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O60568 (PLOD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 130. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3

EC=1.14.11.4
Alternative name(s):
Lysyl hydroxylase 3
Short name=LH3
Gene names
Name:PLOD3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length738 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Cofactor

Iron.

Ascorbate.

Subunit structure

Homodimer.

Subcellular location

Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side.

Involvement in disease

Lysyl hydroxylase 3 deficiency (LH3 deficiency) [MIM:612394]: Connective 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.
Note: The disease is caused by mutations affecting the gene represented in this entry.

Sequence similarities

Contains 1 Fe2OG dioxygenase domain.

Ontologies

Keywords
   Cellular componentEndoplasmic reticulum
Membrane
   Coding sequence diversityPolymorphism
   DiseaseDisease mutation
   DomainSignal
   LigandIron
Metal-binding
Vitamin C
   Molecular functionDioxygenase
Oxidoreductase
   PTMGlycoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processbasement membrane assembly

Inferred from electronic annotation. Source: Ensembl

cellular protein modification process

Traceable author statement Ref.2. Source: ProtInc

cellular response to hormone stimulus

Inferred from electronic annotation. Source: Ensembl

collagen fibril organization

Inferred from electronic annotation. Source: Ensembl

endothelial cell morphogenesis

Inferred from electronic annotation. Source: Ensembl

epidermis morphogenesis

Inferred from electronic annotation. Source: Ensembl

extracellular matrix organization

Traceable author statement. Source: Reactome

in utero embryonic development

Inferred from electronic annotation. Source: Ensembl

lung morphogenesis

Inferred from electronic annotation. Source: Ensembl

neural tube development

Inferred from electronic annotation. Source: Ensembl

protein localization

Inferred from electronic annotation. Source: Ensembl

vasodilation

Inferred from electronic annotation. Source: Ensembl

   Cellular_componentendoplasmic reticulum

Traceable author statement Ref.2. Source: ProtInc

endoplasmic reticulum membrane

Traceable author statement. Source: Reactome

extracellular vesicular exosome

Inferred from direct assay PubMed 19056867PubMed 19199708. Source: UniProt

rough endoplasmic reticulum membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionL-ascorbic acid binding

Inferred from electronic annotation. Source: UniProtKB-KW

iron ion binding

Inferred from electronic annotation. Source: InterPro

procollagen galactosyltransferase activity

Traceable author statement. Source: Reactome

procollagen glucosyltransferase activity

Traceable author statement. Source: Reactome

procollagen-lysine 5-dioxygenase activity

Traceable author statement Ref.2. Source: ProtInc

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

RHOXF2Q9BQY42EBI-741582,EBI-372094

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2424 Potential
Chain25 – 738714Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
PRO_0000024686

Regions

Domain647 – 73892Fe2OG dioxygenase

Sites

Active site7291 Potential
Metal binding6671Iron By similarity
Metal binding6691Iron By similarity
Metal binding7191Iron By similarity

Amino acid modifications

Glycosylation631N-linked (GlcNAc...) Potential
Glycosylation5481N-linked (GlcNAc...) Potential

Natural variations

Natural variant1511A → V.
Corresponds to variant rs35627324 [ dbSNP | Ensembl ].
VAR_051708
Natural variant2231N → S in LH3 deficiency. Ref.10
VAR_054913
Natural variant2861R → W.
Corresponds to variant rs1134907 [ dbSNP | Ensembl ].
VAR_012075

Sequences

Sequence LengthMass (Da)Tools
O60568 [UniParc].

Last modified August 1, 1998. Version 1.
Checksum: 08424B46985941F9

FASTA73884,785
        10         20         30         40         50         60 
MTSSGPGPRF LLLLPLLLPP AASASDRPRG RDPVNPEKLL VITVATAETE GYLRFLRSAE 

        70         80         90        100        110        120 
FFNYTVRTLG LGEEWRGGDV ARTVGGGQKV RWLKKEMEKY ADREDMIIMF VDSYDVILAG 

       130        140        150        160        170        180 
SPTELLKKFV QSGSRLLFSA ESFCWPEWGL AEQYPEVGTG KRFLNSGGFI GFATTIHQIV 

       190        200        210        220        230        240 
RQWKYKDDDD DQLFYTRLYL DPGLREKLSL NLDHKSRIFQ NLNGALDEVV LKFDRNRVRI 

       250        260        270        280        290        300 
RNVAYDTLPI VVHGNGPTKL QLNYLGNYVP NGWTPEGGCG FCNQDRRTLP GGQPPPRVFL 

       310        320        330        340        350        360 
AVFVEQPTPF LPRFLQRLLL LDYPPDRVTL FLHNNEVFHE PHIADSWPQL QDHFSAVKLV 

       370        380        390        400        410        420 
GPEEALSPGE ARDMAMDLCR QDPECEFYFS LDADAVLTNL QTLRILIEEN RKVIAPMLSR 

       430        440        450        460        470        480 
HGKLWSNFWG ALSPDEYYAR SEDYVELVQR KRVGVWNVPY ISQAYVIRGD TLRMELPQRD 

       490        500        510        520        530        540 
VFSGSDTDPD MAFCKSFRDK GIFLHLSNQH EFGRLLATSR YDTEHLHPDL WQIFDNPVDW 

       550        560        570        580        590        600 
KEQYIHENYS RALEGEGIVE QPCPDVYWFP LLSEQMCDEL VAEMEHYGQW SGGRHEDSRL 

       610        620        630        640        650        660 
AGGYENVPTV DIHMKQVGYE DQWLQLLRTY VGPMTESLFP GYHTKARAVM NFVVRYRPDE 

       670        680        690        700        710        720 
QPSLRPHHDS STFTLNVALN HKGLDYEGGG CRFLRYDCVI SSPRKGWALL HPGRLTHYHE 

       730 
GLPTTWGTRY IMVSFVDP 

« Hide

References

« Hide 'large scale' references
[1]"Primary structure, tissue distribution, and chromosomal localization of a novel isoform of lysyl hydroxylase (lysyl hydroxylase 3)."
Valtavaara M., Szpirer C., Szpirer J., Myllylae R.
J. Biol. Chem. 273:12881-12886(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Cloning and characterization of a third human lysyl hydroxylase isoform."
Passoja K., Rautavuoma K., Ala-Kokko L., Kosonen T., Kivirikko K.I.
Proc. Natl. Acad. Sci. U.S.A. 95:10482-10486(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"Complete exon-intron organization of the gene for human lysyl hydroxylase 3 (LH3)."
Rautavuoma K., Passoja K., Helaakoski T., Kivirikko K.I.
Matrix Biol. 19:73-79(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]"A gene upregulated by HBVX and is similar to LH3."
Lian Z., Feitelson M.
Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[5]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Small intestine.
[6]"The DNA sequence of human chromosome 7."
Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. expand/collapse author list , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]"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].
Tissue: Pancreas.
[9]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"A connective tissue disorder caused by mutations of the lysyl hydroxylase 3 gene."
Salo A.M., Cox H., Farndon P., Moss C., Grindulis H., Risteli M., Robins S.P., Myllylae R.
Am. J. Hum. Genet. 83:495-503(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT LH3 DEFICIENCY SER-223.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001075.1. NM_001084.4.
UniGeneHs.153357.

3D structure databases

ProteinModelPortalO60568.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114467. 25 interactions.
IntActO60568. 11 interactions.
MINTMINT-1438117.
STRING9606.ENSP00000223127.

Chemistry

DrugBankDB00139. Succinic acid.
DB00126. Vitamin C.

PTM databases

PhosphoSiteO60568.

Proteomic databases

PaxDbO60568.
PeptideAtlasO60568.
PRIDEO60568.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000223127; ENSP00000223127; ENSG00000106397.
GeneID8985.
KEGGhsa:8985.
UCSCuc003uyd.3. human.

Organism-specific databases

CTD8985.
GeneCardsGC07M100849.
HGNCHGNC:9083. PLOD3.
HPAHPA001236.
MIM603066. gene.
612394. phenotype.
neXtProtNX_O60568.
Orphanet300284. Connective tissue disorder due to lysyl hydroxylase-3 deficiency.
PharmGKBPA33413.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG311199.
HOGENOMHOG000231099.
HOVERGENHBG053618.
InParanoidO60568.
KOK13646.
OMALRYDCVI.
OrthoDBEOG79PJNP.
PhylomeDBO60568.
TreeFamTF313826.

Enzyme and pathway databases

ReactomeREACT_118779. Extracellular matrix organization.

Gene expression databases

ArrayExpressO60568.
BgeeO60568.
CleanExHS_PLOD3.
GenevestigatorO60568.

Family and domain databases

InterProIPR005123. Oxoglu/Fe-dep_dioxygenase.
IPR006620. Pro_4_hyd_alph.
IPR001006. Procol_lys_dOase.
[Graphical view]
PfamPF03171. 2OG-FeII_Oxy. 1 hit.
[Graphical view]
SMARTSM00702. P4Hc. 1 hit.
[Graphical view]
PROSITEPS51471. FE2OG_OXY. 1 hit.
PS01325. LYS_HYDROXYLASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPLOD3. human.
GeneWikiPLOD3.
GenomeRNAi8985.
NextBio33693.
PROO60568.
SOURCESearch...

Entry information

Entry namePLOD3_HUMAN
AccessionPrimary (citable) accession number: O60568
Secondary accession number(s): B2R6W6, Q540C3
Entry history
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: August 1, 1998
Last modified: April 16, 2014
This is version 130 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM