PDBsum entry 2an7

DNA binding protein

PDB id: 2an7

Contents

Protein chains

83 a.a.

PDB id:

2an7

Name:

DNA binding protein

Title:

Solution structure of the bacterial antidote pard

Structure:

Protein pard. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

NMR struc:

24 models

Authors:

M.Oberer,K.Zangger,K.Gruber,W.Keller

Key ref:

M.Oberer et al. (2007). The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding. Protein Sci, 16, 1676-1688. PubMed id: 17656583 DOI: 10.1110/ps.062680707

Date:

11-Aug-05 Release date: 05-Sep-06

Protein chains

P22995  (PARD_ECOLX) -  Antitoxin ParD from Escherichia coli

Seq: 83 a.a.

Struc: 83 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1110/ps.062680707

Protein Sci 16:1676-1688 (2007)

PubMed id: 17656583

The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.

M.Oberer, K.Zangger, K.Gruber, W.Keller.

ABSTRACT

ParD is the antidote of the plasmid-encoded toxin-antitoxin (TA) system ParD-ParE. These modules rely on differential stabilities of a highly expressed but labile antidote and a stable toxin expressed from one operon. Consequently, loss of the coding plasmid results in loss of the protective antidote and poisoning of the cell. The antidote protein usually also exhibits an autoregulatory function of the operon. In this paper, we present the solution structure of ParD. The repressor activity of ParD is mediated by the N-terminal half of the protein, which adopts a ribbon-helix-helix (RHH) fold. The C-terminal half of the protein is unstructured in the absence of its cognate binding partner ParE. Based on homology with other RHH proteins, we present a model of the ParD-DNA interaction, with the antiparallel beta-strand being inserted into the major groove of DNA. The fusion of the N-terminal DNA-binding RHH motif to the toxin-binding unstructured C-terminal domain is discussed in its evolutionary context.

Selected figure(s)

Figure 1.
The experimentally derived restraints per residue reflect the two-domain architecture of ParD protein. The shading is hatched, light gray, dark gray, black, and dotted for intraresidue, sequential, short-range (d[ij], j < i + 5), long-range (d[ij], j > i + 4), and intermonomer NOEs, respectively.

Figure 5.
Model of the ParD --DNA complex. The ParD --DNA complex is shown in a ribbon presentation: (blue and light blue) the two chains of the ParD dimer, and (green and pale green) the two strands of the 10-bp inverted repeat. Residues involved in protein --DNA interactions are shown in stick presentation: (gray) those pointing into the major groove of the DNA (Arg3, Thr5, and Asp7), (yellow) those interacting with the phosphate backbone. (A) View along the [beta]-ribbon protruding the major groove. (B) View approximately along the twofold axis of the dimer. The line drawing of the nucleotides was omitted for clarity. (C) The superposition of two ParD dimers with the MetJ --DNA complex (PDB entry: 1mjo). The ParD dimers are shown as ribbon drawing: (blue) chain A, (pale green) chain B, (pink) the hydrophobic patches positioned at the dimer --dimer interface above the minor groove. The DNA represents the original 19-mer repressor site of MetJ (Garvie and Phillips 2000). (D) The ParD promoter sequence from [minus sign]32 to +17, showing the inverted repeat (solid boxes) and the flanking half sites (half tone).

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2007, 16, 1676-1688) copyright 2007.

Figures were selected by the author.