Human PLD structures enable drug design and characterization of isoenzyme selectivity

Metrick, C.M.; Peterson, Emily A.; Santoro, Joseph C.; Enyedy, Istvan; Murugan, Param; Chen, T.; Michelsen, Klaus; Cullivan, Mike; Spilker, Kerri; Kumar, P. Rajesh; May‐Dracka, Tricia L.; Chodaparambil, J.V.

doi:10.1038/s41589-019-0458-4

Cited by 30 publications

(25 citation statements)

References 59 publications

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“…PLD belongs to the PLD superfamily and is widely distributed in prokaryotes and eukaryotes. Members of the PLD superfamily usually contain a conserved region of the catalytic HKD motif, H-x-K-(x)4-D, where x is any amino acid ( Metrick et al, 2020 ). The sequence alignment results of the PLD family protein in K. pneumoniae (by Phyre2 fold recognition server) demonstrated 26% identity with known PLD alpha (PLDα; PDB:6KZ9) of Arabidopsis thaliana and 25% identity with phospholipase D2 (PLD2) catalytic domain (PDB:6OHM) of Homo sapiens .…”

Section: Resultsmentioning

confidence: 99%

Identification and Comparative Genomic Analysis of Type VI Secretion Systems and Effectors in Klebsiella pneumoniae

Liu

Tsui

et al. 2022

Front. Microbiol.

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Klebsiella pneumoniae is a nosocomial opportunistic pathogen that can cause pneumonia, liver abscesses, and infections of the bloodstream. The resistance and pathogenicity of K. pneumoniae pose major challenges to clinical practice. However, the ecology and pathogenic mechanisms of K. pneumoniae have not been fully elucidated. Among these mechanisms, the secretion systems encoded by strains of the bacteria confer adaptive advantages depending on the niche occupied. The type VI secretion system (T6SS) is a multi-protein complex that delivers effector proteins to the extracellular environment or directly to eukaryotic or prokaryotic cells. T6SSs are widely distributed in Gram-negative bacteria and play an important role in bacterial virulence and the interactions between bacteria and other microorganisms or the environment. This study aimed to enhance the understanding of the characteristics of T6SSs in K. pneumoniae through an in-depth comparative genomic analysis of the T6SS in 241 sequenced strains of K. pneumoniae. We identified the T6SS loci, the synteny of the loci in different species, as well as the effectors and core T6SS-related genes in K. pneumoniae. The presence of a T6SS was a common occurrence in K. pneumoniae, and two T6SS clusters are the most prevalent. The variable region downstream of the gene vgrG usually encodes effector proteins. Conserved domain analysis indicated that the identified putative effectors in K. pneumoniae had the functions of lipase, ribonuclease, deoxyribonuclease, and polysaccharide hydrolase. However, some effectors did not contain predicted functional domains, and their specific functions have yet to be elucidated. This in silico study represents a detailed analysis of T6SS-associated genes in K. pneumoniae and provides a foundation for future studies on the mechanism(s) of T6SSs, especially effectors, which may generate new insights into pathogenicity and lead to the identification of proteins with novel antimicrobial properties.

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Section: Resultsmentioning

confidence: 99%

Identification and Comparative Genomic Analysis of Type VI Secretion Systems and Effectors in Klebsiella pneumoniae

Liu

Tsui

et al. 2022

Front. Microbiol.

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“…strain PMF (Leiros et al, 2000). Then, protein crystals of other PLD superfamily members have been reported, including endonucleases and several bacterial enzymes, and for human PLD (Bowling et al, 2020;Metrick et al, 2020). PLD enzymes act in two steps.…”

Section: Discussionmentioning

confidence: 99%

Human Tyrosyl-DNA Phosphodiesterase 1 Possesses Transphosphooligonucleotidation Activity With Primary Alcohols

Dyrkheeva

Anarbaev

Лебедева

et al. 2020

Front. Cell Dev. Biol.

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Human tyrosyl-DNA phosphodiesterase 1 (TDP1) belongs to the phospholipase D superfamily, whose members contain paired catalytic histidine and lysine residues within two conserved motifs and hydrolyze phosphodiester bonds. TDP1 is a DNA repair enzyme that processes 3′ DNA end blocking lesions and a wide range of synthetic DNA adducts as a substrate. TDP1 hydrolyzes DNA-adducts via two coordinated SN2 nucleophilic attacks mediated by the action of two histidine residues and leads to the formation of the covalent intermediate. Hydrolysis of this intermediate is proposed to be carried out by a water molecule that is activated by the His493 residue acting as a general base. It was known that phospholipase D enzymes are able to catalyze not only hydrolysis but also a transphosphatidylation reaction in the presence of primary alcohols in which they transfer the substrate to the alcohol instead of water. Here, we first demonstrated that TDP1 is able to undergo a “transphosphooligonucleotidation” reaction, transferring the substrate residue to the alcohol, thus inducing the formation of covalent DNA adducts with different primary alcohol residues. Such adducts can be accumulated in the conditions of high concentration of alcohol. We demonstrated that glycerol residue was efficiently cleaved from the 3′-end by TDP1 but not by its mutant form associated with the disease spinocerebellar ataxia with axonal neuropathy. Therefore, the second reaction step can be carried out not only by a water molecule but also by the other small nucleophilic molecules, e.g., glycerol and ethanol. Thus, in some cases, TDP1 can be regarded not only as a repair enzyme but also as a source of DNA damage especially in the case of mutation. Such damages can make a negative contribution to the stability of cell vitality.

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“…In addition to the two HKD motifs located well in the middle of the sequence, PLDs from eukaryotes typically encode an N-terminal phox homology/pleckstrin homology (PX/PH) or C2 domain 23 – 25 . Based on their N-terminal domains, PLDs can be grouped into PX/PH-PLDs and C2-PLDs.…”

Section: Introductionmentioning

confidence: 99%

Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA

Yang

Zhao

et al. 2022

Nat Commun

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PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids—the main component of cell membranes—and assists the invasion of the opportunistic pathogen Pseudomonas aeruginosa. As a cognate immunity protein, PA3488 can inhibit the activity of PldA to avoid self-toxicity. However, the precise inhibitory mechanism remains elusive. We determine the crystal structures of full-length and truncated PldA and the cryogenic electron microscopy structure of the PldA–PA3488 complex. Structural analysis reveals that there are different intermediates of PldA between the “open” and “closed” states of the catalytic pocket, accompanied by significant conformational changes in the “lid” region and the peripheral helical domain. Through structure-based mutational analysis, we identify the key residues responsible for the enzymatic activity of PldA. Together, these data provide an insight into the molecular mechanisms of PldA invasion and its neutralization by PA3488, aiding future design of PLD-targeted inhibitors and drugs.

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Human PLD structures enable drug design and characterization of isoenzyme selectivity

Cited by 30 publications

References 59 publications

Identification and Comparative Genomic Analysis of Type VI Secretion Systems and Effectors in Klebsiella pneumoniae

Identification and Comparative Genomic Analysis of Type VI Secretion Systems and Effectors in Klebsiella pneumoniae

Human Tyrosyl-DNA Phosphodiesterase 1 Possesses Transphosphooligonucleotidation Activity With Primary Alcohols

Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA

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