Structural and Functional Characterization of Methicillin-Resistant<i>Staphylococcus aureus’s</i>Class IIb Fructose 1,6-Bisphosphate Aldolase

Capodagli, Glenn C.; Lee, Stephen A.; Boehm, Kyle J.; Brady, Kristin M.; Pegan, Scott D.

doi:10.1021/bi501141t

Cited by 13 publications

(10 citation statements)

References 69 publications

(175 reference statements)

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“…The resultant conformer facilitates relocation of the Zn 2ϩ cofactor that advances the reaction by its stabilization of the nascent enediolate species. Our finding of a catalytic His residue on the mobile loop ␤6-␣8 reinforces recent efforts to inhibit class II aldolases by interference with this loop displacement (50,51). Furthermore, our proposed mechanism offers new insights into understanding substrate specificity and conformational states requisite for catalysis, critical knowledge in drug design, protein engineering, and more recently the synthesis of rare sugars (52).…”

Section: Tbp Inhibitionsupporting

confidence: 76%

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases

Jacques¹,

Coincon²,

Sygusch

2018

Journal of Biological Chemistry

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Crystal structures of two bacterial metal (Zn)-dependent d-fructose-1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 Å resolution. The ligand complexes cryotrapped in native or mutant aldolase crystals enabled a novel mechanistic description of FBP C3-C4 bond cleavage. The reaction mechanism uses active site remodeling during the catalytic cycle, implicating relocation of the Zn cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes triggered upon P1 phosphate binding, which liberates the Zn-chelating His-180, allowing it to act as a general base for the proton abstraction at the FBP C4 hydroxyl group. A second zinc-chelating His-83 hydrogen bonds the substrate C4 hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface-exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu-142 is essential for protonation of the enediolate form prior to product release. A d-tagatose 1,6-bisphosphate enzymatic complex reveals how His-180-mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and d-glyceraldehyde 3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp-82 and Asp-255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops β5-α7 and β6-α8 (containing catalytic residues Glu-142 and His-180, respectively) drive active site remodeling, enabling the relocation of the metal cofactor.

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Section: Tbp Inhibitionsupporting

confidence: 76%

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases

Jacques¹,

Coincon²,

Sygusch

2018

Journal of Biological Chemistry

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“…Of the 11 positively selected proteins with known functions, two affect bacterial growth, i.e., phosphoribosylaminoimidazole-succinocarboxamide synthase purC which has been described to affect the growth of M. tuberculosis ( Brown et al, 2005 ) and Fructose-bisphosphate aldolase, frequently reported to be important for growth in pathogens such as M. tuberculosis and multidrug-resistant Staphylococcus aureus ( Capodagli et al, 2014 ; Puckett et al, 2014 ). The remaining nine proteins are associated with cell membrane entry (mce), transcription regulation (IclR family), reaction to heat shock (Hsp20), metabolic reactions ( trans- aconitate methyl transferase, 5-methyltetrahydropteroyltriglutamate–homocysteine methyltransferase), and probable endonuclease activity (as described for protein S16 in the 30S ribosomal subunit, by Oberto et al, 1996 ).…”

Section: Resultsmentioning

confidence: 99%

Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies

Tan

Ong

et al. 2017

Front. Microbiol.

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Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear. We compared genome data from 243 M. abscessus strains downloaded from the NCBI ftp Refseq database to understand how the microevolutionary processes of homologous recombination and positive selection influenced the diversification of the M. abscessus complex at the subspecies level. The three subspecies are clearly separated in the Minimum Spanning Tree. Their MUMi-based genomic distances support the separation of M. massiliense and M. bolletii into two subspecies. Maximum Likelihood analysis through dN/dS (the ratio of number of non-synonymous substitutions per non-synonymous site, to the number of synonymous substitutions per synonymous site) identified distinct genes in each subspecies that could have been affected by positive selection during evolution. The results of genome-wide alignment based on concatenated locally-collinear blocks suggest that (a) recombination has affected the M. abscessus complex more than mutation and positive selection; (b) recombination occurred more frequently in M. massiliense than in the other two subspecies; and (c) the recombined segments in the three subspecies have come from different intra-species and inter-species origins. The results lead to the identification of possible gene sets that could have been responsible for the subspecies-specific features and suggest independent evolution among the three subspecies, with recombination playing a more significant role than positive selection in the diversification among members in this complex.

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“…The decreased expression of mnhABCDEHF, specifically responsible for Na + /H + antiporter, suggested a decline of ΔΨ and energy biosynthesis (Castro et al 2016). The genes (nreB, ftnA, narGHT, nasD, pflAB, adh1, ldhAB, and natA) for energy metabolism were upregulated (1.3 to 7.8-fold), while trxAB (encoding thioredoxin and thioredoxin reductase) (Villanueva et al 2016), glpD (encoding glycerol-3phosphate dehydrogenase) (Szalus-Jordanow et al 2018), fda (encoding fructose-bisphosphate aldolase class 1) (Capodagli et al 2014), pgk (encoding phosphoglycerate kinase) (Liew et al 2015), and eno (encoding enolase) (Dai et al 2019) were downregulated. The results indicated that ID13 might negatively affect the endergonic processes such as ATP synthesis through mnhABCDEHF inhibition.…”

Section: Id13 Regulated S Aureus Cvcc 546 Gene Expressionmentioning

confidence: 99%

Therapeutic potential of a designed CSαβ peptide ID13 in Staphylococcus aureus-induced endometritis of mice

Yang

Shan

et al. 2020

Appl Microbiol Biotechnol

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Staphylococcus aureus is a common pathogen that can cause clinical and subclinical endometritis in humans and animals. In this study, a designed CSαβ peptide ID13 from DLP4 exhibited high stable antibacterial activity in simulated gastric fluid (90.79%), serum (99.54%), and different pH buffers (> 99%) against S. aureus CVCC 546 and lower cytotoxicity (89.62% viability) than its parent peptide DLP4 (74.14% viability) toward mouse endometrial epithelial cells (MEECs). ID13 caused a depolarization of bacterial membrane and downregulation of the expression of genes involved in membrane potential maintenance and biofilm formation. The in vitro efficacy analysis of ID13 showed a synergistic effect with vancomycin, ampicillin, rifampin, and ciprofloxacin; intracellular antimicrobial activity against S. aureus CVCC 546 in MEECs; and the ability to inhibit lipoteichoic acid-induced pro-inflammatory cytokines from RAW 264.7. In the S. aureus-induced endometritis of mice, similar to vancomycin, ID13 remarkably alleviated pathological conditions, inhibited the production of cytokines (TNF-α, IL-1ß, IL-6, and IL-10), and suppressed the TLR2-NF-κB signal pathway. Collectively, these results suggest that ID13 could be a potential candidate peptide for therapeutic application in S. aureus-induced endometritis. Key Points•Higher antibacterial activity and lower hemolysis of ID13 than DLP4. •ID13 could downregulate the genes of bacterial survival and infection.•ID13 could alleviate the S. aureus-induced endometritis of mice.•ID13 could regulate the cytokines and suppress the TLR2-NF-κB signal pathway.

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Structural and Functional Characterization of Methicillin-ResistantStaphylococcus aureus’sClass IIb Fructose 1,6-Bisphosphate Aldolase

Cited by 13 publications

References 69 publications

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases

Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies

Therapeutic potential of a designed CSαβ peptide ID13 in Staphylococcus aureus-induced endometritis of mice

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