PDBsum entry: 2ivh

Hydrolase

PDB id: 2ivh

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 DOI: 10.1093/nar/gkl621

Date:

13-Jun-06 Release date: 02-Jan-07

Protein chain

Q47112  (CEA7_ECOLX) -  Colicin-E7

Seq: 576 a.a.

Struc: 124 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Biological process: cytolysis (3 terms)
• Biochemical function: receptor binding (2 terms)

DOI no: 10.1093/nar/gkl621

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.