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Protein

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3

Gene

PLOD3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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.By similarity

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • Fe2+By similarity
  • L-ascorbateBy similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi667IronPROSITE-ProRule annotation1
Metal bindingi669IronPROSITE-ProRule annotation1
Metal bindingi719IronPROSITE-ProRule annotation1
Active sitei729Sequence analysis1

GO - Molecular functioni

  • iron ion binding Source: InterPro
  • L-ascorbic acid binding Source: UniProtKB-KW
  • procollagen galactosyltransferase activity Source: Reactome
  • procollagen glucosyltransferase activity Source: CAFA
  • procollagen-lysine 5-dioxygenase activity Source: CAFA

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BRENDAi1.14.11.4 2681
2.4.1.50 2681
2.4.1.66 2681
ReactomeiR-HSA-1650814 Collagen biosynthesis and modifying enzymes

Protein family/group databases

MoonProtiO60568

Names & Taxonomyi

Protein namesi
Recommended name:
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 (EC:1.14.11.4By similarity)
Alternative name(s):
Lysyl hydroxylase 3
Short name:
LH3
Gene namesi
Name:PLOD3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

EuPathDBiHostDB:ENSG00000106397.11
HGNCiHGNC:9083 PLOD3
MIMi603066 gene
neXtProtiNX_O60568

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

Lysyl hydroxylase 3 deficiency (LH3 deficiency)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionConnective tissue disorder. The syndrome is characterized by congenital malformations severely affecting many tissues and organs and revealing features of several collagen disorders, most of them involving COL2A1 (type II collagen). The findings suggest that the failure of lysyl hydroxylation and hydroxylysyl carbohydrate addition, which affects many collagens, is the molecular basis of this syndrome.
See also OMIM:612394
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_054913223N → S in LH3 deficiency. 1 PublicationCorresponds to variant dbSNP:rs121434414EnsemblClinVar.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi8985
MalaCardsiPLOD3
MIMi612394 phenotype
OpenTargetsiENSG00000106397
Orphaneti300284 Connective tissue disorder due to lysyl hydroxylase-3 deficiency
PharmGKBiPA33413

Chemistry databases

DrugBankiDB00139 Succinic acid
DB00126 Vitamin C

Polymorphism and mutation databases

BioMutaiPLOD3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 24Sequence analysisAdd BLAST24
ChainiPRO_000002468625 – 738Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3Add BLAST714

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi63N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi548N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiO60568
MaxQBiO60568
PaxDbiO60568
PeptideAtlasiO60568
PRIDEiO60568

PTM databases

iPTMnetiO60568
PhosphoSitePlusiO60568

Expressioni

Gene expression databases

BgeeiENSG00000106397
CleanExiHS_PLOD3
ExpressionAtlasiO60568 baseline and differential
GenevisibleiO60568 HS

Organism-specific databases

HPAiHPA001236

Interactioni

Subunit structurei

Homodimer.By similarity

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi114467, 57 interactors
IntActiO60568, 33 interactors
MINTiO60568
STRINGi9606.ENSP00000223127

Structurei

3D structure databases

ProteinModelPortaliO60568
SMRiO60568
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini647 – 738Fe2OG dioxygenasePROSITE-ProRule annotationAdd BLAST92

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiKOG1971 Eukaryota
ENOG410Y4QU LUCA
GeneTreeiENSGT00550000074427
HOGENOMiHOG000231099
HOVERGENiHBG053618
InParanoidiO60568
KOiK13646
OMAiLFYTRLY
OrthoDBiEOG091G02DK
PhylomeDBiO60568
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

Sequencei

Sequence statusi: Complete.

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

O60568-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSSGPGPRF LLLLPLLLPP AASASDRPRG RDPVNPEKLL VITVATAETE
60 70 80 90 100
GYLRFLRSAE FFNYTVRTLG LGEEWRGGDV ARTVGGGQKV RWLKKEMEKY
110 120 130 140 150
ADREDMIIMF VDSYDVILAG SPTELLKKFV QSGSRLLFSA ESFCWPEWGL
160 170 180 190 200
AEQYPEVGTG KRFLNSGGFI GFATTIHQIV RQWKYKDDDD DQLFYTRLYL
210 220 230 240 250
DPGLREKLSL NLDHKSRIFQ NLNGALDEVV LKFDRNRVRI RNVAYDTLPI
260 270 280 290 300
VVHGNGPTKL QLNYLGNYVP NGWTPEGGCG FCNQDRRTLP GGQPPPRVFL
310 320 330 340 350
AVFVEQPTPF LPRFLQRLLL LDYPPDRVTL FLHNNEVFHE PHIADSWPQL
360 370 380 390 400
QDHFSAVKLV GPEEALSPGE ARDMAMDLCR QDPECEFYFS LDADAVLTNL
410 420 430 440 450
QTLRILIEEN RKVIAPMLSR HGKLWSNFWG ALSPDEYYAR SEDYVELVQR
460 470 480 490 500
KRVGVWNVPY ISQAYVIRGD TLRMELPQRD VFSGSDTDPD MAFCKSFRDK
510 520 530 540 550
GIFLHLSNQH EFGRLLATSR YDTEHLHPDL WQIFDNPVDW KEQYIHENYS
560 570 580 590 600
RALEGEGIVE QPCPDVYWFP LLSEQMCDEL VAEMEHYGQW SGGRHEDSRL
610 620 630 640 650
AGGYENVPTV DIHMKQVGYE DQWLQLLRTY VGPMTESLFP GYHTKARAVM
660 670 680 690 700
NFVVRYRPDE QPSLRPHHDS STFTLNVALN HKGLDYEGGG CRFLRYDCVI
710 720 730
SSPRKGWALL HPGRLTHYHE GLPTTWGTRY IMVSFVDP
Length:738
Mass (Da):84,785
Last modified:August 1, 1998 - v1
Checksum:i08424B46985941F9
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_051708151A → V. Corresponds to variant dbSNP:rs35627324Ensembl.1
Natural variantiVAR_054913223N → S in LH3 deficiency. 1 PublicationCorresponds to variant dbSNP:rs121434414EnsemblClinVar.1
Natural variantiVAR_012075286R → W. Corresponds to variant dbSNP:rs1134907Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF046889 mRNA Translation: AAC39753.1
AF068229 mRNA Translation: AAC34808.1
AF207069 Genomic DNA Translation: AAF63701.1
AY220458 mRNA Translation: AAO61775.1
AK312743 mRNA Translation: BAG35613.1
AC004876 Genomic DNA Translation: AAD45831.1
CH471197 Genomic DNA Translation: EAW50205.1
BC011674 mRNA Translation: AAH11674.1
CCDSiCCDS5715.1
RefSeqiNP_001075.1, NM_001084.4
UniGeneiHs.153357

Genome annotation databases

EnsembliENST00000223127; ENSP00000223127; ENSG00000106397
GeneIDi8985
KEGGihsa:8985
UCSCiuc003uyd.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiPLOD3_HUMAN
AccessioniPrimary (citable) accession number: O60568
Secondary accession number(s): B2R6W6, Q540C3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: August 1, 1998
Last modified: April 25, 2018
This is version 167 of the entry and version 1 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, Reference proteome

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