PDZ and LIM domain protein 1 (PDLIM1)
The protein contains 329 amino acids for an estimated molecular weight of 36072 Da.
Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton (PubMed:10861853). Involved in assembly, disassembly and directioning of stress fibers in fibroblasts. Required for the localization of ACTN1 and PALLD to stress fibers. Required for cell migration and in maintaining cell polarity of fibroblasts (By similarity). (updated: Dec. 20, 2017)
Protein identification was indicated in the following studies:
- Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
- Lange and co-workers. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J Proteome Res. 13(4), 2028-2044.
- Hegedűs and co-workers. (2015) Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database (Oxford) 1-8.
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.
(right-click above to access to more options from the contextual menu)
| Variant | Description |
|---|---|
| dbSNP:rs2296961 |
Biological Process
Actin cytoskeleton organization
Establishment or maintenance of actin cytoskeleton polarity
Fibroblast migration
Heart development
Maintenance of cell polarity
Muscle structure development
Regulation of transcription by RNA polymerase II
Regulation of transcription, DNA-templated
Response to hypoxia
Response to oxidative stress
Stress fiber assembly
The reference OMIM entry for this protein is 605900
Pdz and lim domain protein 1; pdlim1
Elfin
Clp36, rat, homolog of; clp36
C-terminal lim domain protein 1; clim1
CLONING
Proteins of the Enigma family (see ENIGMA; 605903) possess a PDZ domain at the N terminus and 1 to 3 LIM domains at the C terminus. Enigma PDZ domains have a P/S-W-G-F motif in place of the G-L-G-F signature sequence found in most PDZ domains. LIM domains are cysteine-rich double zinc fingers that are involved in protein-protein interactions. C-terminal LIM domain proteins are cytoplasmic and are associated with the cytoskeleton, and some are involved in protein trafficking. By partial sequencing of cDNA clones isolated from a cardiomyopathic heart cDNA library, followed by searching sequence databases, Kotaka et al. (1999) obtained a cDNA encoding PDLIM1, which they called CLIM1, the human homolog of rat Clp36 (36-kD C-terminal LIM domain protein). Sequence analysis predicted that the 329-amino acid PDLIM1 protein, which is 88% homologous to the rat protein, shares 51 to 61% identity with the PDZ domains of ENIGMA, ALP (605889), ENH (605904), and RIL (603422). SDS-PAGE analysis showed that recombinant PDLIM1 was expressed as a 36-kD protein. Northern blot analysis revealed expression of an approximately 2.0-kb transcript that was most abundant in heart and skeletal muscle, moderate in spleen, small intestine, colon, placenta, and lung, low in liver, thymus, kidney, prostate, and pancreas, and not detectable in brain, testis, ovary, and peripheral blood leukocytes.GENE FUNCTION
By yeast 2-hybrid analysis, Kotaka et al. (2000) showed that the LIM domain of PDLIM1 interacts with the C-terminal EF-hand region of alpha-actinin-2 (ACTN2; 102573). Immunoprecipitation, Western blot analysis, and immunofluorescence microscopy demonstrated that the 36-kD PDLIM1 protein colocalizes with ACTN2 in the Z discs of myocardial sarcomeres, particularly at intercalated discs, and with vinculin (VCL; 193065), which is localized in the fascia adherens of intercalated discs. Vallenius et al. (2000) demonstrated that CLP36 localizes to actin stress fibers via its PDZ domain through its association with cellular alpha-actinin-1 (ACTN1; 102575) and alpha-actinin-4 (ACTN4; 604638). By yeast 2-hybrid analysis, Vallenius and Makela (2002) showed that CLP36 interacts with CLIK1 (STK35; 609370) through the LIM domain. Transfection experiments indicated that CLP36 acts as an adaptor, recruiting the CLIK1 kinase to actin stress fibers in nonmuscle cells.MAPPING
By FISH, radiation hybrid analysis, and somatic cell hybrid analysis, Kotaka et al. (1999) mapped the PDLIM1 gene to 10q26. ... More on the omim web site
Feb. 10, 2018: Protein entry updated
Automatic update: Entry updated from uniprot information.
Feb. 2, 2018: Protein entry updated
Automatic update: Uniprot description updated
Dec. 19, 2017: Protein entry updated
Automatic update: Uniprot description updated
Nov. 23, 2017: Protein entry updated
Automatic update: Uniprot description updated
March 16, 2016: Protein entry updated
Automatic update: OMIM entry 605900 was added.
Jan. 25, 2016: Protein entry updated
Automatic update: model status changed