PDBsum entry: 1d5y

Transcription/DNA

PDB id: 1d5y

Contents

Protein chains

288 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1d5y

Name:

Transcription/DNA

Title:

Crystal structure of the e. Coli rob transcription factor in complex with DNA

Structure:

DNA (5'- d( Tp Gp Ap Cp Ap Gp Cp Ap Cp Tp Gp Ap Ap Tp Gp Tp Cp Ap Ap Ap G)-3'). Chain: m, o. Engineered: yes. DNA (5'- d( Ap Cp Tp Tp Tp Gp Ap Cp Ap Tp Tp Cp Ap Gp Tp Gp Cp Tp Gp Tp C)-3'). Chain: n, p.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.70Å R-factor: 0.254 R-free: 0.302

Authors:

H.J.Kwon,M.H.J.Bennik,B.Demple,T.Ellenberger

Key ref:

H.J.Kwon et al. (2000). Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Nat Struct Biol, 7, 424-430. PubMed id: 10802742 DOI: 10.1038/75213

Date:

12-Oct-99 Release date: 24-Apr-00

Protein chains

P0ACI0  (ROB_ECOLI) -  Right origin-binding protein

Seq: 289 a.a.

Struc: 288 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: regulation of transcription (2 terms)
• Biochemical function: DNA binding (3 terms)

DOI no: 10.1038/75213

Nat Struct Biol 7:424-430 (2000)

PubMed id: 10802742

Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA.

H.J.Kwon, M.H.Bennik, B.Demple, T.Ellenberger.

ABSTRACT

The Escherichia coli Rob protein is a transcription factor belonging to the AraC/XylS protein family that regulates genes involved in resistance to antibiotics, organic solvents and heavy metals. The genes encoding these proteins are activated by the homologous proteins MarA and SoxS, although the level of activation can vary for the different transcription factors. Here we report a 2.7 A crystal structure of Rob in complex with the micF promoter that reveals an unusual mode of binding to DNA. The Rob-DNA complex differs from the previously reported structure of MarA bound to the mar promoter, in that only one of Rob's dual helix-turn-helix (HTH) motifs engages the major groove of the binding site. Biochemical studies show that sequence specific interactions involving only one of Rob's HTH motifs are sufficient for high affinity binding to DNA. The two different modes of DNA binding seen in crystal structures of Rob and MarA also match the distinctive patterns of DNA protection by AraC at several sites within the pBAD promoter. These and other findings suggest that gene activation by AraC/XylS transcription factors might involve two alternative modes of binding to DNA in different promoter contexts.

Selected figure(s)

Figure 1.
Figure 1. The structure of Rob in complex with the micF promotor. a, Ribbon diagrams of the Rob -micF DNA complex and the MarA -mar DNA complex13. The structurally similar N-terminal DNA binding domains of Rob and MarA are colored orange and Rob's unique C-terminal domain is shaded blue. Only the N-terminal HTH motif of Rob directly contacts bases of the binding site. Sequences of the micF and mar promotors used in the crystal structure determinations are shown with the A-box and B-box sequences colored red and blue, respectively. Rob's C-terminal HTH motif contacts the DNA backbone, but it is relatively exposed. In contrast, MarA bends its DNA site so that both HTH modules are situated in adjacent major groove surfaces on one side of the DNA. b, Stereo view of the Rob protein with the DNA removed for clarity. c, C trace of the two Rob protomers bound to one of the two DNA duplexes in the asymmetric unit. The protomer bound specifically to the consensus binding site is colored orange. The nonspecifically bound protomer (green) contacts the major groove at the junction of two DNA molecules packed end-to-end in the crystals. Crystallographically related molecules are shown in gray. Electron density is not present for the side chains of residues facing the DNA in the nonspecific complex. Figs 1, 2, 4, 6, and 7 were prepared with SETOR39.

Figure 4.
Figure 4. Rob's C-terminal domain might restrict DNA bending. The structure of Rob is shown in complex with DNA from the crystal structure (yellow), and with the DNA from the MarA crystal structure^13 (red) superimposed on the Rob protein. The bent DNA from the MarA complex clashes with the acidic 3- 4 loop (compare Fig. 3) that projects from the C-terminal domain of Rob (right side of diagram). The loop and the -strands on either side of the loop would have to rearrange to accommodate the modeled interaction of Rob with bent DNA.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 424-430) copyright 2000.

Figures were selected by the author.