scholarly journals C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Takahiro Mori ◽  
Takuto Kumano ◽  
Haibing He ◽  
Satomi Watanabe ◽  
Miki Senda ◽  
...  
Keyword(s):  
Bond Cleavage ◽  
Structural Basis ◽  
Electron Microscopic ◽  
Intestinal Microbes ◽  
X Ray ◽  
Sugar Moiety ◽  
Structural Details ◽  
Catalytic Mechanisms ◽  
Cleavage Reactions ◽  
Biochemical Analyses

AbstractC-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and the resulting aglycones exert various bioactivities. Although the enzymes responsible for the reactions have been identified, their catalytic mechanisms and the generality of the reactions in nature remain to be explored. Here, we present the identification and structural basis for the activation of xenobiotic C-glycosides by heterocomplex C-deglycosylation enzymes from intestinal and soil bacteria. They are found to be metal-dependent enzymes exhibiting broad substrate specificity toward C-glycosides. X-ray crystallographic and cryo-electron microscopic analyses, as well as structure-based mutagenesis, reveal the structural details of these enzymes and the detailed catalytic mechanisms of their remarkable C-C bond cleavage reactions. Furthermore, bioinformatic and biochemical analyses suggest that the C-deglycosylation enzymes are widely distributed in the gut, soil, and marine bacteria.

scholarly journals Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhiwen Liu ◽  
Fanglong Zhao ◽  
Boyang Zhao ◽  
Jie Yang ◽  
Joseph Ferrara ◽  
...  
Keyword(s):  
High Resolution ◽  
Organic Synthesis ◽  
Indole Alkaloids ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Directed Mutagenesis ◽  
Computational Studies ◽  
X Ray ◽  
Evolutionary Branch ◽  
Catalytic Mechanisms

AbstractPrenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.

scholarly journals Structural basis for the unusual carbohydrate-binding specificity of jacalin towards galactose and mannose

2002 ◽  
Vol 364 (1) ◽  
pp. 173-180 ◽  
Author(s):  
Yves BOURNE ◽  
Corinne Houlès ASTOUL ◽  
Véronique ZAMBONI ◽  
Willy J. PEUMANS ◽  
Laurence MENU-BOUAOUICHE ◽  
...  
Keyword(s):  
Surface Plasmon Resonance ◽  
T Antigen ◽  
Structural Basis ◽  
Carbohydrate Binding ◽  
X Ray ◽  
Acetylneuraminic Acid ◽  
Large Size ◽  
Biochemical Analyses ◽  
Carbohydrate Binding Site

Evidence is presented that the specificity of jacalin, the seed lectin from jack fruit (Artocarpus integrifolia), is not directed exclusively against the T-antigen disaccharide Galβ1,3GalNAc, lactose and galactose, but also against mannose and oligomannosides. Biochemical analyses based on surface-plasmon-resonance measurements, combined with the X-ray-crystallographic determination of the structure of a jacalin—α-methyl-mannose complex at 2Å resolution, demonstrated clearly that jacalin is fully capable of binding mannose. Besides mannose, jacalin also interacts readily with glucose, N-acetylneuraminic acid and N-acetylmuramic acid. Structural analyses demonstrated that the relatively large size of the carbohydrate-binding site enables jacalin to accommodate monosaccharides with different hydroxyl conformations and provided unambiguous evidence that the β-prism structure of jacalin is a sufficiently flexible structural scaffold to confer different carbohydrate-binding specificities to a single lectin.

Cluster Chemistry. XLIII. Sulfur-Carbon Bond Cleavage Reactions in the Hydrogenation of Some Sulfur-Containing Ruthenium Carbonyl Cluster Complexes: X-Ray Structure of Ru3(μ-H)2(μ3-S)(μ-(Z)-Ph2PCH=CHPPH2)(CO)7

1986 ◽  
Vol 39 (7) ◽  
pp. 1109 ◽  
Author(s):  
MI Bruce ◽  
OB Shawkataly ◽  
MR Snow ◽  
ERT Tiekink
Keyword(s):  
Least Squares Method ◽  
Bond Cleavage ◽  
Unit Cell Parameters ◽  
Tertiary Phosphine ◽  
Cluster Chemistry ◽  
X Ray ◽  
Cell Parameters ◽  
Ruthenium Carbonyl ◽  
Cleavage Reactions ◽  
Sulfur Containing

Reactions between Ru3(μ-H)(μ3-SBut)(CO)9 and dppm have given Ru3(μ-H)(μn- SBut)(μ-dppm)(CO)10-n(n = 2,3); hydrogenation of all three complexes resulted in S-C bond cleavage and formation of Ru3(μ-H)2(μ3-S)(CO)7(L2) [L2 = (CO)2, μ-dppm]. Facile substitution of 2CO in Ru3(μ-H)2(μ3-S)(CO)9 by dppm, dpam or ebdp (L2), catalysed by Na+[Ph2CO]- or [ppn][OAc], gave Ru3(μ-H)2(μ3-S)(μ-L2)(CO)7, in which the bis-tertiary phosphine (or arsine) bridges an edge of the Ru3 triangle, with the P (or As) atoms occupying equatorial positions. In the case of L2 = ebdp, this edge is also bridged by H, as shown by a single-crystal X-ray structure determination. Crystals of the title compound are mcnoclinic, space group P21/n, with unit cell parameters a 13.454(3), b 17.748(2), c 14.706(2) Ǻ, and β 94.50(1)°. The structure was refined by a full-matrix least-squares method; at convergence R and Rw were 0.036 and 0.038, respectively, for 4729 reflections with I ≥ 3.0σ(I).

scholarly journals A requirement for an active proton delivery network supports a compound I-mediated C–C bond cleavage in CYP51 catalysis

2020 ◽  
Vol 295 (29) ◽  
pp. 9998-10007 ◽  
Author(s):  
Tatiana Y. Hargrove ◽  
Zdzislaw Wawrzak ◽  
F. Peter Guengerich ◽  
Galina I. Lepesheva
Keyword(s):  
Bond Cleavage ◽  
Cytochromes P450 ◽  
Relay Network ◽  
Compound I ◽  
X Ray ◽  
Proton Relay ◽  
Multistep Reactions ◽  
Biochemical Analyses ◽  
Ferric Peroxo ◽  
Delivery Network

CYP51 enzymes (sterol 14α-demethylases) are cytochromes P450 that catalyze multistep reactions. The CYP51 reaction occurs in all biological kingdoms and is essential in sterol biosynthesis. It removes the 14α-methyl group from cyclized sterol precursors by first forming an alcohol, then an aldehyde, and finally eliminating formic acid with the introduction of a Δ14–15 double bond in the sterol core. The first two steps are typical hydroxylations, mediated by an electrophilic compound I mechanism. The third step, C–C bond cleavage, has been proposed to involve either compound I (i.e. FeO3+) or, alternatively, a proton transfer-independent nucleophilic ferric peroxo anion (compound 0, i.e. Fe3+O2–). Here, using comparative crystallographic and biochemical analyses of WT human CYP51 (CYP51A1) and its D231A/H314A mutant, whose proton delivery network is destroyed (as evidenced in a 1.98-Å X-ray structure in complex with lanosterol), we demonstrate that deformylation of the 14α-carboxaldehyde intermediate requires an active proton relay network to drive the catalysis. These results indicate a unified, compound I-based mechanism for all three steps of the CYP51 reaction, as previously established for CYP11A1 and CYP19A1. We anticipate that our approach can be applied to mechanistic studies of other P450s that catalyze multistep reactions, such as C–C bond cleavage.

scholarly journals Te–Te and Te–C bond cleavage reactions using a monovalent gallanediyl

2015 ◽  
Vol 44 (11) ◽  
pp. 5153-5159 ◽  
Author(s):  
Chelladurai Ganesamoorthy ◽  
Georg Bendt ◽  
Dieter Bläser ◽  
Christoph Wölper ◽  
Stephan Schulz
Keyword(s):  
Ir Spectroscopy ◽  
Single Crystal ◽  
Heteronuclear Nmr ◽  
Bond Cleavage ◽  
X Ray ◽  
Cleavage Reactions

Te–Te and Te–C bond cleavage occurs in reactions of monovalent LGa (L = [(2,6-i-Pr2-C6H3)NC(Me)]2CH) with Te, Ph2Te2 and i-Pr2Te. (LGa-μ-Te)21, LGa(TePh)22 and LGa(i-Pr)Tei-Pr 3 were characterized by heteronuclear NMR (1H, 13C, 125Te) and IR spectroscopy and by single crystal X-ray analyses.

scholarly journals Novel W(CO)6-Promoted C-S Bond Cleavage Reactions of Dithianes. X-Ray Structure of 9,9′:9,9′-Terfluorene

1991 ◽  
Vol 38 (1) ◽  
pp. 35-38 ◽  
Author(s):  
Chi-Hong Kuo ◽  
Tien-Yau Lnh ◽  
Ming-Chu Cheng ◽  
Shie-Ming Peng
Keyword(s):  
Bond Cleavage ◽  
X Ray ◽  
Cleavage Reactions

scholarly journals Molecular and structural basis for Lewis glycan recognition by a cancer-targeting antibody

2020 ◽  
Vol 477 (17) ◽  
pp. 3219-3235
Author(s):  
Caroline Soliman ◽  
Andrew J. Guy ◽  
Jia Xin Chua ◽  
Mireille Vankemmelbeke ◽  
Richard S. McIntosh ◽  
...  
Keyword(s):  
Cross Reactivity ◽  
Structural Basis ◽  
Cancer Targeting ◽  
Antigen Binding ◽  
X Ray ◽  
Colorectal Cancer Cells ◽  
Structural Details ◽  
Dynamics Simulations ◽  
Fragment Antigen Binding ◽  
Insight Into

Immunotherapy has been successful in treating many tumour types. The development of additional tumour-antigen binding monoclonal antibodies (mAbs) will help expand the range of immunotherapeutic targets. Lewis histo-blood group and related glycans are overexpressed on many carcinomas, including those of the colon, lung, breast, prostate and ovary, and can therefore be selectively targeted by mAbs. Here we examine the molecular and structural basis for recognition of extended Lea and Lex containing glycans by a chimeric mAb. Both the murine (FG88.2) IgG3 and a chimeric (ch88.2) IgG1 mAb variants showed reactivity to colorectal cancer cells leading to significantly reduced cell viability. We determined the X-ray structure of the unliganded ch88.2 fragment antigen-binding (Fab) containing two Fabs in the unit cell. A combination of molecular docking, glycan grafting and molecular dynamics simulations predicts two distinct subsites for recognition of Lea and Lex trisaccharides. While light chain residues were exclusively used for Lea binding, recognition of Lex involved both light and heavy chain residues. An extended groove is predicted to accommodate the Lea–Lex hexasaccharide with adjoining subsites for each trisaccharide. The molecular and structural details of the ch88.2 mAb presented here provide insight into its cross-reactivity for various Lea and Lex containing glycans. Furthermore, the predicted interactions with extended epitopes likely explains the selectivity of this antibody for targeting Lewis-positive tumours.

Direct visualization of phase-separated domains in lipid membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 290-291
Author(s):  
S. W. Hui ◽  
T. P. Stewart
Keyword(s):  
Lipid Membranes ◽  
Structural Information ◽  
Freeze Fracture ◽  
Biological Molecules ◽  
Vacuum Drying ◽  
Direct Visualization ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
X Ray ◽  
Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

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