PDBsum entry: 1bl0

Transcription/DNA

PDB id: 1bl0

Contents

Protein chain

116 a.a. *

DNA/RNA

Waters ×144

* Residue conservation analysis

PDB id:

1bl0

Name:

Transcription/DNA

Title:

Multiple antibiotic resistance protein (mara)/DNA complex

Structure:

DNA (5'- d( Gp Gp Gp Gp Ap Tp Tp Tp Ap Gp Cp Ap Ap Ap Ap Cp Gp Tp Gp Gp Cp Ap Tp C)-3'). Chain: b. Engineered: yes. DNA (5'- d( Cp Cp Gp Ap Tp Gp Cp Cp Ap Cp Gp Tp Tp Tp Tp Gp Cp Tp Ap Ap Ap Tp Cp C)-3'). Chain: c.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Strain: bl21(lamdade3). Gene: mara. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.30Å R-factor: 0.225 R-free: 0.303

Authors:

S.Davies,R.G.Rhee,J.L.Martin,D.R.Rosner

Key ref:

S.Rhee et al. (1998). A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc Natl Acad Sci U S A, 95, 10413-10418. PubMed id: 9724717 DOI: 10.1073/pnas.95.18.10413

Date:

22-Jul-98 Release date: 02-Sep-98

Protein chain

P0ACH5  (MARA_ECOLI) -  Multiple antibiotic resistance protein marA

Seq: 127 a.a.

Struc: 116 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: response to antibiotic (4 terms)
• Biochemical function: DNA binding (3 terms)

DOI no: 10.1073/pnas.95.18.10413

Proc Natl Acad Sci U S A 95:10413-10418 (1998)

PubMed id: 9724717

A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator.

S.Rhee, R.G.Martin, J.L.Rosner, D.R.Davies.

ABSTRACT

A crystal structure for a member of the AraC prokaryotic transcriptional activator family, MarA, in complex with its cognate DNA-binding site is described. MarA consists of two similar subdomains, each containing a helix-turn-helix DNA-binding motif. The two recognition helices of the motifs are inserted into adjacent major groove segments on the same face of the DNA but are separated by only 27 A thereby bending the DNA by approximately 35 degrees. Extensive interactions between the recognition helices and the DNA major groove provide the sequence specificity.

Selected figure(s)

Figure 3.
Fig. 3. A stereo diagram of the relative orientations of the four helices and the hydrophobic core in the C subdomain. The view, from the top of Fig. 2A, shows the antiparallel orientations of helix-4 and -5 and the perpendicular location of helix-6 relative to the preceding helices. The putative hydrophobic residues from one face of each helix are indicated with their side chains. This figure was prepared by using the RIBBONS program (34).

Figure 5.
Fig. 5. Stereo close-up view of the interface between DNA and MarA. The interactions are for the N subdomain (A) and the C subdomain (C) of MarA. This orientation is similar to that in Fig. 2B. Hydrogen bonds in Fig. 4 are represented with black dashed lines between the interacting atoms (red for oxygen, blue for nitrogen, yellow for phosphorous, and silver for carbon) and the C32 and T8 bases are colored green. Water molecules at the interface of the C subdomain correspond to balls in magenta. Molecular surfaces of the N subdomain (B) and the C subdomain (D) of MarA are shown docked into the major groove of DNA. Arg-46 and Arg-96 protrude from the recognition helices and penetrate into the major groove. Figures A and C were prepared by using RIBBONS (34), and B and D were prepared by using GRASP (35).

Figures were selected by the author.