PDBsum entry 3eip

Immune system

PDB id: 3eip

Contents

Protein chains

84 a.a. *

Metals

_ZN

Waters ×118

* Residue conservation analysis

PDB id:

3eip

Name:

Immune system

Title:

Crystal structure of colicin e3 immunity protein: an inhibitor to a ribosome-inactivating rnase

Structure:

Protein (colicin e3 immunity protein). Chain: a, b. Engineered: yes. Other_details: zinc bound between cys 47 of a and b chains

Source:

Escherichia coli str. K12 substr.. Organism_taxid: 316407. Strain: w3110. Expressed in: escherichia coli str. K12 substr. W3110. Expression_system_taxid: 316407. Other_details: overexpression by addtion of mitomycin c during log phase of growth

Resolution:

1.80Å R-factor: 0.218 R-free: 0.265

Authors:

C.Li,D.Zhao,A.Djebli,M.Shoham

Key ref:

C.Li et al. (1999). Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase. Structure, 7, 1365-1372. PubMed id: 10574790 DOI: 10.1016/S0969-2126(00)80026-X

Date:

29-Mar-99 Release date: 10-Nov-99

Protein chains

P02984  (IMM3_ECOLX) -  Colicin E3 immunity protein from Escherichia coli

Seq: 85 a.a.

Struc: 84 a.a.

DOI no: 10.1016/S0969-2126(00)80026-X

Structure 7:1365-1372 (1999)

PubMed id: 10574790

Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase.

C.Li, D.Zhao, A.Djebli, M.Shoham.

ABSTRACT

BACKGROUND: Colicins are antibiotic-like proteins of Escherichia coli that kill related strains. Colicin E3 acts as an RNase that specifically cleaves 16S rRNA, thereby inactivating the ribosomes in the infected cell. The producing organism is protected against colicin E3 by a specific inhibitor, the immunity protein Im3, which forms a tight 1:1 complex with colicin E3 and renders it inactive. Crystallographic studies on colicin E3 and Im3 have been undertaken to unravel the structural basis for the ribonucleolytic activity and its inhibition. RESULTS: The crystal structure of Im3 has been determined to a resolution of 1.8 A. The structure consists of a four-standard antiparallel beta sheet flanked by three alpha helices on one side of the sheet. Thr7, Phe9, Phe16 and Phe74 form a hydrophobic cluster on the surface of the protein in the vicinity of Cys47. This cluster is part of a putative binding pocket which also includes nine polar residues. CONCLUSIONS: The putative binding pocket of Im3 is the probable site of interaction with colicin E3. The six acidic residues in the pocket may interact with some of the numerous basic residues of colicin E3. The involvement of hydrophobic moieties in the binding is consistent with the observation that the tight complex can only be dissociated by denaturation. The structure of Im3 resembles those of certain nucleic acid binding proteins, in particular domain II of topoisomerase I and RNA-binding proteins that contain the ribonucleoprotein (RNP) sequence motif. This observation suggests that Im3 has a nucleic acid binding function in addition to binding colicin E3.

Selected figure(s)

Figure 3.
Figure 3. The molecular interface of the Im3 dimer. Monomers A and B are depicted as Ca traces. Residues at the interface are shown in ball-and-stick representation in green (monomer A) and blue (monomer B). A major intermolecular interaction is the covalent cross-link of the thiols via a zinc ion, shown in yellow. Additional interactions include two intermolecular hydrogen bonds as well as hydrophobic interactions involving the nonpolar atoms of nine residues from monomer A, and seven residues from monomer B (see text). Furthermore, there are two water molecules, shown in red, that mediate the interaction between the monomers. (This figure was made with the program MOLSCRIPT [43].)

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1365-1372) copyright 1999.

Figure was selected by an automated process.