Synaptobrevin homolog YKT6 (YKT6)
The protein contains 198 amino acids for an estimated molecular weight of 22418 Da.
Vesicular soluble NSF attachment protein receptor (v-SNARE) mediating vesicle docking and fusion to a specific acceptor cellular compartment. Functions in endoplasmic reticulum to Golgi transport; as part of a SNARE complex composed of GOSR1, GOSR2 and STX5. Functions in early/recycling endosome to TGN transport; as part of a SNARE complex composed of BET1L, GOSR1 and STX5. Has a S-palmitoyl transferase activity. (updated: Feb. 4, 2015)
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.
- 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.
- Bryk and co-workers. (2017) Quantitative Analysis of Human Red Blood Cell Proteome. J Proteome Res. 16(8), 2752-2761.
- D'Alessandro and co-workers. (2017) Red blood cell proteomics update: is there more to discover? Blood Transfus. 15(2), 182-187.
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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Biological Process
Endoplasmic reticulum to Golgi vesicle-mediated transport
Metabolic process
Protein transport
Retrograde transport, endosome to Golgi
Vesicle docking involved in exocytosis
Vesicle fusion
Vesicle targeting
Cellular Component
Apical dendrite
Basal dendrite
Cytoplasm
Cytoplasmic vesicle membrane
Cytosol
Endoplasmic reticulum
Endoplasmic reticulum-Golgi intermediate compartment membrane
Endosome
Extracellular exosome
Golgi apparatus
Golgi membrane
Integral component of plasma membrane
Mitochondrion
Neuronal cell body
Obsolete cell
SNARE complex
Transport vesicle
The reference OMIM entry for this protein is 606209
Ykt6, s. cerevisiae, homolog of; ykt6
DESCRIPTION
For an explanation of the SNARE hypothesis, see 603215. YKT6 is a v-SNARE involved in endoplasmic reticulum-Golgi transport.CLONING
McNew et al. (1997) isolated S. cerevisiae Ykt6p as an interacting partner of the cis Golgi target membrane-associated SNARE Sed5p. They identified human YKT6 by comparison of the yeast sequence with an EST database, and cloned the human cDNA by PCR from a pancreatic cDNA library. Ykt6 and its homologs are highly conserved from yeast to human. Human YKT6 protein shares 47% and 57% sequence identity with S. cerevisiae and C. elegans homologs, respectively.GENE FUNCTION
Ykt6 is an essential gene that codes for a novel vesicle-associated SNARE functioning at the endoplasmic reticulum/Golgi transport step in the yeast secretory pathway. McNew et al. (1997) demonstrated that depletion of Ykt6p results in the accumulation of the p1 precursor of the vacuolar enzyme carboxypeptidase Y and morphologic abnormalities consistent with a defect in secretion. Membrane localization of Ykt6p is essential for protein function and is normally mediated by isoprenylation. However, replacement of the isoprenylation motif with a bona fide transmembrane anchor results in a functional protein confirming that membrane localization, but not isoprenylation per se, is required for function. McNew et al. (1997) demonstrated that human YKT6 could complement the loss of Ykt6p. Tochio et al. (2001) performed in vitro studies which revealed that the N-terminal domain of Ykt6p plays an important biologic role in its function, which includes influencing the kinetics and proper assembly of SNARE complexes.BIOCHEMICAL FEATURES
- Atomic Structure By nuclear magnetic resonance (NMR) spectroscopy, Tochio et al. (2001) reported the atomic structure of the N-terminal domain of Ykt6p. The N-terminal structure of Ykt6p differed entirely from that of syntaxin (see 186590) and resembled the overall fold of the actin regulatory protein profilin (see 176610). Like some syntaxins, Ykt6p adopted a folded-back conformation in which the Ykt6p N-terminus bound to its C-terminal core domain. ... More on the omim web site
Feb. 2, 2018: Protein entry updated
Automatic update: Uniprot description updated
Dec. 19, 2017: Protein entry updated
Automatic update: Uniprot description updated
June 20, 2017: Protein entry updated
Automatic update: comparative model was added.
March 16, 2016: Protein entry updated
Automatic update: OMIM entry 606209 was added.