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PDBsum entry 4esj

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protein dna_rna ligands metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
4esj
Jmol
Contents
Protein chains
246 a.a.
DNA/RNA
Ligands
AZI
UNX ×2
GOL
Metals
_ZN ×3
Waters ×197
PDB id:
4esj
Name: Hydrolase/DNA
Title: Restriction endonuclease dpni in complex with target DNA
Structure: Type-2 restriction enzyme dpni. Chain: a, b. Synonym: r.Dpni, endonuclease dpni, type ii restriction enz engineered: yes. DNA (5'-d( Cp Tp Gp Gp (6Ma)p Tp Cp Cp Ap G)-3'). Chain: c, d, e, f. Engineered: yes
Source: Streptococcus pneumoniae. Organism_taxid: 170187. Strain: tigr4. Gene: dpnc, spr1665. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 32630. Other_details: synthetic oligonucleotide
Resolution:
2.05Å     R-factor:   0.199     R-free:   0.218
Authors: W.Siwek,H.Czapinska,M.Bochtler,J.M.Bujnicki,K.Skowronek
Key ref: W.Siwek et al. (2012). Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI. Nucleic Acids Res, 40, 7563-7572. PubMed id: 22610857
Date:
23-Apr-12     Release date:   13-Jun-12    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A460  (T2D1_STRR6) -  Type-2 restriction enzyme DpnI
Seq:
Struc:
254 a.a.
246 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: Mg(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
Nucleic Acids Res 40:7563-7572 (2012)
PubMed id: 22610857  
 
 
Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.
W.Siwek, H.Czapinska, M.Bochtler, J.M.Bujnicki, K.Skowronek.
 
  ABSTRACT  
 
No abstract given.