Computational protocol: Three Dimensional Structure of the MqsR:MqsA Complex: A Novel TA Pair Comprised of a Toxin Homologous to RelE and an Antitoxin with Unique Properties

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Protocol publication

[…] MqsA-F: Molecular replacement (Phaser ) using the structures of the MqsA individual domains (MqsA-N and MqsA-C; structure determination of MqsA-N and MqsA-C described in , and , ) as search models resulted in a single solution, with two molecules of each domain present in the asymmetric unit. The resulting electron density maps were readily interpretable. Model building was performed in Coot followed by restrained refinement in REFMAC 5.2.0019 . As observed for the structure of MqsA C-terminal domain alone (), Gln108 is methylated at N5. MqsR:MqsA-N complex: SOLVE was used to determine the positions of the two expected zinc atoms. Initial phases to 2.0 Å were improved with density modification in RESOLVE. An initial model built by ARP/wARP served as the basis for subsequent manual model building and refinement. Iterative cycles of refinement in REFMAC against the high energy remote data were used to complete and refine the model. Data collection, model and refinement statistics for both structures are reported in . Structure validation and stereochemistry analysis was performed with Molprobity and SFCHECK . [...] The P22 C2 repressor protein (PDBID 2R1J) was identified as the closest structural homolog to the MqsA C-terminal domain (DALI Z-score  = 6.0), whose DNA-bound structure was known. The MqsA:DNA complex was modeled by superimposing the conserved HTH-XRE helices from both proteins (MqsA residues 98–105; P22R residues 34–41) and mapping the rotated DNA coordinates onto one MqsA monomer. This MqsA monomer:DNA complex was then superimposed onto the symmetry-related MqsA monomer to obtain the rotated DNA coordinates for the second monomer. […]

Pipeline specifications

Software tools Coot, ARP/wARP, MolProbity, DALI
Application Protein structure analysis
Organisms Escherichia coli
Diseases Bacterial Infections, Drug-Related Side Effects and Adverse Reactions
Chemicals Zinc