...) Reviewed prediction
Glycosylationi197 – 1971N-linked (GlcNAc...) Inferred
Glycosylationi538 – 5381N-linked (GlcNAc...) Inferred
Glycosylationi686 – 6861N-linked (GlcNAc...) Reviewed prediction

Keywords - PTMi

Glycoprotein

Proteomic databases

MaxQBiQ02809.
PaxDbiQ02809.
PeptideAtlasiQ02809.
PRIDEiQ02809.

PTM databases

PhosphoSiteiQ02809.

Expressioni

Gene expression databases

ArrayExpressiQ02809.
BgeeiQ02809.
CleanExiHS_PLOD1.
GenevestigatoriQ02809.

Organism-specific databases

HPAiHPA049137.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi111366. 31 interactions.
IntActiQ02809. 14 interactions.
MINTiMINT-1134973.
STRINGi9606.ENSP00000196061.

Structurei

3D structure databases

ProteinModelPortaliQ02809.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini636 – 72792Fe2OG dioxygenaseAdd
BLAST

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiNOG311199.
HOGENOMiHOG000231099.
HOVERGENiHBG053618.
InParanoidiQ02809.
KOiK00473.
OrthoDBiEOG79PJNP.
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]

Sequencei

Sequence statusi: Complete.

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

Q02809-1 [UniParc]FASTAAdd to Basket

« Hide

MRPLLLLALL GWLLLAEAKG DAKPEDNLLV LTVATKETEG FRRFKRSAQF    50
FNYKIQALGL GEDWNVEKGT SAGGGQKVRL LKKALEKHAD KEDLVILFAD 100
SYDVLFASGP RELLKKFRQA RSQVVFSAEE LIYPDRRLET KYPVVSDGKR 150
FLGSGGFIGY APNLSKLVAE WEGQDSDSDQ LFYTKIFLDP EKREQINITL 200
DHRCRIFQNL DGALDEVVLK FEMGHVRARN LAYDTLPVLI HGNGPTKLQL 250
NYLGNYIPRF WTFETGCTVC DEGLRSLKGI GDEALPTVLV GVFIEQPTPF 300
VSLFFQRLLR LHYPQKHMRL FIHNHEQHHK AQVEEFLAQH GSEYQSVKLV 350
GPEVRMANAD ARNMGADLCR QDRSCTYYFS VDADVALTEP NSLRLLIQQN 400
KNVIAPLMTR HGRLWSNFWG ALSADGYYAR SEDYVDIVQG RRVGVWNVPY 450
ISNIYLIKGS ALRGELQSSD LFHHSKLDPD MAFCANIRQQ DVFMFLTNRH 500
TLGHLLSLDS YRTTHLHNDL WEVFSNPEDW KEKYIHQNYT KALAGKLVET 550
PCPDVYWFPI FTEVACDELV EEMEHFGQWS LGNNKDNRIQ GGYENVPTID 600
IHMNQIGFER EWHKFLLEYI APMTEKLYPG YYTRAQFDLA FVVRYKPDEQ 650
PSLMPHHDAS TFTINIALNR VGVDYEGGGC RFLRYNCSIR APRKGWTLMH 700
PGRLTHYHEG LPTTRGTRYI AVSFVDP 727
Length:727
Mass (Da):83,550
Last modified:October 25, 2005 - v2
Checksum:i6C3E0C11B15D598C
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti67 – 671E → D.
Corresponds to variant rs7551068 [ dbSNP | Ensembl ].
VAR_032754
Natural varianti84 – 841A → T.
Corresponds to variant rs34878020 [ dbSNP | Ensembl ].
VAR_032755
Natural varianti99 – 991A → T.2 Publications
Corresponds to variant rs7551175 [ dbSNP | Ensembl ].
VAR_014220
Natural varianti120 – 1201A → S.1 Publication
Corresponds to variant rs2273285 [ dbSNP | Ensembl ].
VAR_032756
Natural varianti123 – 1231Q → H in a breast cancer sample; somatic mutation. 1 Publication
VAR_035479
Natural varianti367 – 3715Missing in EDS6.
VAR_009269
Natural varianti446 – 4461W → G in EDS6. 1 Publication
VAR_023466
Natural varianti532 – 5321Missing in EDS6. 1 Publication
VAR_006354
Natural varianti612 – 6121W → C in EDS6. 1 Publication
VAR_006355
Natural varianti667 – 6671A → T in EDS6. 1 Publication
Corresponds to variant rs199730384 [ dbSNP | Ensembl ].
VAR_023467
Natural varianti678 – 6781G → R in EDS6. 1 Publication
VAR_006356
Natural varianti706 – 7061H → R in EDS6. 1 Publication
VAR_023468

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
AL096840 Genomic DNA. Translation: CAC19722.1.
BC016657 mRNA. Translation: AAH16657.1.
CCDSiCCDS142.1.
PIRiA38206.
RefSeqiNP_000293.2. NM_000302.3.
UniGeneiHs.75093.

Genome annotation databases

EnsembliENST00000196061; ENSP00000196061; ENSG00000083444.
GeneIDi5351.
KEGGihsa:5351.
UCSCiuc001atm.3. human.

Polymorphism databases

DMDMi78099790.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
AL096840 Genomic DNA. Translation: CAC19722.1 .
BC016657 mRNA. Translation: AAH16657.1 .
CCDSi CCDS142.1.
PIRi A38206.
RefSeqi NP_000293.2. NM_000302.3.
UniGenei Hs.75093.

3D structure databases

ProteinModelPortali Q02809.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 111366. 31 interactions.
IntActi Q02809. 14 interactions.
MINTi MINT-1134973.
STRINGi 9606.ENSP00000196061.

Chemistry

DrugBanki DB00350. Minoxidil.
DB00139. Succinic acid.
DB00126. Vitamin C.

PTM databases

PhosphoSitei Q02809.

Polymorphism databases

DMDMi 78099790.

Proteomic databases

MaxQBi Q02809.
PaxDbi Q02809.
PeptideAtlasi Q02809.
PRIDEi Q02809.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000196061 ; ENSP00000196061 ; ENSG00000083444 .
GeneIDi 5351.
KEGGi hsa:5351.
UCSCi uc001atm.3. human.

Organism-specific databases

CTDi 5351.
GeneCardsi GC01P011994.
GeneReviewsi PLOD1.
HGNCi HGNC:9081. PLOD1.
HPAi HPA049137.
MIMi 153454. gene.
225400. phenotype.
neXtProti NX_Q02809.
Orphaneti 1900. Ehlers-Danlos syndrome, kyphoscoliotic type.
PharmGKBi PA33411.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG311199.
HOGENOMi HOG000231099.
HOVERGENi HBG053618.
InParanoidi Q02809.
KOi K00473.
OrthoDBi EOG79PJNP.
PhylomeDBi Q02809.
TreeFami TF313826.

Enzyme and pathway databases

Reactomei REACT_121139. Collagen biosynthesis and modifying enzymes.

Miscellaneous databases

ChiTaRSi PLOD1. human.
GenomeRNAii 5351.
NextBioi 20742.
PROi Q02809.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q02809.
Bgeei Q02809.
CleanExi HS_PLOD1.
Genevestigatori Q02809.

Family and domain databases

InterProi IPR029044. Nucleotide-diphossugar_trans.
IPR005123. Oxoglu/Fe-dep_dioxygenase.
IPR006620. Pro_4_hyd_alph.
IPR001006. Procol_lys_dOase.
[Graphical view ]
Pfami PF03171. 2OG-FeII_Oxy. 1 hit.
[Graphical view ]
SMARTi SM00702. P4Hc. 1 hit.
[Graphical view ]
SUPFAMi SSF53448. SSF53448. 1 hit.
PROSITEi PS51471. FE2OG_OXY. 1 hit.
PS01325. LYS_HYDROXYLASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning of human lysyl hydroxylase: complete cDNA-derived amino acid sequence and assignment of the gene (PLOD) to chromosome 1p36.3-p36.2."
    Hautala T., Byers M.G., Eddy R.L., Shows T.B., Kivirikko K.I., Myllylae R.
    Genomics 13:62-69(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 19-28 AND 332-34, VARIANT THR-99.
    Tissue: Placenta.
  2. "Structure and expression of the human lysyl hydroxylase gene (PLOD): introns 9 and 16 contain Alu sequences at the sites of recombination in Ehlers-Danlos syndrome type VI patients."
    Heikkinen J., Hautala T., Kivirikko K.I., Myllylae R.
    Genomics 24:464-471(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS THR-99 AND SER-120.
    Tissue: Skin.
  5. "Site-directed mutagenesis of human lysyl hydroxylase expressed in insect cells. Identification of histidine residues and an aspartic acid residue critical for catalytic activity."
    Pirskanen A., Kaimio A.M., Myllylae R., Kivirikko K.I.
    J. Biol. Chem. 271:9398-9402(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS.
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "A patient with Ehlers-Danlos syndrome type VI is a compound heterozygote for mutations in the lysyl hydroxylase gene."
    Ha V.T., Marshall M.K., Elsas L.J., Pinnell S.R., Yeowell H.N.
    J. Clin. Invest. 93:1716-1721(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS EDS6 GLU-532 DEL AND ARG-678.
  8. "Ehlers-Danlos syndrome type VI: lysyl hydroxylase deficiency due to a novel point mutation (W612C)."
    Brinckmann J., Acil Y., Feshchenko S., Katzer E., Brenner R., Kulozik A., Kugler S.
    Arch. Dermatol. Res. 290:181-186(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT EDS6 CYS-612.
  9. "Deletion of cysteine 369 in lysyl hydroxylase 1 eliminates enzyme activity and causes Ehlers-Danlos syndrome type VI."
    Yeowell H.N., Allen J.D., Walker L.C., Overstreet M.A., Murad S., Thai S.F.
    Matrix Biol. 19:37-46(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT EDS6 367-ASP--GLN-371 DEL, MUTAGENESIS OF CYS-369.
  10. "Nevo syndrome is allelic to the kyphoscoliotic type of the Ehlers-Danlos syndrome (EDS VIA)."
    Giunta C., Randolph A., Al-Gazali L.I., Brunner H.G., Kraenzlin M.E., Steinmann B.
    Am. J. Med. Genet. A 133:158-164(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN EDS6.
  11. "A novel mutation in the lysyl hydroxylase 1 gene causes decreased lysyl hydroxylase activity in an Ehlers-Danlos VIA patient."
    Walker L.C., Overstreet M.A., Siddiqui A., De Paepe A., Ceylaner G., Malfait F., Symoens S., Atsawasuwan P., Yamauchi M., Ceylaner S., Bank R.A., Yeowell H.N.
    J. Invest. Dermatol. 124:914-918(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT EDS6 GLY-446.
  12. "Mutation analysis of the PLOD1 gene: an efficient multistep approach to the molecular diagnosis of the kyphoscoliotic type of Ehlers-Danlos syndrome (EDS VIA)."
    Giunta C., Randolph A., Steinmann B.
    Mol. Genet. Metab. 86:269-276(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS EDS6 THR-667 AND ARG-706.
  13. Cited for: VARIANT [LARGE SCALE ANALYSIS] HIS-123.

Entry informationi

Entry nameiPLOD1_HUMAN
AccessioniPrimary (citable) accession number: Q02809
Secondary accession number(s): Q96AV9, Q9H132
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: October 25, 2005
Last modified: September 3, 2014
This is version 168 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

External Data

Dasty 3

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