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0  structures 17  species 0  interactions 20  sequences 1  architecture

Family: RE_Alw26IDE (PF09665)

Summary: Type II restriction endonuclease (RE_Alw26IDE)

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Type II restriction endonuclease (RE_Alw26IDE) Provide feedback

Members of this entry are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterised specificities of the three members are GGTCTC, CGTCTC and the shared subsequence GTCTC.

This tab holds annotation information from the InterPro database.

InterPro entry IPR014328

Type II restriction endonucleases ( EC ) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin [ PUBMED:15770420 ]. However, there is still considerable diversity amongst restriction endonucleases [ PUBMED:14576294 , PUBMED:11827971 ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone [ PUBMED:11557805 ].

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [ PUBMED:15121719 , PUBMED:12665693 ], as summarised below:

  • Type I enzymes ( EC ) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase ( EC ) activities.
  • Type II enzymes ( EC ) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
  • Type III enzymes ( EC ) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase ( EC ).
  • Type IV enzymes target methylated DNA.

This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [ PUBMED:12172806 ], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).

Domain organisation

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(3)
Full
(20)
Representative proteomes UniProt
(154)
RP15
(4)
RP35
(11)
RP55
(22)
RP75
(34)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(3)
Full
(20)
Representative proteomes UniProt
(154)
RP15
(4)
RP35
(11)
RP55
(22)
RP75
(34)
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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
(3)
Full
(20)
Representative proteomes UniProt
(154)
RP15
(4)
RP35
(11)
RP55
(22)
RP75
(34)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: TIGRFAMs
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: TIGRFAMs, Coggill P
Number in seed: 3
Number in full: 20
Average length of the domain: 429.7 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 89.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.1 23.1
Trusted cut-off 52.0 51.9
Noise cut-off 21.3 19.7
Model length: 507
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;