Summary: Survival protein SurE
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This is the Wikipedia entry entitled "SurE, survival protein E". More...
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SurE, survival protein E Edit Wikipedia article
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Crystal structure of SurE protein from T.maritima in complex with tungstate.
In molecular biology, the protein domain surE refers to survival protein E. It was originally found that cells that did not contain this protein, could not survive in the stationary phase, at above normal temperatures, and in high-salt media. Hence the name, survival protein E. It is a metal ion-dependent phosphatase that is found in bacteria, and eukaryotes. It is an important stress response protein. This domain is found in acid phosphatases (EC), 5'-nucleotidases (EC), 3'-nucleotidases (EC) and exopolyphosphatases (EC).
Interaction with pcm gene
The gene, surE, is part of a bicistronic operon found upstream of the pcm gene. When mutated, their phenotypes, or physical characteristics, are very similar and indicate that both gene products are important for survival under stressful conditions.
The C-terminal domain is important mainly for maintaining the oligomeric state of the protein, SurE. The N-terminal domain is thought to be part of the functional domain. Since the SurE is a phosphatase enzyme it removes a phosphate group from a substance, affecting that substance's role in signal transduction.
The N-terminal domain contains a three-layer alpha/beta/alpha sandwich that is homologous with the Rossmann fold (CATH class 184.108.40.206) of which the major feature is a long beta sheet that is composed of nine mostly parallel beta strands. SurEstructural domain has a similar topology to the N-terminal protein domain of the glutaminase/asparaginase family.
- Li C, Ichikawa JK, Ravetto JJ, Kuo HC, Fu JC, Clarke S (1994). "A new gene involved in stationary-phase survival located at 59 minutes on the Escherichia coli chromosome.". J Bacteriol. 176 (19): 6015–22. PMC . PMID 7928962.
- Iwasaki W, Miki K (2007). "Crystal structure of the stationary phase survival protein SurE with metal ion and AMP.". J Mol Biol. 371 (1): 123–36. PMID 17561111. doi:10.1016/j.jmb.2007.05.007.
- Zhang RG, Skarina T, Katz JE, Beasley S, Khachatryan A, Vyas S, et al. (2001). "Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase.". Structure. 9 (11): 1095–106. PMC . PMID 11709173. doi:10.1016/s0969-2126(01)00675-x.
- Lee JY, Kwak JE, Moon J, Eom SH, Liong EC, Pedelacq JD, et al. (2001). "Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family.". Nat Struct Biol. 8 (9): 789–94. PMID 11524683. doi:10.1038/nsb0901-789.
- Mura C, Katz JE, Clarke SG, Eisenberg D (March 2003). "Structure and function of an archaeal homolog of survival protein E (SurEalpha): an acid phosphatase with purine nucleotide specificity". J. Mol. Biol. 326 (5): 1559–75. PMID 12595266. doi:10.1016/S0022-2836(03)00056-1.
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.
Survival protein SurE Provide feedback
E. coli cells with the surE gene disrupted are found to survive poorly in stationary phase . It is suggested that SurE may be involved in stress response. Yeast also contains a member of the family P38254. P30887 can complement a mutation in acid phosphatase, suggesting that members of this family could be phosphatases.
Li C, Ichikawa JK, Ravetto JJ, Kuo HC, Fu JC, Clarke S; , J Bacteriol 1994;176:6015-6022.: A new gene involved in stationary-phase survival located at 59 minutes on the Escherichia coli chromosome PUBMED:7928962 EPMC:7928962
Treton BY, Le Dall MT, Gaillardin CM; , Curr Genet 1992;22:345-355.: Complementation of Saccharomyces cerevisiae acid phosphatase mutation by a genomic sequence from the yeast Yarrowia lipolytica identifies a new phosphatase. PUBMED:1423722 EPMC:1423722
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002828
This entry represents a SurE-like structural domain with a 3-layer alpha/bete/alpha topology that bears some topological similarity to the N-terminal domain of the glutaminase/asparaginase family. This domain is found in the stationary phase survival protein SurE, a metal ion-dependent phosphatase found in eubacteria, archaea and eukaryotes. In Escherichia coli, SurE also has activity as a nucleotidase and exopolyphosphatase, and may be involved in the stress response [PUBMED:17561111]. E. coli cells with mutations in the surE gene survive poorly in stationary phase [PUBMED:11709173]. The structure of SurE homologues have been determined from Thermotoga maritima [PUBMED:11524683] and the archaea Pyrobaculum aerophilum [PUBMED:12595266]. The T. maritima SurE homologue has phosphatase activity that is inhibited by vanadate or tungstate, both of which bind adjacent to the divalent metal ion.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||hydrolase activity (GO:0016787)|
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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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:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
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- 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:
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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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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
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|Seed source:||Enright A|
|Author:||Enright A , Ouzounis C , Bateman A|
|Number in seed:||761|
|Number in full:||6733|
|Average length of the domain:||191.50 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||64.52 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|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.
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:
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 SurE domain has been found. There are 95 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 sequence.
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