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PDBsum entry 2ivh

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protein dna_rna metals links
Hydrolase PDB id
2ivh
Jmol
Contents
Protein chain
124 a.a. *
DNA/RNA
Metals
_ZN
Waters ×87
* Residue conservation analysis
PDB id:
2ivh
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
Resolution:
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
Date:
13-Jun-06     Release date:   02-Jan-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q47112  (CEA7_ECOLX) -  Colicin-E7
Seq:
Struc:
 
Seq:
Struc:
576 a.a.
124 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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.
 
  ABSTRACT  
 
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
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.