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PDBsum entry 1cfr

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Restriction endonuclease PDB id
1cfr
Jmol
Contents
Protein chain
283 a.a.
Waters ×294
PDB id:
1cfr
Name: Restriction endonuclease
Title: Crystal structure of citrobacter freundii restriction endonu cfr10i at 2.15 angstroms resolution.
Structure: Restriction endonuclease. Chain: a. Fragment: residues 1 - 283. Synonym: cfr10i. Engineered: yes. Other_details: characterization of cfr10i restriction endon janulaitis et al. (1983)
Source: Citrobacter freundii. Organism_taxid: 546. Strain: rfl10i. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.15Å     R-factor:   0.196    
Authors: D.Bozic,S.Grazulis,V.Siksnys,R.Huber
Key ref:
D.Bozic et al. (1996). Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution. J Mol Biol, 255, 176-186. PubMed id: 8568865 DOI: 10.1006/jmbi.1996.0015
Date:
02-Feb-96     Release date:   27-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56200  (T2CX_CITFR) -  Type-2 restriction enzyme Cfr10I
Seq:
Struc:
285 a.a.
283 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.21.4  - 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: Magnesium
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     hydrolase activity     6 terms  

 

 
DOI no: 10.1006/jmbi.1996.0015 J Mol Biol 255:176-186 (1996)
PubMed id: 8568865  
 
 
Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution.
D.Bozic, S.Grazulis, V.Siksnys, R.Huber.
 
  ABSTRACT  
 
The X-ray crystal structure of Citrobacter freundii restriction endonuclease Cfr10I has been determined at a resolution of 2.15 A by multiple isomorphous replacement methods and refined to an R-factor of 19.64%. The structure of Cfr10I represents the first structure of a restriction endonuclease recognizing a degenerated nucleotide sequence. Structural comparison of Cfr10I with previously solved structures of other restriction enzymes suggests that recognition of specific sequence occurs through contacts in the major and the minor grooves of DNA. The arrangement of the putative active site residues shows some striking differences from previously described restriction endonucleases and supports a two-metal-ion mechanism of catalysis.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Topological diagrams of Cfr10I (a), EcoRI (b) and EcoRV (c) at the same orientation as in Figure 3. Common structural elements are shadowed. Dimerisation regions are emphasised in blue and structural elements that contact DNA are in red.
Figure 5.
Figure 5. Stereo view of the superimposition of the DNA-recognition region of Cfr10I (red) on BamHI (purple). Residue R155 in BamHI is supposed to contact the outer base-pair of the recognition sequence.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 255, 176-186) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21465555 M.Sikora, and M.Cieplak (2011).
Mechanical stability of multidomain proteins and novel mechanical clamps.
  Proteins, 79, 1786-1799.  
20071747 F.Khan, Y.Furuta, M.Kawai, K.H.Kaminska, K.Ishikawa, J.M.Bujnicki, and I.Kobayashi (2010).
A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).
  Nucleic Acids Res, 38, 3019-3030.  
20375162 S.K.Menon, B.J.Eilers, M.J.Young, and C.M.Lawrence (2010).
The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.
  J Virol, 84, 5890-5897.
PDB code: 2w8m
19307723 P.W.Dunten, E.J.Little, and N.C.Horton (2009).
The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases.
  Acta Crystallogr D Biol Crystallogr, 65, 393-398.  
19793866 R.M.Smith, J.Josephsen, and M.D.Szczelkun (2009).
An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI.
  Nucleic Acids Res, 37, 7231-7238.  
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.  
18367450 S.Takahashi, H.Matsuno, H.Furusawa, and Y.Okahata (2008).
Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII.
  J Biol Chem, 283, 15023-15030.  
17308914 G.A.Papadakos, H.Nastri, P.Riggs, and C.M.Dupureur (2007).
Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis.
  J Biol Inorg Chem, 12, 557-569.  
17584608 P.M.Gordon, R.Fong, and J.A.Piccirilli (2007).
A second divalent metal ion in the group II intron reaction center.
  Chem Biol, 14, 607-612.  
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.  
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
15667656 A.A.Chmiel, J.M.Bujnicki, and K.J.Skowronek (2005).
A homology model of restriction endonuclease SfiI in complex with DNA.
  BMC Struct Biol, 5, 2.  
16308566 E.S.Vanamee, H.Viadiu, R.Kucera, L.Dorner, S.Picone, I.Schildkraut, and A.K.Aggarwal (2005).
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
  EMBO J, 24, 4198-4208.
PDB codes: 2ezv 2f03
15590682 H.Hashimoto, T.Shimizu, T.Imasaki, M.Kato, N.Shichijo, K.Kita, and M.Sato (2005).
Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.
  J Biol Chem, 280, 5605-5610.
PDB codes: 1wtd 1wte
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
15563460 V.Pingoud, A.Sudina, H.Geyer, J.M.Bujnicki, R.Lurz, G.Lüder, R.Morgan, E.Kubareva, and A.Pingoud (2005).
Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences.
  J Biol Chem, 280, 4289-4298.  
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
15383647 H.Geyer, R.Geyer, and V.Pingoud (2004).
A novel strategy for the identification of protein-DNA contacts by photocrosslinking and mass spectrometry.
  Nucleic Acids Res, 32, e132.  
12876363 H.Viadiu, E.S.Vanamee, E.M.Jacobson, I.Schildkraut, and A.K.Aggarwal (2003).
Crystallization of restriction endonuclease SfiI in complex with DNA.
  Acta Crystallogr D Biol Crystallogr, 59, 1493-1495.  
12732532 I.Mruk, and T.Kaczorowski (2003).
Genetic organization and molecular analysis of the EcoVIII restriction-modification system of Escherichia coli E1585-68 and its comparison with isospecific homologs.
  Appl Environ Microbiol, 69, 2638-2650.  
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.  
11818524 J.Bitinaite, and I.Schildkraut (2002).
Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease.
  Proc Natl Acad Sci U S A, 99, 1164-1169.  
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.  
11842098 S.Grazulis, M.Deibert, R.Rimseliene, R.Skirgaila, G.Sasnauskas, A.Lagunavicius, V.Repin, C.Urbanke, R.Huber, and V.Siksnys (2002).
Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
  Nucleic Acids Res, 30, 876-885.
PDB code: 1knv
11827971 V.Pingoud, E.Kubareva, G.Stengel, P.Friedhoff, J.M.Bujnicki, C.Urbanke, A.Sudina, and A.Pingoud (2002).
Evolutionary relationship between different subgroups of restriction endonucleases.
  J Biol Chem, 277, 14306-14314.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11179886 C.M.Lukacs, and A.K.Aggarwal (2001).
BglII and MunI: what a difference a base makes.
  Curr Opin Struct Biol, 11, 14-18.  
11250198 M.J.van der Woerd, J.J.Pelletier, S.Xu, and A.M.Friedman (2001).
Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
  Structure, 9, 133-144.
PDB code: 1dc1
11327870 S.L.Reid, D.Parry, H.H.Liu, and B.A.Connolly (2001).
Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization.
  Biochemistry, 40, 2484-2494.  
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
10666447 E.A.Kubareva, H.Thole, A.S.Karyagina, T.S.Oretskaya, A.Pingoud, and V.Pingoud (2000).
Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.
  Nucleic Acids Res, 28, 1085-1091.  
10715131 J.J.Hlavaty, J.S.Benner, L.J.Hornstra, and I.Schildkraut (2000).
Identification of the metal-binding sites of restriction endonucleases by Fe2+-mediated oxidative cleavage.
  Biochemistry, 39, 3097-3105.  
10982859 L.Aravind, K.S.Makarova, and E.V.Koonin (2000).
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
  Nucleic Acids Res, 28, 3417-3432.  
10648519 P.C.Hsieh, J.P.Xiao, D.O'loane, and S.Y.Xu (2000).
Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.
  J Bacteriol, 182, 949-955.  
10856254 Q.Huai, J.D.Colandene, Y.Chen, F.Luo, Y.Zhao, M.D.Topal, and H.Ke (2000).
Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
  EMBO J, 19, 3110-3118.
PDB code: 1ev7
11092936 T.J.O'Loughlin, Q.Xu, R.B.Kucera, L.F.Dorner, S.Sweeney, I.Schildkraut, and H.C.Guo (2000).
Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.
  Acta Crystallogr D Biol Crystallogr, 56, 1652-1655.  
10103058 C.M.Dupureur, and L.M.Hallman (1999).
Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases.
  Eur J Biochem, 261, 261-268.  
10593932 D.T.Bilcock, L.E.Daniels, A.J.Bath, and S.E.Halford (1999).
Reactions of type II restriction endonucleases with 8-base pair recognition sites.
  J Biol Chem, 274, 36379-36386.  
10531503 N.C.Horton, L.F.Dorner, I.Schildkraut, and J.J.Perona (1999).
Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease-DNA complex.
  Acta Crystallogr D Biol Crystallogr, 55, 1943-1945.  
10508668 R.A.Kovall, and B.W.Matthews (1999).
Type II restriction endonucleases: structural, functional and evolutionary relationships.
  Curr Opin Chem Biol, 3, 578-583.  
10360178 S.E.Tsutakawa, T.Muto, T.Kawate, H.Jingami, N.Kunishima, M.Ariyoshi, D.Kohda, M.Nakagawa, and K.Morikawa (1999).
Crystallographic and functional studies of very short patch repair endonuclease.
  Mol Cell, 3, 621-628.
PDB code: 1vsr
10586498 T.Dahai, S.Ando, Y.Takasaki, and J.Tadano (1999).
Site-directed mutagenesis of restriction endonuclease HindIII.
  Biosci Biotechnol Biochem, 63, 1703-1707.  
9548954 F.Stahl, W.Wende, C.Wenz, A.Jeltsch, and A.Pingoud (1998).
Intra- vs intersubunit communication in the homodimeric restriction enzyme EcoRV: Thr 37 and Lys 38 involved in indirect readout are only important for the catalytic activity of their own subunit.
  Biochemistry, 37, 5682-5688.  
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
9736624 M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, and S.E.Phillips (1998).
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
  EMBO J, 17, 5466-5476.
PDB code: 1dmu
9705308 N.C.Horton, and J.J.Perona (1998).
Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
  J Biol Chem, 273, 21721-21729.
PDB code: 1bgb
9653111 R.A.Kovall, and B.W.Matthews (1998).
Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.
  Proc Natl Acad Sci U S A, 95, 7893-7897.  
9287151 A.Lagunavicius, and V.Siksnys (1997).
Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity.
  Biochemistry, 36, 11086-11092.  
9210460 A.Pingoud, and A.Jeltsch (1997).
Recognition and cleavage of DNA by type-II restriction endonucleases.
  Eur J Biochem, 246, 1.  
9325303 H.G.Nastri, P.D.Evans, I.H.Walker, and P.D.Riggs (1997).
Catalytic and DNA binding properties of PvuII restriction endonuclease mutants.
  J Biol Chem, 272, 25761-25767.  
9200708 S.G.Erskine, G.S.Baldwin, and S.E.Halford (1997).
Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease.
  Biochemistry, 36, 7567-7576.  
9063456 S.Windolph, and J.Alves (1997).
Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI.
  Eur J Biochem, 244, 134-139.  
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.