Reviewed,
UniProtKB/Swiss-Prot O60568 (PLOD3_HUMAN)
Last modified
July 7, 2009.
Version 82.
History...
Clusters with 100%,
90%,
50% identity |
Documents (5) |
Third-party data |
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Names and origin
| Protein names | Recommended name: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 EC=1.14.11.4 Alternative name(s): Lysyl hydroxylase 3 Short name=LH3 | ||
| Gene names |
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| Organism | Homo sapiens (Human) [Complete proteome] | ||
| Taxonomic identifier | 9606 [NCBI] | ||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 738 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is further processed into a mature form. |
| Protein existence | Evidence 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 | Procollagen L-lysine + 2-oxoglutarate + O2 = procollagen 5-hydroxy-L-lysine + succinate + CO2. |
| Cofactor | Iron. Ascorbate. |
| Subunit structure | Homodimer. |
| Subcellular location | Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side. |
| Involvement in disease | Defects in PLOD3 are the cause of lysyl hydroxylase 3 deficiency (LH3 deficiency) [MIM:612394]; also called bone fragility with contractures arterial rupture and deafness. LH3 deficiency is a 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. |
| Sequence similarities | Contains 1 PKHD (prolyl/lysyl hydroxylase) domain. |
Ontologies
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Signal peptide | 1 – 24 | 24 | Potential | ||||||
| Chain | 25 – 738 | 714 | Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 | PRO_0000024686 | |||||
Regions | |||||||||
| Domain | 565 – 738 | 174 | PKHD | ||||||
Sites | |||||||||
| Active site | 729 | 1 | Potential | ||||||
| Metal binding | 667 | 1 | Iron By similarity | ||||||
| Metal binding | 669 | 1 | Iron By similarity | ||||||
| Metal binding | 719 | 1 | Iron By similarity | ||||||
Amino acid modifications | |||||||||
| Glycosylation | 63 | 1 | N-linked (GlcNAc...) Potential | ||||||
| Glycosylation | 548 | 1 | N-linked (GlcNAc...) Potential | ||||||
Natural variations | |||||||||
| Natural variant | 151 | 1 | A → V: dbSNP rs35627324. | VAR_051708 | |||||
| Natural variant | 223 | 1 | N → S in LH3 deficiency. | VAR_054913 | |||||
| Natural variant | 286 | 1 | R → W: dbSNP rs1134907. | VAR_012075 | |||||
Sequences
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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: 9582318] [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: 9724729] [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: 10686427] [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] | "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. Wilson R.K.Nature 424:157-164(2003) [PubMed: 12853948] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [6] | "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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Pancreas. |
| [7] | Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY. |
| [8] | "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: 18834968] [Abstract] Cited for: VARIANT LH3 DEFICIENCY SER-223. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |
|---|---|
| AF046889 mRNA. Translation: AAC39753.1. AF068229 mRNA. Translation: AAC34808.1. AF207069 Genomic DNA. Translation: AAF63701.1. AY220458 mRNA. Translation: AAO61775.1. AC004876 Genomic DNA. Translation: AAD45831.1. BC011674 mRNA. Translation: AAH11674.1. | |
| IPI | IPI00030255. |
| RefSeq | NP_001075.1. |
| UniGene | Hs.153357 |
3D structure databases | |
| ModBase | Search... |
Protein-protein interaction databases | |
| IntAct | O60568. 6 interactions. |
PTM databases | |
| PhosphoSite | O60568. |
Proteomic databases | |
| PeptideAtlas | O60568. |
| PRIDE | O60568. |
Genome annotation databases | |
| Ensembl | ENSG00000106397. Homo sapiens. [Contig view] |
| GeneID | 8985. |
| KEGG | hsa:8985. |
| UCSC | uc003uyd.1. human. |
Organism-specific databases | |
| GeneCards | GC07M100635. |
| H-InvDB | HIX0006947. |
| HGNC | HGNC:9083. PLOD3. |
| MIM | 603066. gene. 612394. phenotype. |
| PharmGKB | PA33413. |
| GenAtlas | Search... |
Phylogenomic databases | |
| HOGENOM | O60568. |
| HOVERGEN | O60568. |
| OMA | O60568. SAEFFNY. |
Enzyme and pathway databases | |
| BRENDA | 1.14.11.4. 247. |
Gene expression databases | |
| ArrayExpress | O60568. |
| Bgee | O60568. |
| CleanEx | HS_PLOD3. |
| GermOnline | ENSG00000106397. Homo sapiens. |
Family and domain databases | |
| InterPro | IPR005123. Oxoglutarate/Fe-dep_Oase. IPR006620. Pro_4_hyd_alph. IPR001006. Procol_lys_dOase. [Graphical view] |
| Pfam | PF03171. 2OG-FeII_Oxy. 1 hit. [Graphical view] |
| ProDom | PD011578. ProcolLys_dioxy. 1 hit. [Graphical view] [Entries sharing at least one domain] |
| SMART | SM00702. P4Hc. 1 hit. [Graphical view] |
| PROSITE | PS01325. LYS_HYDROXYLASE. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other Resources | |
| DrugBank | DB00139. Succinic acid. DB00126. Vitamin C. |
| NextBio | 33693. |
| SOURCE | Search... |
Entry information
| Entry name | PLOD3_HUMAN | ||||||||
| Accession | Primary (citable) accession number: O60568 Secondary accession number(s): Q540C3 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
Relevant documents
| Human chromosome 7 Human chromosome 7: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| SIMILARITY comments Index of protein domains and families |

Clusters with


