T00055
type: Enzyme
rlcp: p1180
cath: FokI Restriction Endonuclease; Chain A, domain 1
cath: Arc Repressor Mutant, subunit A
cath: Restriction Endonuclease
ec: https://purl.uniprot.org/enzyme/3.1.21.4
csa: 2fok
uniprot: P14870
kegg enzyme: type II site-specific deoxyribonuclease
kegg enzyme: type II restriction enzyme
kegg cofactor: Magnesium
kegg substrate: DNA
kegg substrate: H2O
kegg product: DNA 5'-phosphate
pdb: 1fokA01
pdb: 2fokA01
pdb: 2fokB01
pdb: 1fokA02
pdb: 2fokA02
pdb: 2fokB02
pdb: 1fokA03
pdb: 2fokA03
pdb: 2fokB03
pdb bound state: Unbound
  compound: DNA
  pdb: 2fokA01
pdb bound state: Unbound
  compound: DNA
  pdb: 2fokB01
pdb bound state: Unbound
  compound: DNA
  pdb: 1fokA02
pdb bound state: Unbound
  compound: DNA
  pdb: 2fokA02
pdb bound state: Unbound
  compound: DNA
  pdb: 2fokB02
pdb bound state: Unbound
  compound: DNA
  pdb: 1fokA03
pdb bound state: Unbound
  compound: DNA
  pdb: 2fokA03
pdb bound state: Unbound
  compound: DNA
  pdb: 2fokB03
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1fokA01
pdb bound state: Unbound
  compound: Magnesium
  pdb: 2fokA01
pdb bound state: Unbound
  compound: Magnesium
  pdb: 2fokB01
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1fokA02
pdb bound state: Unbound
  compound: Magnesium
  pdb: 2fokA02
pdb bound state: Unbound
  compound: Magnesium
  pdb: 2fokB02
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1fokA03
pdb bound state: Unbound
  compound: Magnesium
  pdb: 2fokA03
pdb bound state: Unbound
  compound: Magnesium
  pdb: 2fokB03
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 1fokA01
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 2fokA01
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 2fokB01
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 1fokA02
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 2fokA02
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 2fokB02
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 1fokA03
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 2fokA03
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 2fokB03
active site residues resources: Insertion and deletion mutants of FokI restriction endonuclease.
active site residues resources: Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain.
active site residues resources: A detailed study of the substrate specificity of a chimeric restriction enzyme.
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 15
  reference section: Fig.2, p.580-582
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 20
  reference section: Fig.1, p.6
references: Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase.
references: Functional domains in Fok I restriction endonuclease.
references: Alteration of the cleavage distance of Fok I restriction endonuclease by insertion mutagenesis.
references: Single amino acid substitutions uncouple the DNA binding and strand scission activities of Fok I endonuclease.
references: Insertion and deletion mutants of FokI restriction endonuclease.
references: Chimeric restriction endonuclease.
references: Crystallization and preliminary X-ray analysis of restriction endonuclease FokI bound to DNA.
references: Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions.
references: Structure of the multimodular endonuclease FokI bound to DNA.
references: Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain.
references: The mechanism of DNA cleavage by the type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis.
references: Novel site-specific DNA endonucleases.
references: FokI dimerization is required for DNA cleavage.
references: Structure of FokI has implications for DNA cleavage.
references: Type II restriction endonucleases: structural, functional and evolutionary relationships.
references: A detailed study of the substrate specificity of a chimeric restriction enzyme.
references: Identification of the metal-binding sites of restriction endonucleases by Fe2+-mediated oxidative cleavage.
references: Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures.
references: Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.
references: Substrate-assisted catalysis: molecular basis and biological significance.
references: FokI requires two specific DNA sites for cleavage.
references: Stimulation of homologous recombination through targeted cleavage by chimeric nucleases.
references: Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.
references: How the BfiI restriction enzyme uses one active site to cut two DNA strands.
references: In vitro selection of restriction endonucleases by in vitro compartmentalization.
comment: Although the detailed mechanism of the reaction has not been elucidated, the catalytic site is similar to the other Type II restriction enzymes, such as EcoRV (S00403 in EzCatDB) and BglI (S00405 in EzCatDB). Thus, the catalytic mechanism of this enzyme might be similar to that of those enzymes. More recent paper [20] supported the substrate-assisted mechanism for the related enzymes (type II restriction enzymes), ruling out the two-metal-ion mechanism. Thus, we concluded that this enzyme adopts the substrate-assisted mechanism with only one metal ion for catalysis (see EcoRV; S00404 in EzCatDB).

FokI Restriction Endonuclease; Chain A, domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.90.241.10

Arc Repressor Mutant, subunit A
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/1.10.10.10

Restriction Endonuclease
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.91.30
catalytic domain: index.html

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

DNA
type: KeggSubstrate
references: KEGG:C00039
compound type: nucleic acids

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

DNA 5'-phosphate
type: KeggProduct
references: KEGG:C00578
compound type: nucleic acids
compound type: phosphate group/phosphate ion

1fokA03
type: Pdb
references: 1fok
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1fok
catalytic residue: LYS 469
cofactor binding residue: ASP 450;ASP 467(two Mg2+ binding)

2fokA03
type: Pdb
references: 2fok
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2fok
catalytic residue: LYS 469
cofactor binding residue: ASP 450;ASP 467(two Mg2+ binding)

2fokB03
type: Pdb
references: 2fok
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2fok
catalytic residue: LYS 469
cofactor binding residue: ASP 450;ASP 467(two Mg2+ binding)

Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2684765
journal: Gene
volume: 80
pages: 193-208
published year: 1989
authors:
  item: Looney MC
  item: Moran LS
  item: Jack WE
  item: Feehery GR
  item: Benner JS
  item: Slatko BE
  item: Wilson GG

Functional domains in Fok I restriction endonuclease.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1584761
journal: Proc Natl Acad Sci U S A
volume: 89
pages: 4275-9
published year: 1992
authors:
  item: Li L
  item: Wu LP
  item: Chandrasegaran S

Alteration of the cleavage distance of Fok I restriction endonuclease by insertion mutagenesis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8464886
journal: Proc Natl Acad Sci U S A
volume: 90
pages: 2764-8
published year: 1993
authors:
  item: Li L
  item: Chandrasegaran S

Single amino acid substitutions uncouple the DNA binding and strand scission activities of Fok I endonuclease.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8415747
journal: Proc Natl Acad Sci U S A
volume: 90
pages: 9596-600
published year: 1993
authors:
  item: Waugh DS
  item: Sauer RT

Insertion and deletion mutants of FokI restriction endonuclease.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7989374
journal: J Biol Chem
volume: 269
pages: 31978-82
published year: 1994
authors:
  item: Kim YG
  item: Li L
  item: Chandrasegaran S

Chimeric restriction endonuclease.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7905633
journal: Proc Natl Acad Sci U S A
volume: 91
pages: 883-7
published year: 1994
authors:
  item: Kim YG
  item: Chandrasegaran S

Crystallization and preliminary X-ray analysis of restriction endonuclease FokI bound to DNA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9042953
journal: FEBS Lett
volume: 403
pages: 136-8
published year: 1997
authors:
  item: Hirsch JA
  item: Wah DA
  item: Dorner LF
  item: Schildkraut I
  item: Aggarwal AK

Site-specific cleavage of DNA-RNA hybrids by zinc finger/FokI cleavage domain fusions.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9426005
journal: Gene
volume: 203
pages: 43-9
published year: 1997
authors:
  item: Kim YG
  item: Shi Y
  item: Berg JM
  item: Chandrasegaran S

Structure of the multimodular endonuclease FokI bound to DNA.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
medline id: 97357159
references: http://www.ncbi.nlm.nih.gov/pubmed/9214510
journal: Nature
volume: 388
pages: 97-100
published year: 1997
authors:
  item: Wah DA
  item: Hirsch JA
  item: Dorner LF
  item: Schildkraut I
  item: Aggarwal AK
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P14870

Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9628342
journal: Biol Chem
volume: 379
pages: 489-95
published year: 1998
authors:
  item: Kim YG
  item: Smith J
  item: Durgesha M
  item: Chandrasegaran S

The mechanism of DNA cleavage by the type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9628339
journal: Biol Chem
volume: 379
pages: 467-73
published year: 1998
authors:
  item: Stahl F
  item: Wende W
  item: Jeltsch A
  item: Pingoud A

Novel site-specific DNA endonucleases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9519292
journal: Curr Opin Struct Biol
volume: 8
pages: 19-25
published year: 1998
authors:
  item: Aggarwal AK
  item: Wah DA

FokI dimerization is required for DNA cleavage.
type: BibliographicResource
comment: SUBUNIT.
references: http://www.ncbi.nlm.nih.gov/pubmed/9724744
journal: Proc Natl Acad Sci U S A
volume: 95
pages: 10570-5
published year: 1998
authors:
  item: Bitinaite J
  item: Wah DA
  item: Aggarwal AK
  item: Schildkraut I

Structure of FokI has implications for DNA cleavage.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
medline id: 98393684
references: http://www.ncbi.nlm.nih.gov/pubmed/9724743
journal: Proc Natl Acad Sci U S A
volume: 95
pages: 10564-9
published year: 1998
authors:
  item: Wah DA
  item: Bitinaite J
  item: Schildkraut I
  item: Aggarwal AK
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P14870

Type II restriction endonucleases: structural, functional and evolutionary relationships.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10508668
journal: Curr Opin Chem Biol
volume: 3
pages: 578-83
published year: 1999
authors:
  item: Kovall RA
  item: Matthews BW

A detailed study of the substrate specificity of a chimeric restriction enzyme.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9862996
journal: Nucleic Acids Res
volume: 27
pages: 674-81
published year: 1999
authors:
  item: Smith J
  item: Berg JM
  item: Chandrasegaran S

Identification of the metal-binding sites of restriction endonucleases by Fe2+-mediated oxidative cleavage.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10715131
journal: Biochemistry
volume: 39
pages: 3097-105
published year: 2000
authors:
  item: Hlavaty JJ
  item: Benner JS
  item: Hornstra LJ
  item: Schildkraut I

Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10654258
journal: J Mol Evol
volume: 50
pages: 39-44
published year: 2000
authors:
  item: Bujnicki JM

Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10954606
journal: Nucleic Acids Res
volume: 28
pages: 3361-9
published year: 2000
authors:
  item: Smith J
  item: Bibikova M
  item: Whitby FG
  item: Reddy AR
  item: Chandrasegaran S
  item: Carroll D

Substrate-assisted catalysis: molecular basis and biological significance.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10739241
journal: Protein Sci
volume: 9
pages: 1-9
published year: 2000
authors:
  item: Dall'Acqua W
  item: Carter P

FokI requires two specific DNA sites for cleavage.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11491302
journal: J Mol Biol
volume: 309
pages: 69-78
published year: 2001
authors:
  item: Vanamee ES
  item: Santagata S
  item: Aggarwal AK

Stimulation of homologous recombination through targeted cleavage by chimeric nucleases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11113203
journal: Mol Cell Biol
volume: 21
pages: 289-97
published year: 2001
authors:
  item: Bibikova M
  item: Carroll D
  item: Segal DJ
  item: Trautman JK
  item: Smith J
  item: Kim YG
  item: Chandrasegaran S

Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11729187
journal: J Biol Chem
volume: 277
pages: 4024-33
published year: 2002
authors:
  item: Bath AJ
  item: Milsom SE
  item: Gormley NA
  item: Halford SE

How the BfiI restriction enzyme uses one active site to cut two DNA strands.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12750473
journal: Proc Natl Acad Sci U S A
volume: 100
pages: 6410-5
published year: 2003
authors:
  item: Sasnauskas G
  item: Halford SE
  item: Siksnys V

In vitro selection of restriction endonucleases by in vitro compartmentalization.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15247328
journal: Nucleic Acids Res
volume: 32
pages: e95
published year: 2004
authors:
  item: Doi N
  item: Kumadaki S
  item: Oishi Y
  item: Matsumura N
  item: Yanagawa H