PDBsum entry 2kc8

Toxin/toxin repressor

PDB id: 2kc8

Contents

Protein chains

95 a.a. *

33 a.a. *

* Residue conservation analysis

PDB id:

2kc8

Name:

Toxin/toxin repressor

Title:

Structure of e. Coli toxin rele (r81a/r83a) mutant in complex with antitoxin relbc (k47-l79) peptide

Structure:

Toxin rele. Chain: a. Engineered: yes. Mutation: yes. Antitoxin relb. Chain: b. Fragment: unp residues 47-79. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: rele, b1563, jw1555. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: de3. Other_details: rele is expressed with his-tag fusion. The his-tag is removed by thrombin afterward.

NMR struc:

20 models

Authors:

G.Li,Y.Zhang,M.Inouye,M.Ikura

Key ref:

G.Y.Li et al. (2009). Inhibitory mechanism of E. coli RelE/RelB toxin/antitoxin module involves a helix displacement near a mRNA interferase active site. J Biol Chem, 284, 14628-14636. PubMed id: 19297318 DOI: 10.1074/jbc.M809656200

Date:

17-Dec-08 Release date: 17-Mar-09

Protein chain

P0C077  (RELE_ECOLI) -  mRNA interferase toxin RelE from Escherichia coli (strain K12)

Seq: 95 a.a.

Struc: 95 a.a.*

Protein chain

P0C079  (RELB_ECOLI) -  Antitoxin RelB from Escherichia coli (strain K12)

Seq: 79 a.a.

Struc: 33 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.3.1.-.-
• Enzyme class 3: Chain B: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1074/jbc.M809656200

J Biol Chem 284:14628-14636 (2009)

PubMed id: 19297318

Inhibitory mechanism of E. coli RelE/RelB toxin/antitoxin module involves a helix displacement near a mRNA interferase active site.

G.Y.Li, Y.Zhang, M.Inouye, M.Ikura.

ABSTRACT

In E. coli, RelE toxin participates in growth arrest and cell death by inducing mRNA degradation at the ribosomal A-site under stress conditions. The NMR structures of a mutant of E. coli RelE toxin, RelE(R81A/R83A), with reduced toxicity and its complex with an inhibitory peptide from RelB antitoxin, RelB(C) (K47-L79) have been determined. In the free RelE(R81A/R83A) structure, helix alpha4 at the carboxyl terminus adopts a closed conformation contacting with the beta-sheet core and adjacent loops. In the RelER(81A/R83A):RelB(C) complex, an helix alpha3(*) of RelB(C) displaces alpha4 of RelE(R81A/R83A) from the binding site on the beta-sheet core. This helix replacement results in neutralization of a conserved positively charged cluster of RelE by acidic residues from alpha3(*) of RelB. The released helix alpha4 becomes unfolded, adopting an open conformation with increased mobility. The displacement of alpha4 disrupts the geometry of critical residues, including R81 and Y87, in a putative active site of RelE toxin. Our structures indicate that RelB counteracts the toxic activity of RelE by displacing alpha4 helix from the catalytically competent position found in the free RelE structure.

Selected figure(s)

Figure 4.
The interface and electrostatic properties of RelE^R81A/R83A and RelB[C]. A, helix α4 occupies the surface of the central β-meander motif and interacts with the α3-β2 loop and β1-α1 junction region. Helix α4 is colored in cyan, and the remaining core structure of RelE is colored in gray. B, interface site I. The helix α3^* of RelB (magenta) occupies the surface of β-sheet core of RelE (gray). C, interface site II. The C-terminal extended region of RelB (magenta) anchors on the surface of the RelE β1, α1, and α2(gray). The electrostatic surface analysis of free RelE^R81A/R83A (D), RelB[C]-bound RelE^R81A/R83A (E), and RelE^R81A/R83A-bound RelB[C] (F). G-I, opposite views of D--F with a rotation of 180°. Two positively charged clusters on the RelE^R81A/R83A surface are complemented by negatively charged clusters from RelB[C], which are denoted by light green circles. The main positive cluster of the RelE^R81A/R83A protein shown in D-F is the putative mRNA-binding site.

Figure 5.
RelB induced conformation change in the active site of RelE. A, active conformation of the E. coli RelE mRNA-binding site in the absence of RelB antitoxin. The side chain of Arg^81 was modeled based on the orientation of Ala^81 in the structure of RelE^R81A/R83A. B, active site of RNase SA shows the catalytic triad (Glu^54, Arg^69, and His^85) and the hydrophobic site (Phe^37 and Tyr^86) for base packing. C, catalytic site of YoeB in the YefM-free conformation shows the catalytic triad (Glu^46, Arg^65, and His^83) and base anchor residues (Leu^48, Leu^52, and Tyr^84). D, putative mRNA-binding site of E. coli RelE in the presence of RelB[C] shows a large conformation disruption to the active site. The side chain of Arg^81 is modeled based on the orientation of Ala^81 in the structure of RelE^R81A/R83A-RelB[C]. E, active site of archaeal aRelE in the aRelB-aRelE complex shows an inactive conformation similar to the RelE^R81A/R83A-RelB[C] complex. The C-terminal residues (Tyr^89 and Lys^90) of aRelE are missing in the crystal structure; they were arbitrarily rebuilt to estimate the position of Tyr^89. F, catalytic active site of YoeB in the YoeB-YefM complex shows the conformational change altered by YefM binding.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 14628-14636) copyright 2009.

Figures were selected by an automated process.