Substrate recognition by the Pseudomonas aeruginosa EF-Tu–modifying methyltransferase EftM

Kuiper, Emily G.; Dey, Debayan; LaMore, Paige A.; Owings, Joshua P.; Prezioso, Samantha M.; Goldberg, Joanna B.; Conn, Graeme L.

doi:10.1074/jbc.ra119.011213

Cited by 6 publications

(5 citation statements)

References 38 publications

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“…The few other interesting bacterial PKMTs include the protein EF-Tm which targets EF-Tu as reported in P. aeruginosa, the protein FliB which catalyzes a [4Fe–4S] mediated methyl transfer reaction on flagellin of Salmonella enterica . To our knowledge, there are no known protein lysine demethylases in bacteria.…”

Section: Resultsmentioning

confidence: 99%

“…For example, PrmA (A1S_2184) and PrmB (A1S_1693) of A. baumannii transfer methyl group on the 50S ribosomal subunit protein L11 and L3, respectively. 20 The few other interesting bacterial PKMTs include the protein EF-Tm which targets EF-Tu as reported in P. aeruginosa, 48 the protein FliB which catalyzes a [4Fe−4S] mediated methyl transfer reaction on flagellin of Salmonella enterica. 49 To our knowledge, there are no known protein lysine demethylases in bacteria.…”

Section: Conserved Residues Surrounding the Trimethylated Lysine For ...mentioning

confidence: 99%

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Lysine Trimethylation in Planktonic and Pellicle Modes of Growth in Acinetobacter baumannii

et al. 2023

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Over the past 30 years, Acinetobacter baumannii has been described as an important nosocomial pathogen due to frequent ventilator-associated infections. Many biological processes of A. baumannii remain elusive, such as the formation of an air–liquid biofilm (pellicle). Several studies demonstrated the importance of post-translational modifications (PTMs) in A. baumannii physiology. Here, we investigated K-trimethylation in A. baumannii ATCC 17978 in planktonic and pellicle modes using proteomic analysis. To identify the most high-confidence K-trimethylated peptides, we compared different sample preparation methods (i.e., strong cation exchange, antibody-capture) and processing software (i.e., different database search engines). We identified, for the first time, 84 K-trimethylated proteins, many of which are involved in DNA and protein synthesis (HupB, RplK), transporters (Ata, AdeB), or lipid metabolism processes (FadB, FadD). In comparison with previous studies, several identical lysine residues were observed acetylated or trimethylated, indicating the presence of proteoforms and potential PTM cross-talks. This is the first large-scale proteomic study of trimethylation in A. baumannii and will be an important resource for the scientific community (availability in Pride repository under accession PXD035239).

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Section: Resultsmentioning

confidence: 99%

Section: Conserved Residues Surrounding the Trimethylated Lysine For ...mentioning

confidence: 99%

Lysine Trimethylation in Planktonic and Pellicle Modes of Growth in Acinetobacter baumannii

et al. 2023

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“…We further confirmed the phylogenetic analysis using evolutionary trace method to understand the specificity determining residues in a larger protein family or superfamily. This method was previously utilized in several studies to determine functional residue differences among different phylogenetic clades and compares closely to ML method with less computational calculation time (Dey 2018, Shrilakshmi et al 2019, Nosrati et al 2019, Kuiper et al 2019, Dey et al 2020.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic Studies and Inhibitor Design Targeting Protein Interacting Interface of Nucleoid-Associated Protein HU

Dey

Ramakumar

2020

Preprint

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The formations of nucleoprotein structures by promiscuous DNA binding proteins like HU are assisted with their protein protein interaction capability with other proteins. In E. coli Gal repressosome assembly, GalR piggybacks HU to the critical position on the DNA (hbs site) through a specific GalR-HU interaction using an interface at the bottom of alpha helical region, which we termed as HUpb interface. Similarly, MtbHU also interact with Topoisomerase I with the same interface to enhance its relaxation activity. In an earlier study, we determined the crystal structure of MtbHU, inhibited it using stilbene derivatives which inhibited the cell growth. It motivated us to understand the evolutionary and structural characteristics of the HUpb interface, which has not been investigated previously for HU or for any other NAPs. Our analyses found residue positions corresponding to MtbHU Thr11 to Gln20 form the interface while Ala23 serves the pocket lining residue. Due to ancestral mutations in the duplication event before the HU and IHF split, physicochemical properties of the interface vary among clades. Thus, this interface could engage different proteins in different HU oligomeric states in Proteobacteria. Protein-protein interfaces are usually a challenging target due to its flatter surface. In case of MtbHUpb interface,

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“…The DNA Mtases prefer the “bind and slide” mechanism for locating the target base from a pool of nucleobases, where the Mtase nonspecifically binds to the DNA duplex and then scans for the target base by sliding ( 11 ). Protein Mtases, on the other hand, have diverse strategies for identifying target amino acids, the most common being the “catch and catalyze” strategy, which is adopted by lysine Mtases ( 12 ). This entails globular body recognition, which involves conformational modifications as well as substrate orientation in the methylation catalytic site ( 12 ).…”

mentioning

confidence: 99%

“…Protein Mtases, on the other hand, have diverse strategies for identifying target amino acids, the most common being the “catch and catalyze” strategy, which is adopted by lysine Mtases ( 12 ). This entails globular body recognition, which involves conformational modifications as well as substrate orientation in the methylation catalytic site ( 12 ). For the RNA, the tertiary structure is more malleable, and to facilitate function, several bulges and loops, which distort the duplex structure, are present.…”

mentioning

confidence: 99%

Identification of allosteric hotspots regulating the ribosomal RNA binding by antibiotic resistance-conferring Erm methyltransferases

Bhujbalrao

Gavvala

Singh

et al. 2022

Journal of Biological Chemistry

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Substrate recognition by the Pseudomonas aeruginosa EF-Tu–modifying methyltransferase EftM

Cited by 6 publications

References 38 publications

Lysine Trimethylation in Planktonic and Pellicle Modes of Growth in Acinetobacter baumannii

Lysine Trimethylation in Planktonic and Pellicle Modes of Growth in Acinetobacter baumannii

Phylogenetic Studies and Inhibitor Design Targeting Protein Interacting Interface of Nucleoid-Associated Protein HU

Identification of allosteric hotspots regulating the ribosomal RNA binding by antibiotic resistance-conferring Erm methyltransferases

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