PDBsum entry 2ivh

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protein dna_rna metals links
Hydrolase PDB id
Jmol PyMol
Protein chain
124 a.a. *
Waters ×87
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the nuclease domain of cole7 (h545q mutant) in complex with an 18-bp duplex DNA
Structure: Colcin-e7. Chain: a. Fragment: nuclease domain, residues 449-576. Engineered: yes. Mutation: yes. 5'-d( Gp Gp Ap Ap Tp Tp Cp Gp Ap Tp Cp Gp Ap Ap Tp Tp Cp C)-3'. Chain: b, c
Source: Escherichia coli. Organism_taxid: 562. Strain: w3110. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 562
2.80Å     R-factor:   0.193     R-free:   0.265
Authors: Y.T.Wang,W.J.Yang,C.L.Li,L.G.Doudeva,H.S.Yuan
Key ref: Y.T.Wang et al. (2007). Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases. Nucleic Acids Res, 35, 584-594. PubMed id: 17175542
13-Jun-06     Release date:   02-Jan-07    
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Protein chain
Pfam   ArchSchema ?
Q47112  (CEA7_ECOLX) -  Colicin-E7
576 a.a.
124 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.-.-
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cytolysis   3 terms 
  Biochemical function     receptor binding     2 terms  


Nucleic Acids Res 35:584-594 (2007)
PubMed id: 17175542  
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.
Y.T.Wang, W.J.Yang, C.L.Li, L.G.Doudeva, H.S.Yuan.
Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3'O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the 'preferred complex' of the nuclease domain of ColE7 bound to an 18 bp DNA with a thymine before the scissile phosphate had a more distorted DNA phosphate backbone than the backbones in the non-preferred complexes, so that the scissile phosphate was compositionally closer to the endonuclease active site resulting in more efficient DNA cleavage. On the other hand, in the crystal structure of Vvn in complex with a 16 bp DNA, the DNA phosphate backbone was similar and not distorted in comparison with that of a previously reported complex of Vvn with a different DNA sequence. Taken together these results suggest a general structural basis for the sequence-dependent DNA cleavage catalyzed by nonspecific endonucleases, indicating that nonspecific nucleases could induce DNA to deform to distinctive levels depending on the local sequence leading to different cleavage rates along the DNA chain.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
18391403 B.Altermark, R.Helland, E.Moe, N.P.Willassen, and A.O.Smalås (2008).
Structural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida.
  Acta Crystallogr D Biol Crystallogr, 64, 368-376.
PDB code: 2pu3
18312415 L.Niiranen, B.Altermark, B.O.Brandsdal, H.K.Leiros, R.Helland, A.O.Smalås, and N.P.Willassen (2008).
Effects of salt on the kinetics and thermodynamic stability of endonuclease I from Vibrio salmonicida and Vibrio cholerae.
  FEBS J, 275, 1593-1605.
PDB code: 2vnd
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