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51  structures 2646  species 1  interaction 3045  sequences 9  architectures

Family: SurE (PF01975)

Summary: Survival protein SurE

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This is the Wikipedia entry entitled "SurE, survival protein E". More...

SurE, survival protein E Edit Wikipedia article

SurE
PDB 1j9k EBI.jpg
Crystal structure of SurE protein from T.maritima in complex with tungstate.
Identifiers
Symbol SurE
Pfam PF01975
InterPro IPR002828
SCOP 1j9l
SUPERFAMILY 1j9l

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.[1] It is a metal ion-dependent phosphatase that is found in bacteria, and eukaryotes. It is an important stress response protein.[2] 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.[3]

Function

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.[3] Since the SurE is a phosphatase enzyme it removes a phosphate group from a substance, affecting that substance's role in signal transduction.[4]

Structure

This protein consists of two protein domain. One is a large, globular N-terminal domain and the other is a smaller C-terminal domain.

N-terminal domain

The N-terminal domain contains a three-layer alpha/beta/alpha sandwich that is homologous with the Rossmann fold (CATH class 3.40.50.170) of which the major feature is a long beta sheet that is composed of nine mostly parallel beta strands.[4] SurEstructural domain has a similar topology to the N-terminal protein domain of the glutaminase/asparaginase family.[5]

C-terminal domain

The C-terminal domain, has 3 beta strands and two protrusions; one of which is a C-terminal alpha helix, and the second is a beta hairpin.[3]

References

  1. ^ 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 196819. PMID 7928962. 
  2. ^ 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. doi:10.1016/j.jmb.2007.05.007. PMID 17561111. 
  3. ^ a b c 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. doi:10.1016/s0969-2126(01)00675-x. PMC 2792002. PMID 11709173. 
  4. ^ a b 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. doi:10.1038/nsb0901-789. PMID 11524683. 
  5. ^ 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. doi:10.1016/S0022-2836(03)00056-1. PMID 12595266. 

This article incorporates text from the public domain Pfam and InterPro IPR002828

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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 [1]. 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.

Literature references

  1. 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

  2. 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


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.

This domain is found in acid phosphatases (EC), 5'-nucleotidases (EC), 3'-nucleotidases (EC) and exopolyphosphatases (EC).

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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...

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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.

  Seed
(133)
Full
(3045)
Representative proteomes NCBI
(2370)
Meta
(1174)
RP15
(297)
RP35
(627)
RP55
(859)
RP75
(1005)
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Format an alignment

  Seed
(133)
Full
(3045)
Representative proteomes NCBI
(2370)
Meta
(1174)
RP15
(297)
RP35
(627)
RP55
(859)
RP75
(1005)
Alignment:
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Sequence:
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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.

  Seed
(133)
Full
(3045)
Representative proteomes NCBI
(2370)
Meta
(1174)
RP15
(297)
RP35
(627)
RP55
(859)
RP75
(1005)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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.

HMM logo

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...

Trees

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.

Curation View help on the curation process

Seed source: Enright A
Previous IDs: none
Type: Family
Author: Enright A, Ouzounis C, Bateman A
Number in seed: 133
Number in full: 3045
Average length of the domain: 189.50 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 68.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 21.2 21.3
Noise cut-off 20.8 20.8
Model length: 197
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

SurE

Structures

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 51 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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