PDBsum entry 2f03

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
269 a.a.
_CA ×2
Waters ×111
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of tetrameric restriction endonuclease sfii in complex with cognate DNA (partial bound form)
Structure: DNA (5'- d( Ap Tp G Tp Gp Gp Cp Cp Ap Ap Cp Ap Ap Gp Gp Cp Cp Tp Ap Tp T)-3'). Chain: e, g. Engineered: yes. DNA (5'- d( Ap Ap Tp Ap Gp Gp Cp Cp Tp Tp Gp Tp Tp Gp Gp Cp Cp Ap Cp Ap T)-3'). Chain: f, h.
Source: Synthetic: yes. Other_details: e.Coli
3.05Å     R-factor:   0.241     R-free:   0.293
Ensemble: 2 models
Authors: A.K.Aggarwal,E.S.Vanamee,H Viadiu
Key ref:
E.S.Vanamee et al. (2005). A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J, 24, 4198-4208. PubMed id: 16308566 DOI: 10.1038/sj.emboj.7600880
11-Nov-05     Release date:   16-Jan-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O52512  (T2S1_STRFI) -  Type-2 restriction enzyme SfiI
269 a.a.
269 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   3 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1038/sj.emboj.7600880 EMBO J 24:4198-4208 (2005)
PubMed id: 16308566  
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
E.S.Vanamee, H.Viadiu, R.Kucera, L.Dorner, S.Picone, I.Schildkraut, A.K.Aggarwal.
Many reactions in cells proceed via the sequestration of two DNA molecules in a synaptic complex. SfiI is a member of a growing family of restriction enzymes that can bind and cleave two DNA sites simultaneously. We present here the structures of tetrameric SfiI in complex with cognate DNA. The structures reveal two different binding states of SfiI: one with both DNA-binding sites fully occupied and the other with fully and partially occupied sites. These two states provide details on how SfiI recognizes and cleaves its target DNA sites, and gives insight into sequential binding events. The SfiI recognition sequence (GGCCNNNN[downward arrow]NGGCC) is a subset of the recognition sequence of BglI (GCCNNNN[downward arrow]NGGC), and both enzymes cleave their target DNAs to leave 3-base 3' overhangs. We show that even though SfiI is a tetramer and BglI is a dimer, and there is little sequence similarity between the two enzymes, their modes of DNA recognition are unusually similar.
  Selected figure(s)  
Figure 5.
Figure 5 Change in loop E conformation. (A) Loop E enters the DNA major groove in the native complex (blue), but in the C/D dimer of the Se-Met complex (red) it packs away from the DNA. Black spheres mark the position of Arg 213. (B) View of C/D dimer looking down the DNA axis. In the native complex (blue), loop E's bracket the DNA and help to hold it in place, while in the Se-Met complex (red) the loops are positioned away from the DNA.
Figure 6.
Figure 6 The active sites of SfiI (left) and BglI (right). The DNA and the active site residues of SfiI (Asp 79, Asp100, and Lys102) and BglI (Asp116, Asp142, and Lys144) are shown in 'stick' representation. The scissile phosphodiester is indicated by arrows. The Ca^2+ ions are shown as nonbonded spheres and colored aqua, water molecules are not shown. In SfiI, the second Ca^2+ is missing and the scissile phosphodiester is 3 further away than in BglI, indicating that the enzyme is in an inactive state.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2005, 24, 4198-4208) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21151881 C.K.Park, H.K.Joshi, A.Agrawal, M.I.Ghare, E.J.Little, P.W.Dunten, J.Bitinaite, and N.C.Horton (2010).
Domain swapping in allosteric modulation of DNA specificity.
  PLoS Biol, 8, e1000554.
PDB code: 3mq6
19502597 L.S.Shlyakhtenko, J.Gilmore, A.N.Kriatchko, S.Kumar, P.C.Swanson, and Y.L.Lyubchenko (2009).
Molecular mechanism underlying RAG1/RAG2 synaptic complex formation.
  J Biol Chem, 284, 20956-20965.  
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
19567736 R.D.Morgan, and Y.A.Luyten (2009).
Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity.
  Nucleic Acids Res, 37, 5222-5233.  
19596810 S.R.Bellamy, Y.S.Kovacheva, I.H.Zulkipli, and S.E.Halford (2009).
Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping.
  Nucleic Acids Res, 37, 5443-5453.  
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.  
18831563 J.W.Pavlicek, Y.L.Lyubchenko, and Y.Chang (2008).
Quantitative analyses of RAG-RSS interactions and conformations revealed by atomic force microscopy.
  Biochemistry, 47, 11204-11211.  
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.  
18701646 P.W.Dunten, E.J.Little, M.T.Gregory, V.M.Manohar, M.Dalton, D.Hough, J.Bitinaite, and N.C.Horton (2008).
The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
  Nucleic Acids Res, 36, 5405-5416.
PDB codes: 3dpg 3dvo 3dw9
17125791 A.V.Krasnoslobodtsev, L.S.Shlyakhtenko, and Y.L.Lyubchenko (2007).
Probing Interactions within the synaptic DNA-SfiI complex by AFM force spectroscopy.
  J Mol Biol, 365, 1407-1416.  
17266985 J.J.Marshall, D.M.Gowers, and S.E.Halford (2007).
Restriction endonucleases that bridge and excise two recognition sites from DNA.
  J Mol Biol, 367, 419-431.  
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.  
17410205 L.Zhao, R.P.Bonocora, D.A.Shub, and B.L.Stoddard (2007).
The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.
  EMBO J, 26, 2432-2442.
PDB code: 2ost
17277188 M.A.Karymov, A.V.Krasnoslobodtsev, and Y.L.Lyubchenko (2007).
Dynamics of synaptic SfiI-DNA complex: single-molecule fluorescence analysis.
  Biophys J, 92, 3241-3250.  
17870087 S.R.Bellamy, S.E.Milsom, Y.S.Kovacheva, R.B.Sessions, and S.E.Halford (2007).
A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease.
  J Mol Biol, 373, 1169-1183.  
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
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.  
16628220 M.Bochtler, R.H.Szczepanowski, G.Tamulaitis, S.Grazulis, H.Czapinska, E.Manakova, and V.Siksnys (2006).
Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.
  EMBO J, 25, 2219-2229.
PDB codes: 2fqz 2gb7
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.