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3  structures 21  species 1  interaction 21  sequences 2  architectures

Family: FokI_C (PF02980)

Summary: Restriction endonuclease FokI, catalytic domain

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Restriction endonuclease FokI, catalytic domain Provide feedback

No Pfam abstract.

Literature references

  1. Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK; , Proc Natl Acad Sci U S A. 1998;95:10564-10569.: Structure of FokI has implications for DNA cleavage. PUBMED:9724743 EPMC:9724743

  2. Kovall RA, Matthews BW; , Curr Opin Chem Biol 1999;3:578-583.: Type II restriction endonucleases: structural, functional and evolutionary relationships. PUBMED:10508668 EPMC:10508668


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004233

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.

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].

Thie entry represents the type IIS restriction endonuclease FokI (EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence [PUBMED:9724744]. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition (INTERPRO) and cleavage functions, respectively.

The catalytic domain contains only a single catalytic centre, raising the question of how monomeric FokI manages to cleave both DNA strands. The catalytic domain is sequestered in a 'piggyback' fashion by the recognition domain [PUBMED:9214510].

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(4)
Full
(21)
Representative proteomes NCBI
(25)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(3)
RP75
(3)
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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
(4)
Full
(21)
Representative proteomes NCBI
(25)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(3)
RP75
(3)
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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.

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Trees

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Curation and family details

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Curation View help on the curation process

Seed source: Structural domain
Previous IDs: none
Type: Domain
Author: Griffiths-Jones SR
Number in seed: 4
Number in full: 21
Average length of the domain: 139.00 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 24.27 %

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 25.0 25.0
Trusted cut-off 104.3 103.1
Noise cut-off 19.4 19.0
Model length: 142
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Endonuc-FokI_C

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 FokI_C domain has been found. There are 3 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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