Crystal structure of <i>Escherichia coli</i> EC1530, a glyoxylate induced protein YgbM

Kim, Y; Skarina, T.; Beasley, Steven; Laskowski, Roman A.; Arrowsmith, C.H.; Joachimiak, Andrzej; Edwards, A.M.; Savchenko, Alexei

doi:10.1002/prot.10160

Cited by 4 publications

(2 citation statements)

References 11 publications

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“…Molecular docking of hydroquinine to each of the ADI-pathway-related proteins was performed using the SwissDock web server. Where possible, the solved X-ray crystal structures were used for the docking simulations, as was the case for ADI (encoded by arcA ) and CK (encoded by arcC ) (1RXX and 8CRV, respectively; available from: ) [ 23 , 24 , 25 ]. Unfortunately, as a solved crystal structure for P. aeruginosa , OTC (encoded by arcB ), and AOA (encoded by arcD ), we used Deepmind’s AlphaFold protein structure prediction run from the GitHub site [ 26 ].…”

Section: Resultsmentioning

confidence: 99%

Hydroquinine Inhibits the Growth of Multidrug-Resistant Pseudomonas aeruginosa via the Suppression of the Arginine Deiminase Pathway Genes

Weawsiangsang,

Rattanachak,

Jongjitvimol

et al. 2023

IJMS

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Hydroquinine has antimicrobial potential with demonstrated activity against several bacteria, including multidrug-resistant (MDR) P. aeruginosa reference strains. Despite this, there is limited evidence confirming the antibacterial activity of hydroquinine against clinical isolates and the underlying mechanism of action. Here, we aimed to investigate the antibacterial effect of hydroquinine in clinical P. aeruginosa strains using phenotypic antimicrobial susceptibility testing and synergistic testing. In addition, we examined the potential inhibitory mechanisms against MDR P. aeruginosa isolates using informatic-driven molecular docking analysis in combination with RT-qPCR. We uncovered that hydroquinine inhibits and kills clinical P. aeruginosa at 2.50 mg/mL (MIC) and 5.00 mg/mL (MBC), respectively. Hydroquinine also showed partial synergistic effects with ceftazidime against clinical MDR P. aeruginosa strains. Using SwissDock, we identified potential interactions between arginine deiminase (ADI)-pathway-related proteins and hydroquinine. Furthermore, using RT-qPCR, we found that hydroquinine directly affects the mRNA expression of arc operon. We demonstrated that the ADI-related genes, including the arginine/ornithine antiporter (arcD) and the three enzymes (arginine deiminase (arcA), ornithine transcarbamylase (arcB), and carbamate kinase (arcC)), were significantly downregulated at a half MIC of hydroquinine. This study is the first report that the ADI-related proteins are potential molecular targets for the inhibitory effect of hydroquinine against clinically isolated MDR P. aeruginosa strains.

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Section: Resultsmentioning

confidence: 99%

Hydroquinine Inhibits the Growth of Multidrug-Resistant Pseudomonas aeruginosa via the Suppression of the Arginine Deiminase Pathway Genes

Weawsiangsang,

Rattanachak,

Jongjitvimol

et al. 2023

IJMS

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“…Because Dali, BLAST and Pfam all suggested that PDB entry 1K77 [30] is a xylose isomerase or an epimerase with a 4-digit EC number 5.3.1.22, while ProMOL suggested EC number 3.1.1.29, we were particularly interested in the alignments of 1K77 in Table 4. The alignment is also shown in Figure 4.…”

Section: Resultsmentioning

confidence: 99%

Annotation of proteins of unknown function: initial enzyme results

McKay

Hart

Horn

et al. 2015

J Struct Funct Genomics

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Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having “unknown function”. Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed.

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Structures of the holoenzyme TglHI required for 3-thiaglutamate biosynthesis

Zheng,

Xu,

et al. 2023

Structure

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Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM

Cited by 4 publications

References 11 publications

Hydroquinine Inhibits the Growth of Multidrug-Resistant Pseudomonas aeruginosa via the Suppression of the Arginine Deiminase Pathway Genes

Hydroquinine Inhibits the Growth of Multidrug-Resistant Pseudomonas aeruginosa via the Suppression of the Arginine Deiminase Pathway Genes

Annotation of proteins of unknown function: initial enzyme results

Structures of the holoenzyme TglHI required for 3-thiaglutamate biosynthesis

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