Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis

Capurro, Juan I. Blanco; Hopkins, Chad W.; Sottile, Gustavo Pierdominici; Lebrero, Mariano C. González; Roitberg, Adrián E.; Martí, Marcelo A.

doi:10.1021/acs.jpcb.6b10130

Cited by 11 publications

(9 citation statements)

References 54 publications

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“…The residues responsible of the proper cleavage and spatial location of β-PO 4 are crucial for catalysis, corroborating observations that the β-PO 4 is essential. Nonetheless, further structural and computational evidence is required for PimA. , …”

Section: Discussionmentioning

confidence: 99%

“…Nonetheless, further structural and computational evidence is required for PimA. 44,45 It is well established that for the GT-B superfamily members the acceptor binding site is located at the N-terminal domain whereas the donor substrate binds mainly to the C-terminal domain. The catalytic cleft is formed between the two spatially separated domains upon an "open-to-closed" conformational change.…”

Section: ■ Discussionmentioning

confidence: 99%

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Dissecting the Structural and Chemical Determinants of the “Open-to-Closed” Motion in the Mannosyltransferase PimA from Mycobacteria

et al. 2020

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The phosphatidyl-myo-inositol mannosyltransferase A (PimA) is an essential peripheral membrane glycosyltransferase that initiates the biosynthetic pathway of phosphatidyl-myoinositol mannosides (PIMs), key structural elements and virulence factors of Mycobacterium tuberculosis. PimA undergoes functionally important conformational changes, including (i) -helix-to--strand and -strand-to--helix transitions, and (ii) an 'open-to-closed' motion between the two Rossmann-fold domains, a conformational change necessary to generate a catalytically competent active site. In previous work, we established that GDP-Man and GDP stabilize the enzyme and facilitate the switch to a more compact active state. To determine the structural contribution of the mannose ring in such activation mechanism we analyzed a series of chemical derivatives, including mannose-phosphate (Man-P) and mannose-pyrophosphateribose (Man-PP-RIB), and additional GDP derivatives, as pyrophosphate-ribose (PP-RIB) and GMP, by the combined used of X-ray crystallography, limited proteolysis, circular dichroism, isothermal titration calorimetry and Small Angle X-ray Scattering methods. Although the phosphate is present, we found that the mannose ring, neither covalently attached to phosphate (Man-P) nor to PP-RIB (Man-PP-RIB), does promote the switch to the active compact form of the enzyme. Therefore, the nucleotide moiety of GDP-Man, and not the sugar ring, facilitates the 'open-to-closed' motion, with the -phosphate group providing the high affinity binding to PimA. Altogether, the experimental data, contribute to a better understanding of the structural determinants involved in the 'open-to-closed' motion observed not only in PimA, but also visualized/predicted in other glycosyltransfeases. In addition, the experimental data might prove useful for the discovery/development of PimA and/or glycosyltransferase inhibitors.

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Section: Discussionmentioning

confidence: 99%

Section: ■ Discussionmentioning

confidence: 99%

Dissecting the Structural and Chemical Determinants of the “Open-to-Closed” Motion in the Mannosyltransferase PimA from Mycobacteria

et al. 2020

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“…Upon binding of the sugar nucleotide donor, the enzyme undergoes a conformational change stabilizing the transition state, resulting in the formation of a glycosidic bond and the release of the nucleotide donor. Different reaction mechanisms of glycosyltransferases have been described and reviewed [26,27,44,45,46,47]. The inverting occurs via a S N 2 mechanism, while a retaining transfer can proceed via a concerted or ion-pair intermediate mechanism through a double displacement via a S N 2 mechanism.…”

Section: Glycosyltransferases In Naturementioning

confidence: 99%

Leloir Glycosyltransferases in Applied Biocatalysis: A Multidisciplinary Approach

Mestrom

Przypis

Kowalczykiewicz

et al. 2019

IJMS

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Enzymes are nature's catalyst of choice for the highly selective and efficient coupling of carbohydrates. Enzymatic sugar coupling is a competitive technology for industrial glycosylation reactions, since chemical synthetic routes require extensive use of laborious protection group manipulations and often lack regio-and stereoselectivity. The application of Leloir glycosyltransferases has received considerable attention in recent years and offers excellent control over the reactivity and selectivity of glycosylation reactions with unprotected carbohydrates, paving the way for previously inaccessible synthetic routes. The development of nucleotide recycling cascades has allowed for the efficient production and reuse of nucleotide sugar donors in robust one-pot multi-enzyme glycosylation cascades. In this way, large glycans and glycoconjugates with complex stereochemistry can be constructed. With recent advances, LeLoir glycosyltransferases are close to being applied industrially in multi-enzyme, programmable cascade glycosylations.hydroxynitrile lyases catalyzed the enzymatic hydrolysis of the glycoside amygdalin [3]. Moving almost two centuries forward, the largest volumetric biocatalytic industrial process is the application of glucose isomerase for the production of high fructose syrup for food and drink applications, producing fructose from glucose at 10 7 tons per year [4]. The secret of the success of enzymes in the production or treatment of carbohydrates and glycosides is their exquisite stereo-and regioselectivity. The excellent selectivity of enzymes is required due to the diversity of structural features of carbohydrates [5], comprising d-and l-epimers, ring size, anomeric configuration, linkages, branching, and oxidation state(s). Since drug targets often exhibit specificity for all of these structural features, the production process should not contain any side-products to prevent undesired side-effects [6].The challenge in the synthesis of carbohydrates is their wide variety of functionalities and stereochemistry ( Figure 1). (Poly)hydroxyaldehydes containing a terminal aldehyde are referred to as aldoses and (poly)hydroxyketones are defined as ketoses. In aqueous solutions, monosaccharides form equilibrium mixtures of linear open-chain and ring-closed 5-or 6-membered furanoses or pyranoses, respectively. For aldoses, the asymmetric ring forms at C-1. For ketoses, it closes at C-2 as an axial (α) or equatorial (β) hemiacetal or hemiketal, respectively (commonly defined as the anomeric center). A glycosidic linkage is a covalent O-, S-, N-, or C-bond connecting a monosaccharide to another residue resulting in a glycoside, while glucoside is specific for a glucose moiety. The equatorial or axial position of the glycosidic bond is referred to as α-(axial) or β-linkage (equatorial). The number of carbohydrates linked via glycosidic bonds can be subdivided into oligosaccharides with two to ten linked carbohydrates, while polysaccharides (glycans) contain more than ten glycosidic bonds. A glycan either con...

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“…Then, the phosphate anion directs a nucleophilic attack from the same side on the thionium basal plane, affording the product through TS-B in a stereospecific manner. Path C: By directly transforming from INT A or through INT-B, the generation of covalently bonded phosphate intermediate INT-C , is also considered possible by the addition of phosphate to episulfonium or thionium. Subsequent syn displacement of phosphate by the nucleophile from INT-C affords the product through concerted asynchronous transition state TS-C, namely, the S N i reaction pathway …”

Section: Results and Discussionmentioning

confidence: 99%

“…In addition, intermediate INT-C could not be observed clearly throughout the NMR monitoring process. Therefore, Path C is probably not the plausible pathway, although the concerted S N i reaction is mechanistically intriguing …”

Section: Results and Discussionmentioning

confidence: 99%

Chiral Phosphoric Acid Catalyzed Enantioselective Ring Expansion Reaction of 1,3-Dithiane Derivatives: Case Study of the Nature of Ion-Pairing Interaction

Korenaga

Nakanishi

et al. 2018

J. Am. Chem. Soc.

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Chiral counterion controlled asymmetric catalysis via an ion-pairing interaction has attracted immense attention in recent years. Despite a number of successful studies, the mechanistic elucidation of the stereocontrolling element in the ion-pairing interaction is rarely conducted and hence its nature is still far from being well understood. Herein we report an in-depth mechanistic case study of a newly developed enantioselective ring expansion reaction of 1,3-dithiane derivatives catalyzed by chiral phosphoric acid (CPA). An unprecedented enantioselective 1,2-sulfur rearrangement/stereospecific nucleophilic addition sequence was proven to be the stereoselective pathway. More importantly, by thorough investigation of the intrinsic nature of the stereospecific nucleophilic addition to the cationic thionium intermediate, we discovered that the key interaction in this process is the nonclassical C-H···O hydrogen bonds formed between the conjugate base of the CPA catalyst and the cationic intermediate. These C-H···O hydrogen bonds not only bind the catalyst to the substrates to form energetically favored states throughout the overall processes but also firmly maintain the relative positions of these fragments as the "fixed" contact ion pair to sustain the chiral information generated at the initial sulfur rearrangement step. This mechanistic case study provides a very clear understanding of the nature of the ion-pairing interaction in organocatalysis. The conclusion encourages the further development of the research field with the focus to design new organocatalysts and cultivate novel organocatalytic transformations.

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Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis

Cited by 11 publications

References 54 publications

Dissecting the Structural and Chemical Determinants of the “Open-to-Closed” Motion in the Mannosyltransferase PimA from Mycobacteria

Dissecting the Structural and Chemical Determinants of the “Open-to-Closed” Motion in the Mannosyltransferase PimA from Mycobacteria

Leloir Glycosyltransferases in Applied Biocatalysis: A Multidisciplinary Approach

Chiral Phosphoric Acid Catalyzed Enantioselective Ring Expansion Reaction of 1,3-Dithiane Derivatives: Case Study of the Nature of Ion-Pairing Interaction

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