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O60568

- PLOD3_HUMAN

UniProt

O60568 - PLOD3_HUMAN

Protein

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3

Gene

PLOD3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 135 (01 Oct 2014)
      Sequence version 1 (01 Aug 1998)
      Previous versions | rss
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    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 bindingi667 – 6671IronPROSITE-ProRule annotation
    Metal bindingi669 – 6691IronPROSITE-ProRule annotation
    Metal bindingi719 – 7191IronPROSITE-ProRule annotation
    Active sitei729 – 7291Sequence Analysis

    GO - Molecular functioni

    1. iron ion binding Source: InterPro
    2. L-ascorbic acid binding Source: UniProtKB-KW
    3. procollagen galactosyltransferase activity Source: Reactome
    4. procollagen glucosyltransferase activity Source: Reactome
    5. procollagen-lysine 5-dioxygenase activity Source: ProtInc
    6. protein binding Source: IntAct

    GO - Biological processi

    1. basement membrane assembly Source: Ensembl
    2. cellular protein modification process Source: ProtInc
    3. cellular response to hormone stimulus Source: Ensembl
    4. collagen fibril organization Source: Ensembl
    5. endothelial cell morphogenesis Source: Ensembl
    6. epidermis morphogenesis Source: Ensembl
    7. extracellular matrix organization Source: Reactome
    8. in utero embryonic development Source: Ensembl
    9. lung morphogenesis Source: Ensembl
    10. neural tube development Source: Ensembl
    11. protein localization Source: Ensembl
    12. vasodilation Source: Ensembl

    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 3 (EC:1.14.11.4)
    Alternative name(s):
    Lysyl hydroxylase 3
    Short name:
    LH3
    Gene namesi
    Name:PLOD3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 7

    Organism-specific databases

    HGNCiHGNC:9083. PLOD3.

    Subcellular locationi

    GO - Cellular componenti

    1. endoplasmic reticulum Source: ProtInc
    2. endoplasmic reticulum membrane Source: Reactome
    3. extracellular vesicular exosome Source: UniProt
    4. rough endoplasmic reticulum membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Endoplasmic reticulum, Membrane

    Pathology & Biotechi

    Involvement in diseasei

    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.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti223 – 2231N → S in LH3 deficiency. 1 Publication
    VAR_054913

    Keywords - Diseasei

    Disease mutation

    Organism-specific databases

    MIMi612394. phenotype.
    Orphaneti300284. Connective tissue disorder due to lysyl hydroxylase-3 deficiency.
    PharmGKBiPA33413.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2424Sequence AnalysisAdd
    BLAST
    Chaini25 – 738714Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3PRO_0000024686Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi63 – 631N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi548 – 5481N-linked (GlcNAc...)Sequence Analysis

    Keywords - PTMi

    Glycoprotein

    Proteomic databases

    MaxQBiO60568.
    PaxDbiO60568.
    PeptideAtlasiO60568.
    PRIDEiO60568.

    PTM databases

    PhosphoSiteiO60568.

    Expressioni

    Gene expression databases

    ArrayExpressiO60568.
    BgeeiO60568.
    CleanExiHS_PLOD3.
    GenevestigatoriO60568.

    Organism-specific databases

    HPAiHPA001236.

    Interactioni

    Subunit structurei

    Homodimer.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    RHOXF2Q9BQY42EBI-741582,EBI-372094

    Protein-protein interaction databases

    BioGridi114467. 25 interactions.
    IntActiO60568. 11 interactions.
    MINTiMINT-1438117.
    STRINGi9606.ENSP00000223127.

    Structurei

    3D structure databases

    ProteinModelPortaliO60568.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini647 – 73892Fe2OG dioxygenasePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 Fe2OG dioxygenase domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiNOG311199.
    HOGENOMiHOG000231099.
    HOVERGENiHBG053618.
    InParanoidiO60568.
    KOiK13646.
    OMAiLRYDCVI.
    OrthoDBiEOG79PJNP.
    PhylomeDBiO60568.
    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.

    O60568-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTSSGPGPRF LLLLPLLLPP AASASDRPRG RDPVNPEKLL VITVATAETE    50
    GYLRFLRSAE FFNYTVRTLG LGEEWRGGDV ARTVGGGQKV RWLKKEMEKY 100
    ADREDMIIMF VDSYDVILAG SPTELLKKFV QSGSRLLFSA ESFCWPEWGL 150
    AEQYPEVGTG KRFLNSGGFI GFATTIHQIV RQWKYKDDDD DQLFYTRLYL 200
    DPGLREKLSL NLDHKSRIFQ NLNGALDEVV LKFDRNRVRI RNVAYDTLPI 250
    VVHGNGPTKL QLNYLGNYVP NGWTPEGGCG FCNQDRRTLP GGQPPPRVFL 300
    AVFVEQPTPF LPRFLQRLLL LDYPPDRVTL FLHNNEVFHE PHIADSWPQL 350
    QDHFSAVKLV GPEEALSPGE ARDMAMDLCR QDPECEFYFS LDADAVLTNL 400
    QTLRILIEEN RKVIAPMLSR HGKLWSNFWG ALSPDEYYAR SEDYVELVQR 450
    KRVGVWNVPY ISQAYVIRGD TLRMELPQRD VFSGSDTDPD MAFCKSFRDK 500
    GIFLHLSNQH EFGRLLATSR YDTEHLHPDL WQIFDNPVDW KEQYIHENYS 550
    RALEGEGIVE QPCPDVYWFP LLSEQMCDEL VAEMEHYGQW SGGRHEDSRL 600
    AGGYENVPTV DIHMKQVGYE DQWLQLLRTY VGPMTESLFP GYHTKARAVM 650
    NFVVRYRPDE QPSLRPHHDS STFTLNVALN HKGLDYEGGG CRFLRYDCVI 700
    SSPRKGWALL HPGRLTHYHE GLPTTWGTRY IMVSFVDP 738
    Length:738
    Mass (Da):84,785
    Last modified:August 1, 1998 - v1
    Checksum:i08424B46985941F9
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti151 – 1511A → V.
    Corresponds to variant rs35627324 [ dbSNP | Ensembl ].
    VAR_051708
    Natural varianti223 – 2231N → S in LH3 deficiency. 1 Publication
    VAR_054913
    Natural varianti286 – 2861R → W.
    Corresponds to variant rs1134907 [ dbSNP | Ensembl ].
    VAR_012075

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.3. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    CCDSi CCDS5715.1.
    RefSeqi NP_001075.1. NM_001084.4.
    UniGenei Hs.153357.

    3D structure databases

    ProteinModelPortali O60568.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 114467. 25 interactions.
    IntActi O60568. 11 interactions.
    MINTi MINT-1438117.
    STRINGi 9606.ENSP00000223127.

    Chemistry

    DrugBanki DB00139. Succinic acid.
    DB00126. Vitamin C.

    PTM databases

    PhosphoSitei O60568.

    Proteomic databases

    MaxQBi O60568.
    PaxDbi O60568.
    PeptideAtlasi O60568.
    PRIDEi O60568.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000223127 ; ENSP00000223127 ; ENSG00000106397 .
    GeneIDi 8985.
    KEGGi hsa:8985.
    UCSCi uc003uyd.3. human.

    Organism-specific databases

    CTDi 8985.
    GeneCardsi GC07M100849.
    HGNCi HGNC:9083. PLOD3.
    HPAi HPA001236.
    MIMi 603066. gene.
    612394. phenotype.
    neXtProti NX_O60568.
    Orphaneti 300284. Connective tissue disorder due to lysyl hydroxylase-3 deficiency.
    PharmGKBi PA33413.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG311199.
    HOGENOMi HOG000231099.
    HOVERGENi HBG053618.
    InParanoidi O60568.
    KOi K13646.
    OMAi LRYDCVI.
    OrthoDBi EOG79PJNP.
    PhylomeDBi O60568.
    TreeFami TF313826.

    Enzyme and pathway databases

    Reactomei REACT_121139. Collagen biosynthesis and modifying enzymes.

    Miscellaneous databases

    ChiTaRSi PLOD3. human.
    GeneWikii PLOD3.
    GenomeRNAii 8985.
    NextBioi 33693.
    PROi O60568.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O60568.
    Bgeei O60568.
    CleanExi HS_PLOD3.
    Genevestigatori O60568.

    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

    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.
      , 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.
      , 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. 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. 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.

    Entry informationi

    Entry nameiPLOD3_HUMAN
    AccessioniPrimary (citable) accession number: O60568
    Secondary accession number(s): B2R6W6, Q540C3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: August 1, 1998
    Last modified: October 1, 2014
    This is version 135 of the entry and version 1 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, Reference proteome

    Documents

    1. Human chromosome 7
      Human chromosome 7: 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