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Protein

Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3

Gene

PLOD3

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

Protein has several cofactor binding sites:

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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding, Vitamin C

Enzyme and pathway databases

BRENDAi1.14.11.4. 2681.
2.4.1.50. 2681.
2.4.1.66. 2681.
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 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:9083. PLOD3.

Subcellular locationi

GO - Cellular componenti

  • endoplasmic reticulum Source: ProtInc
  • endoplasmic reticulum membrane Source: Reactome
  • extracellular exosome Source: UniProtKB
  • rough endoplasmic reticulum membrane Source: UniProtKB-SubCell
Complete GO annotation...

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)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.

Chemistry

DrugBankiDB00139. Succinic acid.
DB00126. Vitamin C.

Polymorphism and mutation databases

BioMutaiPLOD3.

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

BgeeiO60568.
CleanExiHS_PLOD3.
ExpressionAtlasiO60568. baseline and differential.
GenevisibleiO60568. HS.

Organism-specific databases

HPAiHPA001236.

Interactioni

Subunit structurei

Homodimer.

Binary interactionsi

WithEntry#Exp.IntActNotes
EFHC2Q5JST63EBI-741582,EBI-2349927
EHMT2A2ABF93EBI-741582,EBI-10174566
RAB3IPQ96QF03EBI-741582,EBI-747844
RHOXF2Q9BQY42EBI-741582,EBI-372094

Protein-protein interaction databases

BioGridi114467. 24 interactions.
IntActiO60568. 15 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.
GeneTreeiENSGT00550000074427.
HOGENOMiHOG000231099.
HOVERGENiHBG053618.
InParanoidiO60568.
KOiK13646.
OMAiTKARAVM.
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

        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)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:
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.3. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliO60568.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114467. 24 interactions.
IntActiO60568. 15 interactions.
MINTiMINT-1438117.
STRINGi9606.ENSP00000223127.

Chemistry

DrugBankiDB00139. Succinic acid.
DB00126. Vitamin C.

PTM databases

PhosphoSiteiO60568.

Polymorphism and mutation databases

BioMutaiPLOD3.

Proteomic databases

MaxQBiO60568.
PaxDbiO60568.
PeptideAtlasiO60568.
PRIDEiO60568.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000223127; ENSP00000223127; ENSG00000106397.
GeneIDi8985.
KEGGihsa:8985.
UCSCiuc003uyd.3. human.

Organism-specific databases

CTDi8985.
GeneCardsiGC07M100849.
HGNCiHGNC:9083. PLOD3.
HPAiHPA001236.
MIMi603066. gene.
612394. phenotype.
neXtProtiNX_O60568.
Orphaneti300284. Connective tissue disorder due to lysyl hydroxylase-3 deficiency.
PharmGKBiPA33413.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG311199.
GeneTreeiENSGT00550000074427.
HOGENOMiHOG000231099.
HOVERGENiHBG053618.
InParanoidiO60568.
KOiK13646.
OMAiTKARAVM.
OrthoDBiEOG79PJNP.
PhylomeDBiO60568.
TreeFamiTF313826.

Enzyme and pathway databases

BRENDAi1.14.11.4. 2681.
2.4.1.50. 2681.
2.4.1.66. 2681.
ReactomeiREACT_121139. Collagen biosynthesis and modifying enzymes.

Miscellaneous databases

ChiTaRSiPLOD3. human.
GeneWikiiPLOD3.
GenomeRNAii8985.
NextBioi33693.
PROiO60568.
SOURCEiSearch...

Gene expression databases

BgeeiO60568.
CleanExiHS_PLOD3.
ExpressionAtlasiO60568. baseline and differential.
GenevisibleiO60568. HS.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: July 22, 2015
This is version 144 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.