PDBsum entry: 2p5l

Transcription repressor

PDB id: 2p5l

Contents

Protein chains

63 a.a. *

DNA/RNA

Ligands

SO4 ×5

Waters ×13

* Residue conservation analysis

PDB id:

2p5l

Name:

Transcription repressor

Title:

Crystal structure of a dimer of n-terminal domains of ahrc i with an 18bp DNA operator site

Structure:

DNA (5'- d( Dcp Dap Dtp Dgp Dap Dap Dtp Dap Dap Dap Dap Dap Dtp Dtp P Dg)-3'). Chain: a, e. Engineered: yes. DNA (5'- d( Dcp Dtp Dtp Dgp Dap Dap Dtp Dtp Dtp Dtp Dtp Dap Dtp Dtp P Dg)-3'). Chain: b, f.

Source:

Synthetic: yes. Other_details: synthesized by mwg-biotech. Bacillus subtilis. Organism_taxid: 1423. Gene: argr, ahrc. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.85Å R-factor: 0.208 R-free: 0.231

Authors:

J.A.Garnett,F.Marincs,S.Baumberg,P.G.Stockley,S.E.V.Phillips

Key ref:

J.A.Garnett et al. (2008). Structure and function of the arginine repressor-operator complex from Bacillus subtilis. J Mol Biol, 379, 284-298. PubMed id: 18455186 DOI: 10.1016/j.jmb.2008.03.007

Date:

15-Mar-07 Release date: 11-Mar-08

Protein chains

P17893  (ARGR_BACSU) -  Arginine repressor

Seq: 149 a.a.

Struc: 63 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription, DNA-dependent (2 terms)
• Biochemical function: sequence-specific DNA binding transcription factor activity (1 term)

DOI no: 10.1016/j.jmb.2008.03.007

J Mol Biol 379:284-298 (2008)

PubMed id: 18455186

Structure and function of the arginine repressor-operator complex from Bacillus subtilis.

J.A.Garnett, F.Marincs, S.Baumberg, P.G.Stockley, S.E.Phillips.

ABSTRACT

In many bacteria, the concentration of L-arginine is controlled by a transcriptional regulator, the arginine repressor. In Bacillus subtilis this transcription factor is called AhrC and has roles in both the repression and activation of the genes involved in arginine metabolism. It interacts with 18 bp ARG boxes in the promoters of arginine biosynthetic and catabolic operons. AhrC is a hexamer and each subunit has two domains. The C-terminal domains form the core, mediating inter-subunit interactions and L-arginine binding, while the N-terminal domains contain a winged helix-turn-helix DNA-binding motif and are arranged around the periphery. Upon binding of the co-repressor L-arginine there is a approximately 15 degrees relative rotation between core C-terminal trimers. Here, we report the X-ray crystal structure of a dimer of the N-terminal domains of AhrC (NAhrC) in complex with an 18 bp DNA ARG box operator, refined to 2.85 A resolution. Comparison of the N-terminal domains within this complex with those of the free domain reveals that the flexible beta-wings of the DNA-binding motif in the free domain form a stable dimer interface in the protein-DNA complex, favouring correct orientation of the recognition helices. These are then positioned to insert into adjacent turns of the major groove of the ARG box, whilst the wings contact the minor groove. There are extensive contacts between the protein and the DNA phosphodiester backbone, as well as a number of direct hydrogen bonds between conserved amino acid side chains and bases. Combining this structure with other crystal structures of other AhrC components, we have constructed a model of the repression complex of AhrC at the B. subtilis biosynthetic argC operator and, along with transcriptome data, analysed the origins of sequence specificity and arginine activation.

Selected figure(s)

Figure 1.
Fig. 1. Structure and symmetry of the N-terminal AhrC-DNA complex in the asymmetric unit. (a) ARG box sequence used in the NAhrC–DNA complex crystal structure. The top strand corresponds to polynucleotide chains A and E of the complex, and the bottom strand to polynucleotide chains B and F. An approximate dyad passes between base pairs 9 and 10. Asymmetric base positions are shaded green and positions that were substituted by 5-bromouracil in the Br-NAhrC–DNA complex are identified by a red asterisk. (b) Electron density showing the orientation of the ARG box DNA in the asymmetric unit for chains A (purple) and B (yellow). Asymmetric bases were removed and the F[o] – F[c] map calculated after refinement (contoured at 5.5 σ). The larger peaks correspond to adenine and are associated with chain A, while the smaller peaks (thymine) belong to chain B. (c) Relationship between the two independent complexes in the asymmetric unit, in a similar orientation to that in (b). ARG box chains A (teal), B (purple), E (red), F (blue) and NAhrC chains C (orange), D (yellow), G (peach), H (green) pack in the asymmetric unit, with chains A–D and chains E–H related by approximate intermolecular twofold NCS. The adjacent complexes in the lattice are stacked end to end, related by twofold crystallographic symmetry to form pseudo-continuous duplexes. (d) The triple base pair formed at the NCS intersection, where two DNA duplexes pack 5′ to 5′, and 3′ to 3′. (e) The structure of the NAhrC-DNA complex, chains A –D. The two half-complexes are related by intramolecular pseudo twofold NCS.

Figure 4.
Fig. 4. Energy minimised model of the AhrC–argC complex. The figure is coloured as in Fig. 3, with ARG boxes blue and the 11 bp spacer coloured purple. The spacer DNA and AhrC linkers were built into the model, energy minimised and the protein stereochemistry analysed with PROCHECK^32 and the DNA curvature with CURVES5. 1.^[34]^ and ^[35] (a) In the holo-AhrC-argC promoter model, argC[01L] and argC[01R], separated by 11 bp of DNA, are bent around AhrC with a helical bend of vert, similar 120°. A third ARG box (argC[02]) bound to AhrC is shown, although it is not certain whether the intervening DNA is wrapped around AhrC or looped out. (b) The view is along the twofold axis of AhrC.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 379, 284-298) copyright 2008.

Figures were selected by the author.