Summary: S-layer protein
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Methanosarcinales S-layer Tile Protein Edit Wikipedia article
|Methanosarcinales S-layer Tile Protein|
The Methanosarcinales S-layer Tile Protein (MSTP) is a protein family found almost exclusively in Methanomicrobia members of the order Methanosarcinales. Typically a tandem repeat of two DUF1608 domains are contained in a single MSTP protein chain and these proteins self-assemble into the protective proteinaceous surface layer (S-layer) structure that encompasses the cell. The S-layer, which is found in most Archaea, and in many bacteria, serves many crucial functions including protection from deleterious extracellular substances.
Discovery of the Methanosarcinales S-layer
The first S-layers were discovered in bacteria in the 1950s and the presence of S-layers in many Archaea was determined through microscopic (both light and electron) studies of Archaea. The presence of an S-layer in a member of the Methanosarcinales was determined in the 1980s by electron microscope (EM) studies examining the cell morphology of Methanosarcina mazei. This, and other EM studies, confirmed that the cell envelope structure of the Methanosarcinales is composed of a cytoplasmic membrane (CM) with an additional barrier (the S-layer) external to the CM. Under conditions of low osmolarity the S-layer is extensively decorated with a polysaccharide, termed methanochondroitin, and the cells tend to grow in multicellular aggregates. Upon adaptation to high osmolarity conditions the cells disaggregate and grow as single cells that lack the methanochondroitin layer.
Identification of the Methanosarcinales S-layer Protein
The identity of the proteins composing the S-layer of these organisms was subsequently determined by a proteomic approach. The major S-layer proteins of M. acetivorans C2A and M. mazei GÃ¶1 were determined to be MA0829 and MM1976, respectively. Additional proteins with similar characteristics as MA0829 and MM1976 were found to be present in the cell envelopes of these organisms in minor amounts. The genomes of all Methanosarcina species examined thus far have 4-10 paralogous DUF1608 containing proteins. The major and minor S-layer proteins of M. acetivorans C2A and M. mazei GÃ¶1 share many common features including: an N-terminal signal peptide, one or two protein domains of the DUF1608 protein family, a negatively charged tether of ~70 amino acids, and a C-terminal transmembrane helix that likely anchors the S-layer to the CM.
Analysis of protein sequences has determined that members of the DUF1608 protein family contain 250-300 amino acids and are found only in Archaea. With the exception of two halophilic archaea the DUF1608 domain is exclusive to the methanogenic Archaea of the order Methanosarcinales. The DUF1608 has been assigned to the protein family (Pfam), pfam07752.
The structure of one of the two tandem DUF1608 repeats that comprise the major MSTP of M. acetivorans (MA0829) has been determined at high resolution by X-ray crystallography. The structure of the C-terminal DUF1608 tandem repeat (CTR) of MA0829 revealed that the DUF1608 protein domain is composed of two structurally similar Î²-sandwich domains connected by a short connector subdomain. The Î²-sandwich domains are structurally similar not only to each other but also to other proteins associated with envelope structures of disparate species including bacterial, fungal, and viral entities.
While the structure of only one of the two DUF1608 domains of the MA0829 protein was determined the structure of the full-length MA0829 tandem DUF1608 repeat protein (minus the N-terminal signal peptide and C-terminal tether and anchor) could be modeled by virtue of the MA0829 CTR forming the same crystallographic dimer in two different crystal forms. The high degree of primary amino acid sequence identity between the N- and C-terminal DUF1608 domains (79% identical and 87% similar) allowed the homology modeling of the N-terminal DUF1608 amino acid sequence onto one of the DUF1608 domains in the crystallographic DUF1608 CTR dimer thus providing the first high-resolution model of an Archaeal S-layer protein.
A model for the quaternary structure of the M. acetivorans S-layer was proposed based on packing of the MA0829 CTR in a hexagonal lattice in one of the two obtained crystal forms (Protein Data Bank accession number 3U2G). The minimal building block of the S-layer sheet is a trimer of crystallographic MA0829 CTR dimers. Lateral translation of the trimeric unit creates a flat 2-dimensional sheet that has features consistent with the molecular properties of hexagonal archaeal S-layers. The overall appearance of the S-layer resembles a honeycomb structure of hexagonal tiles with center to center spacing between the tiles of ~240 Ã… and a height of ~45 Ã….
Three different types of pores are present in the sheet with "Primary pores" situated on the six-fold symmetry axis and "Trimer pores" on the three-fold symmetry axis. Asymmetric pores are located between the adjacent trimeric building blocks. The size of the pores are sufficiently large to allow the exchange of metabolites between the organism and the external environment. Whereas the protein constituents of lipid-based barriers, such as bacterial outer membranes, can be rapidly modified in response to physiological or environmental stimuli, the large pore sizes of the S-layer composed of MSTP protein subunits are presumably required to allow passage of molecules across a protective barrier whose molecular features are difficult to modify. An interesting feature of the model proposed for the M. acetivorans S-layer is the overwhelmingly negative charge of the surfaces of the S-layer including the pores. The S-layer thus presents a substantial size and charge barrier to the free passage of molecules across the S-layer.
The two structures of the MA0829 CTR have been deposited in the Protein Data Bank: 3U2G is the accession code for the selenomethionine-labeled protein in the P622 space group and 3U2H is the accession code for the unlabeled protein structure in the C2 space group.
S-layers have many potential biotechnology applications. The use of the high-resolution MA0829 structure to facilitate such studies is complicated by difficulties in reconstituting archaeal S-layers in vitro.
- KÃ¶nig, H (1998). "Archaeobacterial cell envelopes". Can J Microbiol 34 (4): 395â€“406. doi:10.1139/m88-07.
- Houwink, AL (1953). "A macromolecular mono-layer in the cell wall of Spirillum spec.". Biochim Biophys Acta. 10 (3): 360â€“6. doi:10.1016/0006-3002(53)90266-2. PMID 13058992.
- Aldrich HC, Robinson RW, Williams DS (May 1986). "Ultrastructure of Methanosarcina mazei". Systematic and Applied Microbiology 7 (2-3): 314â€“9. doi:10.1016/S0723-2020(86)80025-X.
- Kreisl P, Kandler, O (May 1986). "Chemical structure of the cell wall polymer of methanosarcina". Systematic and Applied Microbiology 7 (2-3): 293â€“9. doi:10.1016/S0723-2020(86)80022-4.
- Sowers KR, Boone JE, Gunsalus RP (1993). "Disaggregation of Methanosarcina spp. and Growth as Single Cells at Elevated Osmolarity". Appl Environ Microbiol 59 (11): 3832â€“9. PMC 182538. PMID 16349092.
- Francoleon DR, Boontheung P, Yang Y, Kin U, Ytterberg AJ, Denny PA, Denny PC, Loo JA, Gunsalus RP, Loo RR (April 2009). "S-layer, surface-accessible, and concanavalin A binding proteins of Methanosarcina acetivorans and Methanosarcina mazei". J Proteome Res 8 (4): 1972â€“82. doi:10.1021/pr800923e. PMC 2666069. PMID 19228054.
- "PF07752". PFAM. Sanger Institute. Retrieved 11 February 2013.
- Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004). "The Pfam protein families database". Nucleic Acids Res 32 (Database issue): D138â€“41. doi:10.1093/nar/gkh121. PMC 308855. PMID 14681378.
- Rohlin L, Leon DR, Kim U, Loo JA, Ogorzalek Loo RR, Gunsalus RP (2012). "Identification of the major expressed S-layer and cell surface-layer-related proteins in the model methanogenic archaea: Methanosarcina barkeri Fusaro and Methanosarcina acetivorans C2A". Archaea 2012. doi:10.1155/2012/873589. PMC 3361143. PMID 22666082. 873589.
- Arbing MA, Chan S, Shin A, Phan T, Ahn CJ, Rohlin L, Gunsalus RP (2012). "Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans.". Proc Natl Acad Sci U S A. 109 (29): 11812â€“7. doi:10.1073/pnas.1120595109. PMC 3406845. PMID 22753492.
- Sleytr UB, Messner P (1983). "Crystalline surface layers on bacteria". Annu Rev Microbiol 37: 311â€“39. doi:10.1146/annurev.mi.37.100183.001523. PMID 6416145.
- Cheong G-W, Guckenberger R, Fuchs K-H, Gross H, Baumeister W (September 1993). "The structure of the surface layer of Methanoplanus limicola obtained by a combined electron microscopy and scanning tunneling microscopy approach". J Struct Biol 111 (2): 125â€“34. doi:10.1006/jsbi.1993.1043.
- Trachtenberg S, Pinnick B, Kessel M (2000). "The cell surface glycoprotein layer of the extreme halophile Halobacterium salinarum and its relation to Haloferax volcanii: cryo-electron tomography of freeze-substituted cells and projection studies of negatively stained envelopes". J Struct Biol 130 (1): 10â€“26. doi:10.1006/jsbi.2000.4215. PMID 10806087.
- Sleytr UB, Egelseer EM, Ilk N, Pum D, Schuster B (2007). "S-Layers as a basic building block in a molecular construction kit". FEBS J 274 (2): 323â€“34. doi:10.1111/j.1742-4658.2006.05606.x. PMID 17181542.
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S-layer protein Provide feedback
Archaeal S-layer proteins consist of two copies of this domain [1-2].
Francoleon DR, Boontheung P, Yang Y, Kin U, Ytterberg AJ, Denny PA, Denny PC, Loo JA, Gunsalus RP, Loo RR;, J Proteome Res. 2009;8:1972-1982.: S-layer, surface-accessible, and concanavalin A binding proteins of Methanosarcina acetivorans and Methanosarcina mazei. PUBMED:19228054 EPMC:19228054
Rohlin L, Leon DR, Kim U, Loo JA, Ogorzalek Loo RR, Gunsalus RP;, Archaea. 2012;2012:873589.: Identification of the Major Expressed S-Layer and Cell Surface-Layer-Related Proteins in the Model Methanogenic Archaea: Methanosarcina barkeri Fusaro and Methanosarcina acetivorans C2A. PUBMED:22666082 EPMC:22666082
Internal database links
|SCOOP:||DUF1706 GP40 DUF3122|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR006457
This entry represents a domain found tandemly duplicated in two proven archaeal S-layer glycoproteins, MA0829 from Methanosarcina acetivorans C2A and MM1976 from Methanosarcina mazei Go1 [PUBMED:19228054], as well as in several paralogues of those L-layer proteins from both species. Members of the family show regions of local similarity to another known family of archaeal S-layer proteins (). Some members of this family, including the proven S-layer proteins, have the archaeosortase A target motif, PGF-CTERM (), at the protein C terminus.
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We make a range of alignments for each Pfam-A family:
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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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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_2293 (release 14.0)|
|Author:||Fenech M, Eberhardt RY|
|Number in seed:||52|
|Number in full:||185|
|Average length of the domain:||227.20 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||56.24 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|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:
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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.
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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.
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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.
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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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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the S-layer domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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