Structural Analysis and Insights into the Oligomeric State of an Arginine-Dependent Transcriptional Regulator from Bacillus halodurans

The arginine repressor (ArgR) is an arginine-dependent transcription factor that regulates the expression of genes encoding proteins involved in the arginine biosynthesis and catabolic pathways. ArgR is a functional homolog of the arginine-dependent repressor/activator AhrC from Bacillus subtilis, and belongs to the ArgR/AhrC family of transcriptional regulators. In this research, we determined the structure of the ArgR (Bh2777) from Bacillus halodurans at 2.41 Å resolution by X-ray crystallography. The ArgR from B. halodurans appeared to be a trimer in a size exclusion column and in the crystal structure. However, it formed a hexamer in the presence of L-arginine in multi-angle light scattering (MALS) studies, indicating the oligomerization state was dependent on the presence of L-arginine. The trimeric structure showed that the C-terminal domains form the core, which was made by inter-subunit interactions mainly through hydrophobic contacts, while the N-terminal domains containing a winged helix-turn-helix DNA binding motif were arranged around the periphery. The arrangement of trimeric structure in the B. halodurans ArgR was different from those of other ArgR homologs previously reported. We finally showed that the B. halodurans ArgR has an arginine-dependent DNA binding property by an electrophoretic mobility shift assay.

1 Overall quality at a glance i O The reported resolution of this entry is 2.41Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based.

Metric
Whole archive (#Entries) The table below summarises the geometric issues observed across the polymeric chains and their fit to the electron density. The red, orange, yellow and green segments on the lower bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. The upper red bar (where present) indicates the fraction of residues that have poor fit to the electron density.
Mol Chain Length Quality of chain 1 A 146 The following table lists non-polymeric compounds that are outliers for geometric or electrondensity-fit criteria: Mol Type Chain Res Geometry Electron density 2 PGO C 1 -X Page 3 Preliminary wwPDB X-ray Structure Validation Summary Report UNNAMED 2 Entry composition i O There are 3 unique types of molecules in this entry. The entry contains 1229 atoms, of which 0 are hydrogen and 0 are deuterium.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms.
Molecule 1 is a protein. 3 Residue-property plots i O These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for a chain summarises the proportions of errors displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometry and electron density. Residues are colorcoded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dot above a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey.

Mol Chain Residues
• Molecule 1: Clashscore is defined as the number of clashes calculated for the entry per 1000 atoms (including hydrogens) of the entry. The overall clashscore for this entry is 9.
The worst 5 of 20 close contacts within the same asymmetric unit are listed below. There are no Ramachandran outliers to report.

Protein sidechains i O
In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution. The Analysed column shows the number of residues for which the sidechain conformation was analysed, and the total number of residues.

RNA i O
There are no RNA chains in this entry.

5.4
Non-standard residues in protein, DNA, RNA chains i O There are no non-standard protein/DNA/RNA residues in this entry.

Carbohydrates i
O There are no carbohydrates in this entry.

Ligand geometry i
O 1 ligand is modelled in this entry.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogul statistics could be retrieved, the number of bonds (or angles) that are observed in the model and the number of bonds (or angles) that are defined in the chemical component dictionary. The Link column lists molecule types, if any, to which the group is linked. The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles). There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no torsion outliers.
There are no ring outliers.

Other polymers i O
There are no such residues in this entry.

Polymer linkage issues
There are no chain breaks in this entry.