PDBsum entry 3hqg

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protein dna_rna ligands links
Hydrolase/DNA PDB id
Protein chain
222 a.a. *
Waters ×67
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of restriction endonuclease ecorii catalyt terminal domain in complex with cognate DNA
Structure: Type-2 restriction enzyme ecorii. Chain: a. Fragment: c-terminal catalytic domain (unp residues 183-404 synonym: r.Ecorii, type ii restriction enzyme ecorii, endon ecorii. Engineered: yes. 5'-d( Tp Cp Gp Ap Cp Cp Ap Gp Gp Cp Tp A)-3'. Chain: b. Engineered: yes.
Source: Escherichia coli. Organism_taxid: 562. Gene: ecorii, ecoriir. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
2.60Å     R-factor:   0.242     R-free:   0.293
Authors: D.Golovenko,E.Manakova,S.Grazulis,G.Tamulaitiene,V.Siksnys
Key ref: D.Golovenko et al. (2009). Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res, 37, 6613-6624. PubMed id: 19729506
06-Jun-09     Release date:   22-Sep-09    
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Protein chain
Pfam   ArchSchema ?
P14633  (T2E2_ECOLX) -  Type-2 restriction enzyme EcoRII
404 a.a.
222 a.a.
Key:    PfamA domain  Secondary structure

 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     DNA restriction-modification system   1 term 
  Biochemical function     DNA binding     2 terms  


Nucleic Acids Res 37:6613-6624 (2009)
PubMed id: 19729506  
Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.
D.Golovenko, E.Manakova, G.Tamulaitiene, S.Grazulis, V.Siksnys.
EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T); however, it shows no activity on a single recognition site. To activate cleavage it requires binding of an additional target site as an allosteric effector. EcoRII dimer consists of three structural units: a central catalytic core, made from two copies of the C-terminal domain (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically different structural mechanisms to interact with the effector and substrate DNA. The catalytic EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically in a single defined orientation which is determined by specific hydrogen bonding and van der Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the target site recognition is shared by the large class of higher plant transcription factors of the B3 superfamily.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
20571089 M.Zaremba, A.Owsicka, G.Tamulaitis, G.Sasnauskas, L.S.Shlyakhtenko, A.Y.Lushnikov, Y.L.Lyubchenko, N.Laurens, B.van den Broek, G.J.Wuite, and V.Siksnys (2010).
DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.
  Nucleic Acids Res, 38, 7142-7154.  
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