PDBsum entry 2kjc

Transcription regulator

PDB id: 2kjc

Contents

Protein chains

95 a.a. *

* Residue conservation analysis

PDB id:

2kjc

Name:

Transcription regulator

Title:

Solution structure of czra in the zn(ii) state

Structure:

Czra protein. Chain: a, b. Synonym: repressor protein. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Gene: rzca, czra. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

21 models

Authors:

A.I.Arunkumar,G.C.Campanello,D.P.Giedroc

Key ref:

A.I.Arunkumar et al. (2009). Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state. Proc Natl Acad Sci U S A, 106, 18177-18182. PubMed id: 19822742 DOI: 10.1073/pnas.0905558106

Date:

27-May-09 Release date: 10-Nov-09

Protein chains

O85142  (O85142_STAAU) -  ArsR family transcriptional regulator from Staphylococcus aureus

Seq: 106 a.a.

Struc: 95 a.a.

DOI no: 10.1073/pnas.0905558106

Proc Natl Acad Sci U S A 106:18177-18182 (2009)

PubMed id: 19822742

Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state.

A.I.Arunkumar, G.C.Campanello, D.P.Giedroc.

ABSTRACT

Staphylococcus aureus CzrA is a zinc-dependent transcriptional repressor from the ubiquitous ArsR family of metal sensor proteins. Zn(II) binds to a pair of intersubunit C-terminal alpha5-sensing sites, some 15 A distant from the DNA-binding interface, and allosterically inhibits DNA binding. This regulation is characterized by a large allosteric coupling free energy (DeltaGc) of approximately +6 kcal mol(-1), the molecular origin of which is poorly understood. Here, we report the solution quaternary structure of homodimeric CzrA bound to a palindromic 28-bp czr operator, a structure that provides an opportunity to compare the two allosteric "end" states of an ArsR family sensor. Zn(II) binding drives a quaternary structural switch from a "closed" DNA-binding state to a low affinity "open" conformation as a result of a dramatic change in the relative orientations of the winged helical DNA binding domains within the dimer. Zn(II) binding also effectively quenches both rapid and intermediate timescale internal motions of apo-CzrA while stabilizing the native state ensemble. In contrast, DNA binding significantly enhances protein motions in the allosteric sites and reduces the stability of the alpha5 helices as measured by H-D solvent exchange. This study reveals how changes in the global structure and dynamics drive a long-range allosteric response in a large subfamily of bacterial metal sensor proteins, and provides insights on how other structural classes of ArsR sensor proteins may be regulated by metal binding.

Selected figure(s)

Figure 1.
Solution structure of CzrO DNA-bound CzrA. (A) Backbone heavy atom (N, Cα, and C') overlay of 20 lowest-energy structures of DNA bound CzrA (see Table S2 for structure statistics; unstructured residues 100–103 of the bundle are not shown in this view for clarity). The ribbon diagram in the overlay represents the mean structure of the ensemble and the two subunits are shaded salmon and red. (B) Ribbon diagram representation of the global overlay of DNA bound CzrA and the crystal structure of Zn(II) CzrA (8). The subunits of DNA bound CzrA are colored as in A and the two subunits of Zn(II) CzrA are colored slate and blue. Zn(II) ions are colored yellow. (C) Another view of the same overlay as in B (rotated 45°) and the green arrows represent the direction of the quaternary structural change.

Figure 2.
Distinct conformational states of α5 metal sensor proteins. (A) Overlay of the apo SmtB (magenta ribbon), Zn(II)-bound CzrA (light blue ribbon) and DNA-bound CzrA (salmon ribbon). The “right” subunit is overlaid to better show the quaternary structural differences. (B) Effect of binding DNA on apo CzrA structure is mapped using a ^1H HN chemical shift perturbation experiment. Colors on the ribbon are ramped according to Δδ ppm as follows: gray, Δδ<0.2 ppm; magenta, 0.2<Δδ<0.8 and red; 0.8<Δδ<1.5 ppm. (C) A comparison of the short time scale ^15N relaxation dynamics of Zn[2] CzrA vs. apo-CzrA (see Fig. S2 for primary data). Blue, increased S^2 by ≥ 0.02 on Zn(II) binding; yellow, decreased S^2 by ≤ –0.02 on Zn(II) binding; purple, residues in apo-CzrA that exhibit measurable R[ex] ≥ 1 s^−1 that is completely dampened upon Zn(II) binding; orange, the single residue in Zn[2] CzrA for which there is measurable R[ex] ≥ 1 s^−1 (L35).

Figures were selected by the author.