Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein–RNA toxin–antitoxin system

Genes encoding toxin–antitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important aspects of bacterial physiology, including genomic stability, formation of persister cells under antibiotic stress, and resistance to phage infection. The CptIN locus from Eubacterium rectale is a member of the recently-discovered Type III class of TA systems, defined by a protein toxin suppressed by direct interaction with a structured RNA antitoxin. Here, we present the crystal structure of the CptIN protein–RNA complex to 2.2 Å resolution. The structure reveals a new heterotetrameric quaternary organization for the Type III TA class, and the RNA antitoxin bears a novel structural feature of an extended A-twist motif within the pseudoknot fold. The retention of a conserved ribonuclease active site as well as traits normally associated with TA systems, such as plasmid maintenance, implicates a wider functional role for Type III TA systems. We present evidence for the co-variation of the Type III component pair, highlighting a distinctive evolutionary process in which an enzyme and its substrate co-evolve.

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

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There are 4 unique types of molecules in this entry. The entry contains 19478 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 called CptN Toxin. 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: CptN Toxin Chain A: • Molecule 1: CptN Toxin Chain C: • Molecule 2: RNA (45-MER) Chain B: • Molecule 2: RNA (45-MER) Chain D: • Molecule 2: RNA (45-MER) Chain F: • Molecule 2: RNA (45-MER) Chain H: • Molecule 2: RNA (45-MER) Chain L: wwPDB X-ray Structure Validation Summary Report 4RMO • Molecule 2: RNA (45-MER) Chain N: • Molecule 2: RNA (45-MER) Chain P: Xtriage's analysis on translational NCS is as follows: The largest off-origin peak in the Patterson function is 3.45% of the height of the origin peak. No significant pseudotranslation is detected. 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| > 5 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles). Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying if the center is modelled as a planar moiety or with the opposite hand. A planarity outlier is detected by checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of a sidechain that are expected to be planar.

Mol Chain #Chirality outliers #Planarity outliers
Continued from previous page... Mol Chain #Chirality outliers #Planarity outliers All All 0 7 The worst 5 of 29 bond length outliers are listed below:  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 7.
The worst 5 of 221 close contacts within the same asymmetric unit are listed below.

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In the following table, the Percentiles column shows the percent Ramachandran 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 backbone conformation was analysed, and the total number of residues.

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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. There are no chirality outliers.

Mol Chain
There are no torsion outliers.
There are no ring outliers. There are no bond length outliers.

Carbohydrates
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.