PDBsum entry: 1r8e

Transcription/DNA

PDB id: 1r8e

Contents

Protein chain

275 a.a. *

DNA/RNA

Ligands

GOL ×5

P4P

IMD ×11

Waters ×131

* Residue conservation analysis

PDB id:

1r8e

Name:

Transcription/DNA

Title:

Crystal structure of bmrr bound to DNA at 2.4a resolution

Structure:

5'-d( Gp Ap Cp Cp Cp Tp Cp Cp Cp Cp Tp Tp Ap Gp G Gp Gp Gp Tp C)-3'. Chain: b. Engineered: yes. Multidrug-efflux transporter regulator. Chain: a. Engineered: yes

Source:

Synthetic: yes. Bacillus subtilis. Organism_taxid: 1423. Gene: bmrr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.40Å R-factor: 0.227 R-free: 0.267

Authors:

K.J.Newberry,R.G.Brennan

Key ref:

K.J.Newberry and R.G.Brennan (2004). The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus. J Biol Chem, 279, 20356-20362. PubMed id: 14985361 DOI: 10.1074/jbc.M400960200

Date:

23-Oct-03 Release date: 17-Aug-04

Protein chain

P39075  (BMRR_BACSU) -  Multidrug-efflux transporter 1 regulator

Seq: 278 a.a.

Struc: 275 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: transcription, DNA-dependent (2 terms)
• Biochemical function: nucleotide binding (3 terms)

DOI no: 10.1074/jbc.M400960200

J Biol Chem 279:20356-20362 (2004)

PubMed id: 14985361

The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus.

K.J.Newberry, R.G.Brennan.

ABSTRACT

Transcription regulators of the MerR family respond to myriad stress signals to activate sigma70/sigmaA-targeted genes, which contain suboptimal 19-bp spacers between their -35 and -10 promoter elements. The crystal structure of a BmrR-TPP(+)-DNA complex provided initial insight into the transcription activation mechanism of the MerR family, which involves base pair distortion, DNA undertwisting and shortening of the spacer, and realignment of the -35 and -10 boxes. Here, we describe the crystal structure of MerR family member MtaN bound to the mta promoter. Although the global DNA binding modes of MtaN and BmrR differ somewhat, homologous protein-DNA interactions are maintained. Moreover, despite their different sequences, the mta promoter conformation is essentially identical to that of the BmrR-TPP(+)-bound bmr promoter, indicating that this DNA distortion mechanism is common to the entire MerR family. Interestingly, DNA binding experiments reveal that the identity of the two central bases of the mta and bmr promoters, which are conserved as either a thymidine or an adenine in nearly all MerR promoters, is not important for DNA affinity. Comparison of the free and DNA-bound MtaN structures reveals that a conformational hinge, centered at residues N-terminal to the ubiquitous coiled coil, is key for mta promoter binding. Analysis of the structures of BmrR, CueR, and ZntR indicates that this hinge may be common to all MerR family members.

Selected figure(s)

Figure 4.
FIG. 4. Structural mechanism of transcription activation by the MerR family. a, superimposition of the MtaN-DNA and BmrRTPP+-DNA complexes. Helices 1 to 4 of one subunit from each dimer, but not W1, were overlaid. Yellow, BmrR; blue, MtaN. b, overlay of the MtaN-mta and BmrR-bmr promoter structures using all equivalent phosphate backbone groups. Blue, mta DNA; yellow, bmr DNA. c, close up of the superimposed mta and bmr promoters near base pair 1. Notice their nearly identical structures at the site of DNA distortion. Blue sticks, mta promoter DNA; yellow sticks, bmr promoter DNA.

Figure 5.
FIG. 5. Representative DNA binding isotherms. a, equilibrium binding isotherm of BmrR titrated into bmrT[1]A[2] DNA. To ensure equilibrium binding, 0.2 nM fluorescein-labeled DNA was used in this experiment. b, equilibrium binding isotherm of MtaN titrated into MtaN-mtaT[1']T[2'] DNA. To ensure equilibrium binding, 1 nM fluorescein-labeled DNA was used in this experiment. mP, millipolarization.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 20356-20362) copyright 2004.

Figures were selected by an automated process.