PDBsum entry: 2k9s

Transcription

PDB id: 2k9s

Contents

Protein chain

107 a.a. *

* Residue conservation analysis

PDB id:

2k9s

Name:

Transcription

Title:

Solution structure of DNA binding domain of e. Coli arac

Structure:

Arabinose operon regulatory protein. Chain: a. Fragment: DNA binding domain. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: arac, b0064, jw0063. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

M.E.Rodgers,R.F.Schleif

Key ref:

M.E.Rodgers and R.Schleif (2009). Solution structure of the DNA binding domain of AraC protein. Proteins, 77, 202-208. PubMed id: 19422057 DOI: 10.1002/prot.22431

Date:

23-Oct-08 Release date: 25-Nov-08

Protein chain

P0A9E0  (ARAC_ECOLI) -  Arabinose operon regulatory protein

Seq: 292 a.a.

Struc: 107 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: 10.1002/prot.22431

Proteins 77:202-208 (2009)

PubMed id: 19422057

Solution structure of the DNA binding domain of AraC protein.

M.E.Rodgers, R.Schleif.

ABSTRACT

We report the solution structure of the DNA binding domain of the Escherichia coli regulatory protein AraC determined in the absence of DNA. The 20 lowest energy structures, determined on the basis of 1507 unambiguous nuclear Overhauser restraints and 180 angle restraints, are well resolved with a pair wise backbone root mean square deviation of 0.7 A. The protein, free of DNA, is well folded in solution and contains seven helices arranged in two semi-independent sub domains, each containing one helix-turn-helix DNA binding motif, joined by a 19 residue central helix. This solution structure is discussed in the context of extensive biochemical and physiological data on AraC and with respect to the DNA-bound structures of the MarA and Rob homologs.

Selected figure(s)

Figure 1.
Figure 1. Schematic diagram of the AraC protein and the Ara operon. In the minus arabinose repressing state, left, the AraC DNA binding domains are held in a position that favors looping by binding to the two widely separated DNA half-sites araO[2] and araI[1]. Upon binding arabinose, right, the arms reposition on the dimerization domains over the arabinose. This frees the DNA binding domains to reorient and allows binding to the adjacent direct repeat DNA half-sites araI[1] and araI[2] partially overlapping the RNA polymerase binding site p[BAD].

Figure 5.
Figure 5. Overlay of AraC and MarA. The solution structure of AraC-DBD, dark, overlaid with the DNA-bound structure of MarA, light. Only backbone atoms of the C-terminal H-T-H regions were used to calculate the overlay, which had an RMS difference of 1.3 Å.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 77, 202-208) copyright 2009.

Figures were selected by the author.

Author's comment

See related structures: 2aac, 2arc, 2ara and 1xja.
Robert Schleif