PDBsum entry 1wte

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
272 a.a.
_NA ×2
Waters ×627
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of type ii restrcition endonuclease, ecoo109i complexed with cognate DNA
Structure: 5'-d( Ap Cp Cp Gp Gp Gp Cp Cp Cp Tp Gp Cp C)-3'. Chain: x. Engineered: yes. 5'-d( Gp Gp Cp Ap Gp Gp Gp Cp Cp Cp Gp Gp T)-3'. Chain: y. Engineered: yes. Ecoo109ir. Chain: a, b. Synonym: type ii restriction endonuclease.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
1.90Å     R-factor:   0.173     R-free:   0.223
Ensemble: 2 models
Authors: H.Hashimoto,T.Shimizu,T.Imasaki,M.Kato,N.Shichijo,K.Kita, M.Sato
Key ref:
H.Hashimoto et al. (2005). Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA. J Biol Chem, 280, 5605-5610. PubMed id: 15590682 DOI: 10.1074/jbc.M411684200
22-Nov-04     Release date:   14-Dec-04    
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Protein chains
Pfam   ArchSchema ?
Q9RPJ3  (Q9RPJ3_ECOLX) -  EcoO109IR
272 a.a.
272 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.M411684200 J Biol Chem 280:5605-5610 (2005)
PubMed id: 15590682  
Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.
H.Hashimoto, T.Shimizu, T.Imasaki, M.Kato, N.Shichijo, K.Kita, M.Sato.
EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY. Here we describe the crystal structures of EcoO109I and its complex with DNA. A comparison of the two structures shows that the catalytic domain moves drastically to capture the DNA. One metal ion and two water molecules are observed near the active site of the DNA complex. The metal ion is a Lewis acid that stabilizes the pentavalent phosphorus atom in the transition state. One water molecule, activated by Lys-126, attacks the phosphorus atom in an S(N)2 mechanism, whereas the other water interacts with the 3'-leaving oxygen to donate a proton to the oxygen. EcoO109I is similar to EcoRI family enzymes in terms of its DNA cleavage pattern and folding topology of the common motif in the catalytic domain, but it differs in the manner of DNA recognition. Our findings propose a novel classification of the type II restriction endonucleases and lead to the suggestion that EcoO109I represents a new subclass of the EcoRI family.
  Selected figure(s)  
Figure 4.
FIG. 4. Base pair recognition made by EcoO109I. a, recognition of the outer GC pairs. b, recognition of the inner GC pairs. The black arrow indicates the C5 position of Cyt8, which is the site of methylation by EcoO109I methyltransferase. c and d, recognition of degenerate R:Y pairs. In all of the panels, the upper side is the major groove side.
Figure 6.
FIG. 6. Active site structure of the DNA-EcoO109I complex. a, stick representations and 2F[o] - F[c] electron density contoured at 1.0 around DNA. The metal ion (M), which is considered to be Na^+ ion, is shown by a gray sphere, and water molecules are shown by the red spheres. The scissile bond is indicated by the red arrow. The NW for potential nucleophilic water molecule is indicated. The water molecule that may be a proton donor is labeled PDW. b, schematic representation of the active site structure and possible reaction mechanism. The divalent metal ion (M2^+) is indicated along with the two water molecules, NW and PDW.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 5605-5610) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21245035 F.Chen, Z.Yang, M.Yan, J.B.Alvarado, G.Wang, and S.A.Benner (2011).
Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
  Nucleic Acids Res, 39, 3949-3961.  
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
19348764 T.Oroguchi, H.Hashimoto, T.Shimizu, M.Sato, and M.Ikeguchi (2009).
Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and X-ray scattering data analysis.
  Biophys J, 96, 2808-2822.  
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.  
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
16636827 M.V.Petoukhov, and D.I.Svergun (2006).
Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution.
  Eur Biophys J, 35, 567-576.  
16209953 J.Y.Lee, J.Chang, N.Joseph, R.Ghirlando, D.N.Rao, and W.Yang (2005).
MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.
  Mol Cell, 20, 155-166.
PDB codes: 2aoq 2aor
16880975 V.Pingoud, H.Geyer, R.Geyer, E.Kubareva, J.M.Bujnicki, and A.Pingoud (2005).
Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII.
  Mol Biosyst, 1, 135-141.  
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