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This is the Wikipedia entry entitled "Phospholipid scramblase". More...
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Phospholipid scramblase Edit Wikipedia article
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Scramblase is a protein responsible for the translocation of phospholipids between the two monolayers of a lipid bilayer of a cell membrane. In humans, phospholipid scramblases (PLSCRs) constitute a family of five homologous proteins that are named as hPLSCR1–hPLSCR5. Scramblases are members of the general family of transmembrane lipid transporters known as flippases. The inner-leaflet facing the inside of the cell contains negatively charged amino-phospholipids and phosphatidylethanolamine. The outer-leaflet, facing the outside environment, contains phosphatidylcholine and sphingomyelin. Scramblase is an enzyme, present in the cell membrane, that can transport (scramble) the negatively charged phospholipids from the inner-leaflet to the outer-leaflet, and vice versa.
Whereas hPLSCR1, -3, and -4 are expressed in a variety of tissues with few exceptions, expression of hPLSCR2 is restricted only to the testis. hPLSCR4 is not expressed in peripheral blood lymphocytes, whereas hPLSCR1 and -3 were not detected in the brain. However, the functional significance of this differential gene expression is not yet understood. While the gene and the mRNA of hPLSCR5 provide evidence of its existence, the protein has yet to be described in the literature.
 Enzyme activation
The enzymatic activity of scramblase depends on the calcium concentration present inside the cell. The calcium concentration inside cells is, under normal conditions, very low; therefore, scramblase has a low activity under resting conditions. Phospholipid redistribution is triggered by increased cytosolic calcium and seems to be scramblase-dependent, resulting in a symmetric distribution of negatively charged phospholipids between both leaflets of the lipid bilayer. All scramblases contain an EF hand-like Ca2+binding domain that is probably responsible for the calcium activation of the enzyme. The activity of scramblase does not require energy, meaning that there is no contribution of adenosine triphosphate in the process.
Scramblases are cysteine-rich proteins, possessing many cysteinyl sulfhydryl groups that are prone to modifications. Oxidation, nitrosylation, and blockage of these sulfhydril groups produce an enhanced scramblase activity. Patients with sickle cell disease exhibit a fraction of erythrocytes with an aberrantly enhanced exposure of phosphotidyl serine on their surface. As the erythrocytes of these patients have an enhanced oxidative stress, it is probable that increased scramblase activity might play a role in the etiology of the disease. Furthermore, it is well recognized that both reactive oxygen species and intracellular Ca2+ fluxes affect mitochondria at the beginning of the apoptotic program. Sulfhydryl modification of PLSCR3 in mitochondria during apoptosis may be a key regulator initiating the intrinsic apoptotic pathways.
 Nuclear localisation sequence
Phospholipid scramblase 1 (PLSCR1), a lipid-binding protein that enters the nucleus via the nonclassical NLS (257)GKISKHWTGI(266). The structure of the nuclear localisation sequence of scramblase PLSCR1 complexed to importin was determined using X-ray diffraction with a resolution of 2.20 Ångströms. It is found in most mammals including humans. The import sequence lacks a continuous stretch of positively charged residues, and it is enriched in hydrophobic residues. Thus, Scramblase can transport negatively charged phospholipids from the inside of the cell to the outside of the cell. The importin structure is composed of many alpha helices that integrate the protein into membranes. The role of importin is to move proteins such as scramblase into the nucleus.
 Biological roles
 Mitochondrial membrane maintenance
Recent findings suggest that PLSCR3 is involved in regulation of biosynthesis of cardiolipin in mitochondria, and its overexpression in cultured cells resulted in increased cardiolipin synthase, activity. As cardiolipin is synthesized in the luminal side of inner mitochondrial membrane, a major fraction of this newly synthesized pool of cardiolipin has to be translocated from the inner to the outer mitochondrial membrane. PLSCR3 has been proposed to be involved in this translocation from the inner to the outer membrane that is essential for maintaining the mitochondrial architecture, mass, and transmembrane potential.
 Lipid metabolism
Recent findings suggest that PLSCR3 and, to a lesser degree, PLSCR1 are critical to the normal regulation of fat accumulation in mice. In addition to blood cells, PLSCR3 is expressed to a significantly higher level in fat and muscle cells, which are actively involved in fat metabolism. PLSCR3 knockout mice showed an aberrant abdominal fat accumulation, glucose intolerance, insulin resistance, and dyslipidema as compared to controlled mice. Cultured fat cells from PLSCR3 knockout mice were engorged with neutral lipids. Blood plasma of these mice showed elevated levels of non-high-density lipoproteins, cholesterol, triglycerides, non-esterified fatty acids, and leptin, but low adiponectin content. Abdominal fat accumulation with the formation of enlarged lipid engorged adipocytes has emerged as the key risk factor for the onset of type 2 diabetes, which is often a manifestation of a broader underlying metabolic disorder termed as metabolic syndrome. Further studies on the regulation of lipid metabolism by PLSCRs are required to understand the risk for development of similar diseases in humans when PLSCR genes are mutated, leading to a defective expression and/or function of PLSCR proteins.
Upon activation (in platelets) or injury (in erythrocytes, platelets, endothelium, and other cells), certain cells expose the phospholipid phosphatidylserine on their surface and act as catalysts to induce the coagulation cascade. Surface exposure of phosphatidylserine is thought to be brought about by the activation of scramblases. Several enzyme complexes of blood coagulation cascade such as tenase and prothrombinase are activated by the cell surface exposure of the phosphatidylserine. However, the most studied member of the scramblase family PLSCR1 was shown to be defective in translocation of phospholipids when reconstituted into proteoliposomes in vitro. Although recent studies show that PLSCR1 is neither sufficient nor necessary for the phosphatidylserine externalization, the involvement of PLSCR1 in blood coagulation remains elusive, raising the question of additional membrane components in the externalization pathway. To date, no report is available on the involvement of any other identified member of PLSCRs in blood clotting.
Apoptotic cell death is characterized by a proteolytic caspase cascade that emanates from either an extrinsic or an intrinsic pathway. The extrinsic pathway is initiated by membrane bound death receptors, leading to activation of caspase 8, whereas the intrinsic pathway is triggered by DNA damaging drugs and UV radiation, leading to mitochondrial depolarization and subsequent activation of caspase 9. PLSCRs are supposed to play an important role in both intrinsic and extrinsic apoptotic responses that are linked to each other via the activation of caspase 8. Activated caspase 8 causes the cleavage of the amino terminal portion of the cytosolic protein Bid to generate t-Bid that is translocated into mitochondria during apoptosis. hPLSCR1 and its mitochondrial counterpart hPLSCR3 are phosphorylated by PKCδ during PKC-δ-induced apoptosis. While the consequence of hPLSCR1 phosphorylation and its mechanism of action during cellular apoptotic response remain unclear, phosphorylated hPLSCR3 is thought to facilitate mitochondrial targeting of t-Bid that is an essential requirement in caspase 8-mediated apoptosis. The active t-Bid fragment is shown to localize to mitochondria through a positive interaction with cardiolipin. This activated t-Bid induces activation of Bax and Bak proteins to form cytochrome c channels that facilitate the release of cytochrome c during apoptosis.
An early morphological event in both the extrinsic and the intrinsic apoptotic pathways is the surface exposure of the phospholipid phosphatidylserine, about 96% of which normally reside in the cytosolic leaflet of the plasma membrane. Phosphotidyl serine is translocated to the exoplasmic leaflet by the activation of scramblases, leading to pro-coagulant properties and providing a phagocytic signal to the macrophages that engulf and clear the apoptotic cells. The involvement of other associated proteins aiding scrambling activity cannot be ruled out.
- Sahu SK, Gummadi SN, Manoj N, Aradhyam GK (June 2007). "Phospholipid scramblases: an overview". Arch. Biochem. Biophys. 462 (1): 103–14. doi:10.1016/j.abb.2007.04.002. PMID 17481571.
- Zwaal RF, Comfurius P, Bevers EM (May 2005). "Surface exposure of phosphatidylserine in pathological cells". Cell. Mol. Life Sci. 62 (9): 971–88. doi:10.1007/s00018-005-4527-3. PMID 15761668.
- Sims PJ, Wiedmer T (July 2001). "Unraveling the mysteries of phospholipid scrambling". Thromb. Haemost. 86 (1): 266–75. PMID 11487015. http://www.schattauer.de/index.php?id=1268&pii=th01070266&no_cache=1.
- Wiedmer T, Zhou Q, Kwoh DY, Sims PJ (July 2000). "Identification of three new members of the phospholipid scramblase gene family". Biochim. Biophys. Acta 1467 (1): 244–53. doi:10.1016/S0005-2736(00)00236-4. PMID 10930526.
- Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Söding J (January 2009). "Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors". Bioinformatics 25 (2): 159–62. doi:10.1093/bioinformatics/btn595. PMC 2639001. PMID 19010806. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2639001/.
- PDB 1Y2A; Chen MH, Ben-Efraim I, Mitrousis G, Walker-Kopp N, Sims PJ, Cingolani G (March 2005). "Phospholipid scramblase 1 contains a nonclassical nuclear localization signal with unique binding site in importin alpha". J. Biol. Chem. 280 (11): 10599–606. doi:10.1074/jbc.M413194200. PMID 15611084.
- M. Nowicki and M. Frentzen (2005). "Cardiolipin synthase of Arabidopsis thaliana". FEBS Letters 579 (10): 2161–2165. doi:10.1016/j.febslet.2005.03.007. PMID 15811335.
- M. Nowicki (2006). "Characterization of the Cardiolipin Synthase from Arabidopsis thaliana". Ph.D. thesis, RWTH-Aachen University. http://darwin.bth.rwth-aachen.de/opus/volltexte/2006/1629/.
- Greenberg AS, McDaniel ML (June 2002). "Identifying the links between obesity, insulin resistance and beta-cell function: potential role of adipocyte-derived cytokines in the pathogenesis of type 2 diabetes". Eur. J. Clin. Invest. 32 Suppl 3: 24–34. doi:10.1046/j.1365-2362.32.s3.4.x. PMID 12028372.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Scramblase Provide feedback
Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury .
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005552Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury [PUBMED:11487015].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
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- alignment generated by searching the NCBI sequence database using the family HMM
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
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MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:||Pfam-B_3893 (release 7.0)|
|Number in seed:||10|
|Number in full:||783|
|Average length of the domain:||198.70 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||69.98 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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