PDBsum entry 2c1l

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Hydrolase PDB id
Protein chains
358 a.a.
GOL ×4
TLA ×2
SRT ×2
BCT ×2
MES ×2
Waters ×480
PDB id:
Name: Hydrolase
Title: Structure of the bfii restriction endonuclease
Structure: Restriction endonuclease. Chain: a, b. Synonym: bfii restriction endonuclease. Engineered: yes
Source: Bacillus firmus. Organism_taxid: 1399. Strain: s8120. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.90Å     R-factor:   0.188     R-free:   0.217
Authors: S.Grazulis,E.Manakova,M.Roessle,M.Bochtler,G.Tamulaitiene, R.Huber,V.Siksnys
Key ref:
S.Grazulis et al. (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. PubMed id: 16247004 DOI: 10.1073/pnas.0507949102
15-Sep-05     Release date:   07-Oct-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9F4C9  (Q9F4C9_BACFI) -  Restriction endonuclease
358 a.a.
358 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   1 term 
  Biochemical function     endonuclease activity     1 term  


DOI no: 10.1073/pnas.0507949102 Proc Natl Acad Sci U S A 102:15797-15802 (2005)
PubMed id: 16247004  
Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.
S.Grazulis, E.Manakova, M.Roessle, M.Bochtler, G.Tamulaitiene, R.Huber, V.Siksnys.
Among all restriction endonucleases known to date, BfiI is unique in cleaving DNA in the absence of metal ions. BfiI represents a different evolutionary lineage of restriction enzymes, as shown by its crystal structure at 1.9-A resolution. The protein consists of two structural domains. The N-terminal catalytic domain is similar to Nuc, an EDTA-resistant nuclease from the phospholipase D superfamily. The C-terminal DNA-binding domain of BfiI exhibits a beta-barrel-like structure very similar to the effector DNA-binding domain of the Mg(2+)-dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors. BfiI presumably evolved through domain fusion of a DNA-recognition element to a nonspecific nuclease akin to Nuc and elaborated a mechanism to limit DNA cleavage to a single double-strand break near the specific recognition sequence. The crystal structure suggests that the interdomain linker may act as an autoinhibitor controlling BfiI catalytic activity in the absence of a specific DNA sequence. A psi-blast search identified a BfiI homologue in a Mesorhizobium sp. BNC1 bacteria strain, a plant symbiont isolated from an EDTA-rich environment.
  Selected figure(s)  
Figure 1.
Fig. 1. Crystal structure of BfiI dimer. Two N-terminal domains of each monomer depicted in light and dark blue, respectively, make a dimeric catalytic core flanked by C-terminal DNA-binding domains depicted in light and dark red. The linker connecting the N- and C-terminal domains within the monomer is shown in yellow.
Figure 2.
Fig. 2. Comparison of BfiI with EDTA-resistant nonspecific Nuc nuclease from S. typhimurium. (a) Structural superposition of the N-terminal domain dimer of BfiI (light and dark blue) and Nuc nuclease (green). The active-site region of Nuc nuclease is boxed in red. (b) Close-up view of the active-site residues of Nuc nuclease (green) and their structural equivalents in BfiI (light and dark blue) shown in the same orientation as in a. The tungstate molecule coordinated at the putative scissile DNA phosphate-binding site in Nuc is shown in stick representation colored by atom type. Amino acid residues from both subunits of Nuc and BfiI contribute to a single active site located in the intersubunit cleft.
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20935048 M.Sokolowska, H.Czapinska, and M.Bochtler (2011).
Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
  Nucleic Acids Res, 39, 1554-1564.
PDB codes: 3oqg 3or3
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.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20541511 B.W.Shen, D.F.Heiter, S.H.Chan, H.Wang, S.Y.Xu, R.D.Morgan, G.G.Wilson, and B.L.Stoddard (2010).
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
  Structure, 18, 734-743.
PDB codes: 3ldy 3m7k
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.  
19729506 D.Golovenko, E.Manakova, G.Tamulaitiene, S.Grazulis, and V.Siksnys (2009).
Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
  Nucleic Acids Res, 37, 6613-6624.
PDB codes: 3hqf 3hqg
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.  
19380375 M.Sokolowska, H.Czapinska, and M.Bochtler (2009).
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
  Nucleic Acids Res, 37, 3799-3810.
PDB codes: 3fc3 3gox
19400796 M.Szczepek, P.Mackeldanz, E.Möncke-Buchner, J.Alves, D.H.Krüger, and M.Reuter (2009).
Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition.
  Mol Microbiol, 72, 1011-1021.  
18400177 A.R.Lambert, D.Sussman, B.Shen, R.Maunus, J.Nix, J.Samuelson, S.Y.Xu, and B.L.Stoddard (2008).
Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.
  Structure, 16, 558-569.
PDB codes: 3bvq 3c25
18086711 G.Gasiunas, G.Sasnauskas, G.Tamulaitis, C.Urbanke, D.Razaniene, and V.Siksnys (2008).
Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family.
  Nucleic Acids Res, 36, 938-949.  
18515343 G.Sasnauskas, B.A.Connolly, S.E.Halford, and V.Siksnys (2008).
Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme.
  Nucleic Acids Res, 36, 3969-3977.  
18400171 G.Tamulaitiene, and V.Siksnys (2008).
NotI is not boring.
  Structure, 16, 497-498.  
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.  
19014591 K.H.Kaminska, M.Kawai, M.Boniecki, I.Kobayashi, and J.M.Bujnicki (2008).
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.
  BMC Struct Biol, 8, 48.  
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.  
17626614 E.M.Ibryashkina, M.V.Zakharova, V.B.Baskunov, E.S.Bogdanova, M.O.Nagornykh, M.M.Den'mukhamedov, B.S.Melnik, A.Kolinski, D.Gront, M.Feder, A.S.Solonin, and J.M.Bujnicki (2007).
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.
  BMC Struct Biol, 7, 48.  
17267608 G.Sasnauskas, B.A.Connolly, S.E.Halford, and V.Siksnys (2007).
Site-specific DNA transesterification catalyzed by a restriction enzyme.
  Proc Natl Acad Sci U S A, 104, 2115-2120.  
17407166 J.Kosinski, E.Kubareva, and J.M.Bujnicki (2007).
A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.
  Proteins, 68, 324-336.  
17242028 J.Orlowski, M.Boniecki, and J.M.Bujnicki (2007).
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.
  Bioinformatics, 23, 527-530.  
17332011 K.Miyazono, M.Watanabe, J.Kosinski, K.Ishikawa, M.Kamo, T.Sawasaki, K.Nagata, J.M.Bujnicki, Y.Endo, M.Tanokura, and I.Kobayashi (2007).
Novel protein fold discovered in the PabI family of restriction enzymes.
  Nucleic Acids Res, 35, 1908-1918.
PDB code: 2dvy
17192590 P.Schäfer, I.A.Cymerman, J.M.Bujnicki, and G.Meiss (2007).
Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species.
  Protein Sci, 16, 82-91.  
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.  
17392342 R.Sukackaite, A.Lagunavicius, K.Stankevicius, C.Urbanke, C.Venclovas, and V.Siksnys (2007).
Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family.
  Nucleic Acids Res, 35, 2377-2389.  
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.  
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.  
16962970 G.Tamulaitiene, A.Jakubauskas, C.Urbanke, R.Huber, S.Grazulis, and V.Siksnys (2006).
The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.
  Structure, 14, 1389-1400.
PDB code: 2ixs
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 codes are shown on the right.