PDBsum entry: 1m08

Hydrolase

PDB id: 1m08

Contents

Protein chains

131 a.a. *

Ligands

PO4 ×2

Metals

_ZN ×2

Waters ×224

* Residue conservation analysis

PDB id:

1m08

Name:

Hydrolase

Title:

Crystal structure of the unbound nuclease domain of cole7

Structure:

Colicin e7. Chain: a, b. Fragment: nuclease domain. Engineered: yes

Source:

Escherichia coli str. K12 substr.. Organism_taxid: 316407. Strain: w3110. Gene: cole7 or cea. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.187 R-free: 0.240

Authors:

Y.S.Cheng,K.C.Hsia,L.G.Doudeva,K.F.Chak,H.S.Yuan

Key ref:

Y.S.Cheng et al. (2002). The crystal structure of the nuclease domain of colicin E7 suggests a mechanism for binding to double-stranded DNA by the H-N-H endonucleases. J Mol Biol, 324, 227-236. PubMed id: 12441102 DOI: 10.1016/S0022-2836(02)01092-6

Date:

12-Jun-02 Release date: 11-Dec-02

Protein chains

Q47112  (CEA7_ECOLX) -  Colicin-E7

Seq: 576 a.a.

Struc: 131 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: nucleic acid binding (3 terms)

DOI no: 10.1016/S0022-2836(02)01092-6

J Mol Biol 324:227-236 (2002)

PubMed id: 12441102

The crystal structure of the nuclease domain of colicin E7 suggests a mechanism for binding to double-stranded DNA by the H-N-H endonucleases.

Y.S.Cheng, K.C.Hsia, L.G.Doudeva, K.F.Chak, H.S.Yuan.

ABSTRACT

The bacterial toxin ColE7 contains an H-N-H endonuclease domain (nuclease ColE7) that digests cellular DNA or RNA non-specifically in target cells, leading to cell death. In the host cell, protein Im7 forms a complex with ColE7 to inhibit its nuclease activity. Here, we present the crystal structure of the unbound nuclease ColE7 at a resolution of 2.1A. Structural comparison between the unbound and bound nuclease ColE7 in complex with Im7, suggests that Im7 is not an allosteric inhibitor that induces backbone conformational changes in nuclease ColE7, but rather one that inhibits by blocking the substrate-binding site. There were two nuclease ColE7 molecules in the P1 unit cell in crystals and they appeared as a dimer related to each other by a non-crystallographic dyad symmetry. Gel-filtration and cross-linking experiments confirmed that nuclease ColE7 indeed formed dimers in solution and that the dimeric conformation was more favored in the presence of double-stranded DNA. Structural comparison of nuclease ColE7 with the His-Cys box homing endonuclease I-PpoI further demonstrated that H-N-H motifs in dimeric nuclease ColE7 were oriented in a manner very similar to that of the betabetaalpha-fold of the active sites found in dimeric I-PpoI. A mechanism for the binding of double-stranded DNA by dimeric H-N-H nuclease ColE7 is suggested.

Selected figure(s)

Figure 1.
Figure 1. Three molecules of nuclease domain of ColE7 packed in the P1 unit cell. The two nuclease ColE7 molecules (labeled 1 and 2) in one asymmetric unit are displayed in blue with only the H–N–H motif in red. Zinc ions (yellow sphere) and the bound phosphate ions in the center of the H–N–H motif are represented by ball-and-stick models. Molecule 3, displayed in green, is symmetrically identical with molecule 1; however, it makes different contacts with molecule 2. Molecules 1 and 2 are related by a pseudo 2-fold symmetry (position roughly labeled as an ellipsoid).

Figure 6.
Figure 6. The electrostatic molecular surface of dimeric nuclease ColE7 produced with GRASP.[62] Blue and red correspond to positively and negatively charged areas, respectively. The concave surface of the dimeric nuclease ColE7 facing DNA (left panel) is more basic than the opposite side of the molecule.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 324, 227-236) copyright 2002.

Figures were selected by an automated process.