PDBsum entry 4zm2

Transcription

PDB id: 4zm2

Contents

Protein chains

52 a.a.

61 a.a.

55 a.a.

DNA/RNA

PDB id:

4zm2

Name:

Transcription

Title:

Antitoxin phd from phage p1 in complex with its operator DNA inverted repeat in a monoclinic space group

Structure:

Antitoxin phd. Chain: a, b, c, d. Synonym: addiction protein pdh,prevent host death protein. Engineered: yes. DNA (5'-d(gp Cp Tp Tp Gp Tp Gp Tp Ap Cp Ap Cp Ap T)-3'). Chain: e, g. Engineered: yes. DNA (5'-d(cp Ap Tp Gp Tp Gp Tp Ap Cp Ap Cp Ap Ap G)-3'). Chain: f, h.

Source:

Enterobacteria phage p1. Organism_taxid: 10678. Gene: phd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 10678

Resolution:

3.88Å R-factor: 0.262 R-free: 0.271

Authors:

A.Garcia-Pino,R.Loris

Key ref:

A.Garcia-Pino et al. (2016). An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation. Nat Chem Biol, 12, 490-496. PubMed id: 27159580 DOI: 10.1038/nchembio.2078

Date:

02-May-15 Release date: 20-Apr-16

Protein chain

Q06253  (PHD_BPP1) -  Antitoxin phd from Escherichia phage P1

Seq: 73 a.a.

Struc: 52 a.a.

Protein chain

Q06253  (PHD_BPP1) -  Antitoxin phd from Escherichia phage P1

Seq: 73 a.a.

Struc: 61 a.a.

Protein chains

Q06253  (PHD_BPP1) -  Antitoxin phd from Escherichia phage P1

Seq: 73 a.a.

Struc: 55 a.a.

DNA/RNA chains

G-C-T-T-G-T-G-T-A-C-A-C-A-T 14 bases

C-A-T-G-T-G-T-A-C-A-C-A-A-G 14 bases

G-C-T-T-G-T-G-T-A-C-A-C-A-T 14 bases

A-T-G-T-G-T-A-C-A-C-A-A-G 13 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.?

DOI no: 10.1038/nchembio.2078

Nat Chem Biol 12:490-496 (2016)

PubMed id: 27159580

An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation.

A.Garcia-Pino, S.De Gieter, A.Talavera, H.De Greve, R.G.Efremov, R.Loris.

ABSTRACT

Conditional cooperativity is a common mechanism involved in transcriptional regulation of prokaryotic type II toxin-antitoxin operons and is intricately related to bacterial persistence. It allows the toxin component of a toxin-antitoxin module to act as a co-repressor at low doses of toxin as compared to antitoxin. When toxin level exceeds a certain threshold, however, the toxin becomes a de-repressor. Most antitoxins contain an intrinsically disordered region (IDR) that typically is involved in toxin neutralization and repressor complex formation. To address how the antitoxin IDR is involved in transcription regulation, we studied the phd-doc operon from bacteriophage P1. We provide evidence that the IDR of Phd provides an entropic barrier precluding full operon repression in the absence of Doc. Binding of Doc results in a cooperativity switch and consequent strong operon repression, enabling context-specific modulation of the regulatory process. Variations of this theme are likely to be a common mechanism in the autoregulation of bacterial operons that involve intrinsically disordered regions.