Lumican (LUM)
The protein contains 338 amino acids for an estimated molecular weight of 38429 Da.
No function (updated: Oct. 10, 2018)
Protein identification was indicated in the following studies:
Methods
The following articles were analysed to gather the proteome content of erythrocytes.
The gene or protein list provided in the studies were processed using the ID mapping API of Uniprot in September 2018. The number of proteins identified and mapped without ambiguity in these studies is indicated below.
Only Swiss-Prot entries (reviewed) were considered for protein evidence assignation.
| Publication | Identification 1 | Uniprot mapping 2 | Not mapped / Obsolete | TrEMBL | Swiss-Prot |
|---|---|---|---|---|---|
| Goodman (2013) | 2289 (gene list) | 2278 | 53 | 20599 | 2269 |
| Lange (2014) | 1234 | 1234 | 7 | 28 | 1224 |
| Hegedus (2015) | 2638 | 2622 | 0 | 235 | 2387 |
| Wilson (2016) | 1658 | 1528 | 170 | 291 | 1068 |
| d'Alessandro (2017) | 1826 | 1817 | 2 | 0 | 1815 |
| Bryk (2017) | 2090 | 2060 | 10 | 108 | 1942 |
| Chu (2018) | 1853 | 1804 | 55 | 362 | 1387 |
1 as available in the article and/or in supplementary material
2 uniprot mapping returns all protein isoforms as one entry
The compilation of older studies can be retrieved from the Red Blood Cell Collection database.
The data and differentiation stages presented below come from the proteomic study and analysis performed by our partners of the GReX consortium, more details are available in their published work.
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| Variant | Description |
|---|---|
| Found in patients with amyotrophic lateral sclerosis |
No binding partner found
Biological Process
Cartilage development
Collagen fibril organization
Extracellular matrix organization
Keratan sulfate biosynthetic process
Keratan sulfate catabolic process
Positive regulation of transcription by RNA polymerase II
Positive regulation of transforming growth factor beta1 production
Response to growth factor
Response to organic cyclic compound
Visual perception
The reference OMIM entry for this protein is 600616
Lumican; lum
Ldc
DESCRIPTION
Lumican, a member of the small interstitial proteoglycan gene (SIPG) family, is a keratan sulfate proteoglycan present in large quantities in the corneal stroma and in interstitial collagenous matrices of the heart, aorta, skeletal muscle, skin, and intervertebral discs (Chakravarti and Magnuson, 1995). Other SIPG members are decorin (125255), biglycan (301870), and fibromodulin (600245).CLONING
Chakravarti et al. (1995) derived the primary structure of lumican from cDNA sequencing of chicken, bovine, and human clones and demonstrated that lumican shows all the characteristic features of the SIPG family, namely, 4 and 2 cysteines in the N- and C-terminal globular domains, I and III, and a central, cysteine-free domain II, with 9 beta sheet-forming leucine motifs. This human core protein contains 4 putative N-glycosylation sites in the central domains, all or some of which are substituted with keratan sulfate side chains. At the amino acid level, it is 90% identical with the bovine and 72% identical with the chicken core protein. By immunohistochemical staining, Chakravarti et al. (1995) showed that lumican is present not only in the corneal stroma but also in the dermal area of the skin. Grover et al. (1995) used PCR techniques to derive a human lumican cDNA sequence from RNA obtained from intestine, placenta, and articular cartilage. The deduced lumican protein sequence had 338 amino acids, including a putative 18-residue signal peptide. The lumican message is expressed at high levels in adult articular chondrocytes, but at low levels in the young juvenile. It is present in the extracellular matrix of human articular cartilage at all ages, although its abundance is far greater in the adult. In adult cartilage, lumican exists predominantly in a glycoprotein form lacking keratan sulfate, whereas the juvenile form of the molecule is a proteoglycan. Yeh et al. (2010) found that zebrafish Lum existed as a keratan sulfate proteoglycan in corneal stroma and as an unglycanated glycoprotein in sclera.GENE STRUCTURE
Grover et al. (1995) showed that the LDC gene is spread over about 7.5 kb of genomic DNA and consists of 3 exons separated by introns of 2.2 and 3.5 kb.MAPPING
Chakravarti and Magnuson (1995) localized the mouse lumican gene to distal chromosome 10 by segregation analysis of restriction fragment length variants (RFLVs) in recombinant inbred (RI) strains of mice. Chakravarti et al. (1995) localized the lumican gene to human chromosome 12 by hybridizing a cDNA probe to a Southern blot containing a human/hamster monochromosomal mapping panel DNA. Sublocalization to 12q21.3-q22 was performed by fluorescence in situ hybridization. By PCR analysis of human/hamster somatic cell hybrids Grover et al. (1995) mapped the LDC gene to chromosome 12 and regionalized it to chromosome 12q22 by fluorescence in situ hybridization.GENE FUNCTION
Like decorin, lumican interacts with collagen and limits growth of fibrils in diameter (Chakravarti and Magnuson, 1995). In the cornea, lumican not only interacts with collagen molecules to limit fibril growth, but by virtue of its keratan sulfate-containing glycosaminoglycan side chains LDC plays a critical role in the regular spacing of fibrils and acquisition of corneal transparency.MOLECULAR GENETICS
- Association with Myopia For discussion of a possible association between variation in the LUM gene and myopia, see MYP3 (60322 ... More on the omim web site
June 30, 2020: Protein entry updated
Automatic update: OMIM entry 600616 was added.
Feb. 23, 2019: Protein entry updated
Automatic update: comparative model was added.
Feb. 23, 2019: Protein entry updated
Automatic update: model status changed
Oct. 19, 2018: Additional information
Initial protein addition to the database. This entry was referenced in Bryk and co-workers. (2017).