Summary: S-layer protein
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Methanosarcinales S-layer Tile Protein". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
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 Gö1 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 Gö1 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 β-sandwich domains connected by a short connector subdomain. The β-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 Å and a height of ~45 Å.
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.
- König, H (1998). "Archaeobacterial cell envelopes". Can J Microbiol 34 (4): 395–406. doi:10.1139/m88-07.
- Houwink, AL (1953). "A macromolecular mono-layer in the cell wall of Spirillum spec.". Biochim Biophys Acta 10 (3): 360–6. 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): 314–9. 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): 293–9. 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): 3832–9. 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): 1972–82. 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): D138–41. 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): 11812–7. doi:10.1073/pnas.1120595109. PMC 3406845. PMID 22753492.
- Sleytr UB, Messner P (1983). "Crystalline surface layers on bacteria". Annu Rev Microbiol 37: 311–39. doi:10.1146/annurev.mi.37.100183.001523. PMID 6416145.
- Cheong GW, Guckenberger R, Fuchs KH, 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): 125–34. 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): 10–26. 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): 323–34. doi:10.1111/j.1742-4658.2006.05606.x. PMID 17181542.
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.
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
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.
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:
- the number of sequences which exhibit this architecture
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
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
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.
Note: You can also download the data file for the tree.
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:||189|
|Average length of the domain:||228.90 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||57.83 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
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.
Missing taxonomic levels
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.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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.
Loading structure mapping...