PDBsum entry 2fok

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protein Protein-protein interface(s) links
Nucleic acid recognition PDB id
Protein chains
558 a.a.
Waters ×516
PDB id:
Name: Nucleic acid recognition
Title: Structure of restriction endonuclease foki
Structure: Foki restriction endonuclease. Chain: a, b. Fragment: full-length. Synonym: r.Foki. Engineered: yes
Source: Planomicrobium okeanokoites. Organism_taxid: 244. Strain: ifo12536. Atcc: atcc 33414. Collection: atcc 33414. Gene: foki. Expressed in: escherichia coli. Expression_system_taxid: 562
2.30Å     R-factor:   0.211     R-free:   0.306
Authors: D.A.Wah,J.Bitinaite,I.Schildkraut,A.K.Aggarwal
Key ref:
D.A.Wah et al. (1998). Structure of FokI has implications for DNA cleavage. Proc Natl Acad Sci U S A, 95, 10564-10569. PubMed id: 9724743 DOI: 10.1073/pnas.95.18.10564
30-Mar-98     Release date:   17-Jun-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P14870  (T2F1_PLAOK) -  Type-2 restriction enzyme FokI
583 a.a.
558 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Type Ii site-specific deoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
      Cofactor: Mg(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   4 terms 
  Biochemical function     hydrolase activity     6 terms  


DOI no: 10.1073/pnas.95.18.10564 Proc Natl Acad Sci U S A 95:10564-10569 (1998)
PubMed id: 9724743  
Structure of FokI has implications for DNA cleavage.
D.A.Wah, J.Bitinaite, I.Schildkraut, A.K.Aggarwal.
FokI is a member an unusual class of restriction enzymes that recognize a specific DNA sequence and cleave nonspecifically a short distance away from that sequence. FokI consists of an N-terminal DNA recognition domain and a C-terminal cleavage domain. The bipartite nature of FokI has led to the development of artificial enzymes with novel specificities. We have solved the structure of FokI to 2.3 A resolution. The structure reveals a dimer, in which the dimerization interface is mediated by the cleavage domain. Each monomer has an overall conformation similar to that found in the FokI-DNA complex, with the cleavage domain packing alongside the DNA recognition domain. In corroboration with the cleavage data presented in the accompanying paper in this issue of Proceedings, we propose a model for FokI DNA cleavage that requires the dimerization of FokI on DNA to cleave both DNA strands.
  Selected figure(s)  
Figure 1.
Fig. 1. Recognition sequence of FokI. FokI cleaves phosphodiester groups 9 bp away on the 5' strand and 13 bp away on the 3' strand, as indicated by arrows.
Figure 3.
Fig. 3. Comparison of the FokI-DNA complex (8) to a monomer of the FokI dimer. The two structures superimpose with an rms deviation of 1.2 Å using 553 C[ ]atoms. The linker segment (red dashes) is disordered in the FokI dimer.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21428944 S.E.Halford, L.E.Catto, C.Pernstich, D.A.Rusling, and K.L.Sanders (2011).
The reaction mechanism of FokI excludes the possibility of targeting zinc finger nucleases to unique DNA sites.
  Biochem Soc Trans, 39, 584-588.  
20805246 S.H.Chan, B.L.Stoddard, and S.Y.Xu (2011).
Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.
  Nucleic Acids Res, 39, 1.  
20699274 T.Li, S.Huang, W.Z.Jiang, D.Wright, M.H.Spalding, D.P.Weeks, and B.Yang (2011).
TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain.
  Nucleic Acids Res, 39, 359-372.  
21131970 Y.Doyon, T.D.Vo, M.C.Mendel, S.G.Greenberg, J.Wang, D.F.Xia, J.C.Miller, F.D.Urnov, P.D.Gregory, and M.C.Holmes (2011).
Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures.
  Nat Methods, 8, 74-79.  
20594338 D.Davis, and D.Stokoe (2010).
Zinc finger nucleases as tools to understand and treat human diseases.
  BMC Med, 8, 42.  
20047964 G.Sasnauskas, L.Zakrys, M.Zaremba, R.Cosstick, J.W.Gaynor, S.E.Halford, and V.Siksnys (2010).
A novel mechanism for the scission of double-stranded DNA: BfiI cuts both 3'-5' and 5'-3' strands by rotating a single active site.
  Nucleic Acids Res, 38, 2399-2410.  
19955230 P.H.Too, Z.Zhu, S.H.Chan, and S.Y.Xu (2010).
Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.
  Nucleic Acids Res, 38, 1294-1303.  
20444879 Y.Zheng, D.Cohen-Karni, D.Xu, H.G.Chin, G.Wilson, S.Pradhan, and R.J.Roberts (2010).
A unique family of Mrr-like modification-dependent restriction endonucleases.
  Nucleic Acids Res, 38, 5527-5534.  
18997032 J.Nakonieczna, T.Kaczorowski, A.Obarska-Kosinska, and J.M.Bujnicki (2009).
Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.
  Appl Environ Microbiol, 75, 212-223.  
19223323 K.L.Sanders, L.E.Catto, S.R.Bellamy, and S.E.Halford (2009).
Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands.
  Nucleic Acids Res, 37, 2105-2115.  
19591184 M.Zhang, J.Huang, M.Deng, X.Weng, H.Ma, and X.Zhou (2009).
Sensitive and visual detection of adenosine by a rationally designed FokI-based biosensing strategy.
  Chem Asian J, 4, 1420-1423.  
19304757 S.M.Lippow, P.M.Aha, M.H.Parker, W.J.Blake, B.M.Baynes, and D.Lipovsek (2009).
Creation of a type IIS restriction endonuclease with a long recognition sequence.
  Nucleic Acids Res, 37, 3061-3073.  
18456708 J.Orlowski, and J.M.Bujnicki (2008).
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
  Nucleic Acids Res, 36, 3552-3569.  
18276642 L.E.Catto, S.R.Bellamy, S.E.Retter, and S.E.Halford (2008).
Dynamics and consequences of DNA looping by the FokI restriction endonuclease.
  Nucleic Acids Res, 36, 2073-2081.  
18164625 Y.Bao, L.Higgins, P.Zhang, S.H.Chan, S.Laget, S.Sweeney, K.Lunnen, and S.Y.Xu (2008).
Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants.
  Protein Expr Purif, 58, 42-52.  
17524420 E.S.Vanamee, J.Berriman, and A.K.Aggarwal (2007).
An EM view of the FokI synaptic complex by single particle analysis.
  J Mol Biol, 370, 207-212.  
17603475 J.C.Miller, M.C.Holmes, J.Wang, D.Y.Guschin, Y.L.Lee, I.Rupniewski, C.M.Beausejour, A.J.Waite, N.S.Wang, K.A.Kim, P.D.Gregory, C.O.Pabo, and E.J.Rebar (2007).
An improved zinc-finger nuclease architecture for highly specific genome editing.
  Nat Biotechnol, 25, 778-785.  
17914173 J.Nakonieczna, J.W.Zmijewski, B.Banecki, and A.J.Podhajska (2007).
Binding of MmeI restriction-modification enzyme to its specific recognition sequence is stimulated by S-adenosyl-L-methionine.
  Mol Biotechnol, 37, 127-135.  
17763826 J.Wu, K.Kandavelou, and S.Chandrasegaran (2007).
Custom-designed zinc finger nucleases: what is next?
  Cell Mol Life Sci, 64, 2933-2944.  
17603476 M.Szczepek, V.Brondani, J.Büchel, L.Serrano, D.J.Segal, and T.Cathomen (2007).
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases.
  Nat Biotechnol, 25, 786-793.  
17951612 P.Zhang, Y.Bao, L.Higgins, and S.Y.Xu (2007).
Rational design of a chimeric endonuclease targeted to NotI recognition site.
  Protein Eng Des Sel, 20, 497-504.  
17855396 S.H.Chan, Y.Bao, E.Ciszak, S.Laget, and S.Y.Xu (2007).
Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.
  Nucleic Acids Res, 35, 6238-6248.  
17392356 S.M.Horner, and D.DiMaio (2007).
The DNA binding domain of a papillomavirus E2 protein programs a chimeric nuclease to cleave integrated human papillomavirus DNA in HeLa cervical carcinoma cells.
  J Virol, 81, 6254-6264.  
17586812 S.Y.Xu, Z.Zhu, P.Zhang, S.H.Chan, J.C.Samuelson, J.Xiao, D.Ingalls, and G.G.Wilson (2007).
Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI.
  Nucleic Acids Res, 35, 4608-4618.  
16723432 G.J.Gemmen, R.Millin, and D.E.Smith (2006).
DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.
  Nucleic Acids Res, 34, 2864-2877.  
16556912 L.E.Catto, S.Ganguly, S.E.Milsom, A.J.Welsh, and S.E.Halford (2006).
Protein assembly and DNA looping by the FokI restriction endonuclease.
  Nucleic Acids Res, 34, 1711-1720.  
16582101 Q.Liu, V.Derbyshire, M.Belfort, and D.R.Edgell (2006).
Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions.
  Nucleic Acids Res, 34, 1755-1764.  
16195548 Q.S.Xu, R.J.Roberts, and H.C.Guo (2005).
Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
  Protein Sci, 14, 2590-2600.
PDB code: 1yfi
16251401 S.Durai, M.Mani, K.Kandavelou, J.Wu, M.H.Porteus, and S.Chandrasegaran (2005).
Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.
  Nucleic Acids Res, 33, 5978-5990.  
16247004 S.Grazulis, E.Manakova, M.Roessle, M.Bochtler, G.Tamulaitiene, R.Huber, and V.Siksnys (2005).
Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.
  Proc Natl Acad Sci U S A, 102, 15797-15802.
PDB code: 2c1l
15805123 Z.Yang, J.R.Horton, R.Maunus, G.G.Wilson, R.J.Roberts, and X.Cheng (2005).
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
  Nucleic Acids Res, 33, 1892-1901.
PDB code: 1ynm
15247328 N.Doi, S.Kumadaki, Y.Oishi, N.Matsumura, and H.Yanagawa (2004).
In vitro selection of restriction endonucleases by in vitro compartmentalization.
  Nucleic Acids Res, 32, e95.  
15341737 Q.S.Xu, R.B.Kucera, R.J.Roberts, and H.C.Guo (2004).
An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site.
  Structure, 12, 1741-1747.
PDB code: 1sa3
15139802 S.E.Halford, A.J.Welsh, and M.D.Szczelkun (2004).
Enzyme-mediated DNA looping.
  Annu Rev Biophys Biomol Struct, 33, 1.  
12750473 G.Sasnauskas, S.E.Halford, and V.Siksnys (2003).
How the BfiI restriction enzyme uses one active site to cut two DNA strands.
  Proc Natl Acad Sci U S A, 100, 6410-6415.  
14576294 M.Mucke, D.H.Kruger, and M.Reuter (2003).
Diversity of type II restriction endonucleases that require two DNA recognition sites.
  Nucleic Acids Res, 31, 6079-6084.  
12853651 P.M.Skowron, J.Majewski, A.Zylicz-Stachula, S.M.Rutkowska, I.Jaworowska, and R.I.Harasimowicz-Słowińska (2003).
A new Thermus sp. class-IIS enzyme sub-family: isolation of a 'twin' endonuclease TspDTI with a novel specificity 5'-ATGAA(N(11/9))-3', related to TspGWI, TaqII and Tth111II.
  Nucleic Acids Res, 31, e74.  
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
12356742 M.Mücke, G.Grelle, J.Behlke, R.Kraft, D.H.Krüger, and M.Reuter (2002).
EcoRII: a restriction enzyme evolving recombination functions?
  EMBO J, 21, 5262-5268.  
11328872 A.Loria, and T.Pan (2001).
Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein.
  Nucleic Acids Res, 29, 1892-1897.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11520857 C.E.Besnier, and H.Kong (2001).
Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state.
  EMBO Rep, 2, 782-786.  
11410656 L.S.Higgins, C.Besnier, and H.Kong (2001).
The nicking endonuclease N.BstNBI is closely related to type IIs restriction endonucleases MlyI and PleI.
  Nucleic Acids Res, 29, 2492-2501.  
11113203 M.Bibikova, D.Carroll, D.J.Segal, J.K.Trautman, J.Smith, Y.G.Kim, and S.Chandrasegaran (2001).
Stimulation of homologous recombination through targeted cleavage by chimeric nucleases.
  Mol Cell Biol, 21, 289-297.  
11687651 Y.Xu, K.D.Lunnen, and H.Kong (2001).
Engineering a nicking endonuclease N.AlwI by domain swapping.
  Proc Natl Acad Sci U S A, 98, 12990-12995.  
10911996 A.B.Hickman, Y.Li, S.V.Mathew, E.W.May, N.L.Craig, and F.Dyda (2000).
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
  Mol Cell, 5, 1025-1034.
PDB code: 1f1z
10601013 F.Christ, S.Schoettler, W.Wende, S.Steuer, A.Pingoud, and V.Pingoud (1999).
The monomeric homing endonuclease PI-SceI has two catalytic centres for cleavage of the two strands of its DNA substrate.
  EMBO J, 18, 6908-6916.  
10393910 J.Yang, H.S.Malik, and T.H.Eickbush (1999).
Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements.
  Proc Natl Acad Sci U S A, 96, 7847-7852.  
10494832 S.Chandrasegaran, and J.Smith (1999).
Chimeric restriction enzymes: what is next?
  Biol Chem, 380, 841-848.  
9783752 H.Viadiu, and A.K.Aggarwal (1998).
The role of metals in catalysis by the restriction endonuclease BamHI.
  Nat Struct Biol, 5, 910-916.
PDB codes: 2bam 3bam
9724744 J.Bitinaite, D.A.Wah, A.K.Aggarwal, and I.Schildkraut (1998).
FokI dimerization is required for DNA cleavage.
  Proc Natl Acad Sci U S A, 95, 10570-10575.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.