Crystal Structure Determination Research Articles

The synthesis, spectroscopic characterization, and crystallographic study of the tetra-phenylimido-diphosphinates of Sc, Y, La, and Lu

In the present study, we report the synthesis, spectroscopic characterization, and X-ray single crystal structural determination of four rare earth complexes, M[Ph2P(O)NP(O)PPh2]3, M = Sc, Y, La, and Lu. The structural study reveals that the Sc, Y, and Lu complexes have coordination numbers of six, while the La complex shows a coordination number of seven, through the presence of the additional coordination of a water molecule with a square-face-capped geometry, where the water molecule enables the formation of a dimeric structure through OH…O hydrogen bond interactions. The metal ions M3+, Sc, Y, La, and Lu are coordinated to the [Ph2P(O)NP(O)Ph2]− ligand with a delocalized phosphazenic PNP system in an O,O isobidentate manner, generating carbon-free metallo-inorganic six-membered rings, of which one acquires the a (anti-parallel) conformation and the other two the twist-boat conformation. The Y and Lu complexes crystallized with similar unit cells, M…O distances, and O…M…O angles that are consequences of their similar crystal radii related to the lanthanide contraction in Lu, while the La complex has a coordination number of seven through the coordination of a water molecule and a square-face-capped geometry. The O-M-O angles in the complexes suggest that the bite of the ligand depends on the size of the metal ion, the flexibility, and the steric effects of the tetra-phenyl-imidodiphosphinate ligand.

Molecular replacement for small-molecule crystal structure determination from X-ray and electron diffraction data with reduced resolution.

The resolution of 3D electron diffraction (ED) data of small-molecule crystals is often relatively poor, due to either electron-beam radiation damage during data collection or poor crystallinity of the material. Direct methods, used as standard for crystal structure determination, are not applicable when the data resolution falls below the commonly accepted limit of 1.2 Å. Therefore an evaluation was carried out of the performance of molecular replacement (MR) procedures, regularly used for protein structure determination, for structure analysis of small-molecule crystal structures from 3D ED data. In the course of this study, two crystal structures of Bi-3812, a highly potent inhibitor of the oncogenic transcription factor BCL6, were determined: the structure of α-Bi-3812 was determined from single-crystal X-ray data, the structure of β-Bi-3812 from 3D ED data, using direct methods in both cases. These data were subsequently used for MR with different data types, varying the data resolution limit (1, 1.5 and 2 Å) and by using search models consisting of connected or disconnected fragments of BI-3812. MR was successful with 3D ED data at 2 Å resolution using a search model that represented 74% of the complete molecule.

Synthesis, powder diffraction pattern, crystal structure determination of the pharmaceutical co-crystal of levetiracetam and 3,5-dinitrosalicylic acid

(S)-α-Ethyl-2-oxo-1-pyrrolidineacetamide (trade name levetiracetam), a derivative of piracetam, is used clinically as an add-on treatment for partial-onset seizures. In this study, we report the solid-state structure of a new drug co-crystal produced from levetiracetam and 3,5-dinitrosalicylic acid through cooling crystallization. This compound was further characterized by infrared spectroscopy, powder X-ray diffraction, and single-crystal X-ray diffraction. The new co-crystals show a 1:1 stoichiometry and crystallize in the monoclinic system, space group P21, with cell parameters: a = 9.7709(3) Å, b = 6.2202(2) Å, c = 14.7280(4) Å, α = 90°, β = 96.0340(10)°, γ = 90°, V = 890.16(5) Å3, and Z = 2. It is identified that hydrogen bonds are the main interactions between levetiracetam and 3,5-dinitrosalicylic acid, and the contribution of each hydrogen bond in maintaining the stability of the crystal structure was also quantified using Hirshfeld surface analysis.

Determination of the Crystal Structure of the Cell Wall-Anchored Proteins and Pilins.

Surface proteins and pili (or pilus) anchored on the Gram-positive bacterial cell wall play a vital role in adhesion, colonization, biofilm formation, and immunomodulation. The pilus consists of building blocks called pilins or pilus subunits. The surface proteins and pilins share some common sequences and structural features. They contain an N-terminal signal sequence and the C-terminal cell wall sorting region, enabling their transportation across the membrane and covalent attachment to the bacterial cell wall, respectively. The transpeptidase enzymes called sortases facilitate the covalent links between the pilins during the pilus assembly and between surface proteins or basal subunits of pili and peptidoglycan-bridge during the cell wall anchoring. Thus, elucidating three-dimensional structures for the surface proteins and pilins at the atomic level is essential for understanding the mechanism of adhesion, pilus assembly, and host interaction. This chapter aims to provide a general protocol for crystal structure determination of surface proteins and pilins anchored on the Gram-positive bacterial cell wall and substrates for sortases. The protocol involves the production of recombinant protein, crystallization, and structure determination by X-ray crystallography technique.

Base Promoted Three‐component Reaction for Efficient Construction of Spiro[indoline‐3,3′‐quinoline]‐2,5′‐dione

AbstractA convenient synthetic protocol for the construction of spiro[indoline‐3,3′‐quinoline]‐2,5′‐dione motifs was successfully developed by base promoted one‐pot three‐component reaction. In the presence of piperidine, three‐component reaction of ammonium acetate, aromatic aldehydes and the in situ generated 3‐isatyl 1,4‐dicarbonyl compounds, which were derived from base mediated addition of dimedone to 3‐methyleneoxindoles, resulted in two diastereoisomers of spiro[indoline‐3,3′‐quinoline]‐2,5′‐dione derivatives in good yields and with good diastereoselectivity. The stereochemistry of the reaction was clearly elucidated by isolation of two diastereomers and determination of several single crystal structures.

Effect of Extra-Framework Anion Substitution on the Properties of a Chiral Crystalline Sponge.

Chiral metal-organic materials, CMOMs, are of interest as they can offer selective binding sites for chiral guests. Such binding sites can enable CMOMs to serve as chiral crystalline sponges (CCSs) to determine molecular structure and/or purify enantiomers. We recently reported on the chiral recognition properties of a homochiral cationic diamondoid, dia, network {[Ni(S-IDEC)(bipy)(H2O)][NO3]}n (S-IDEC = S-indoline-2-carboxylicate, bipy = 4,4'-bipyridine), CMOM-5[NO3]. The modularity of CMOM-5[NO3] means there are five feasible approaches to fine-tune structures and properties via substitution of one or more of the following components: metal cation (Ni2+); bridging ligand (S-IDEC); linker (bipy); extra-framework anion (NO3-); and terminal ligand (H2O). Herein, we report the effect of anion substitution on the CCS properties of CMOM-5[NO3] by preparing and characterizing {[Ni(S-IDEC)(bipy)(H2O)][BF4]}n, CMOM-5[BF4]. The chiral channels in CMOM-5[BF4] enabled it to function as a CCS for determination of the absolute crystal structures of both enantiomers of three chiral compounds: 1-phenyl-1-butanol (1P1B); methyl mandelate (MM); ethyl mandelate (EM). Chiral resolution experiments revealed CMOM-5[BF4] to be highly selective toward the S-isomers of MM and EM with enantiomeric excess, ee, values of 82.6 and 78.4%, respectively. The ee measured for S-EM surpasses the 64.3% exhibited by [DyNaL(H2O)4] 6H2O and far exceeds that of CMOM-5[NO3] (6.0%). Structural studies of the binding sites in CMOM-5[BF4] provide insight into their high enantioselectivity.

Li4Ln[PS4]2Cl: Chloride-Containing Lithium Thiophosphates with Lanthanoid Participation (Ln = Pr, Nd and Sm)

The synthesis and structural analysis of three new chloride-containing lithium thiophosphates(V) Li4Ln[PS4]2Cl with trivalent lanthanoids (Ln = Pr, Nd and Sm) are presented and discussed. Single crystals of Li4Sm[PS4]2Cl were obtained and used for crystal structure determination by applying X-ray diffraction. The other compounds were found to crystallize isotypically in the monoclinic space group C2/c. Thus, Li4Sm[PS4]2Cl (a = 2089.31(12) pm, b = 1579.69(9) pm, c = 1309.04(8) pm, β = 109.978(3)°, Z = 12) was used as a representative model to further describe the crystal structure in detail since Li4Pr[PS4]2Cl and Li4Nd[PS4]2Cl were confirmed to be isotypic using powder X-ray diffraction measurements (PXRD). In all cases, a trigonal structure in the space group R3¯ (e.g., a = 1579.67(9) pm, c = 2818.36(16) pm, c/a = 1.784, Z = 18, for Li4Sm[PS4]2Cl) displaying almost identical building units worked initially misleadingly. The structure refinement of Li4Sm[PS4]2Cl revealed bicapped trigonal prisms of sulfur atoms coordinating the two crystallographically distinct (Sm1)3+ and (Sm2)3+ cations, which are further coordinated by four anionic [PS4]3− tetrahedra. The compounds also contain chloride anions residing within channel-like pores made of [PS4]3− units. Eight different sites for Li+ cations were identified with various coordination environments (C.N. = 4–6) with respect to chlorine and sulfur. EDXS measurements supported the stoichiometric formula of Li4Ln[PS4]2Cl, and diffuse reflectance spectroscopy revealed optical band gaps of 2.69 eV, 3.52 eV, and 3.49 eV for Li4Sm[PS4]2Cl, Li4Nd[PS4]2Cl, and Li4Pr[PS4]2Cl, respectively. The activation energy for Li+-cation mobility in Li4Sm[PS4]2Cl was calculated as Ea(Li+) = 0.88 eV using BVEL, which indicates potential as a Li+-cation conductor.

Weakly supervised learning for pattern classification in serial femtosecond crystallography.

Serial femtosecond crystallography at X-ray free electron laser facilities opens a new era for the determination of crystal structure. However, the data processing of those experiments is facing unprecedented challenge, because the total number of diffraction patterns needed to determinate a high-resolution structure is huge. Machine learning methods are very likely to play important roles in dealing with such a large volume of data. Convolutional neural networks have made a great success in the field of pattern classification, however, training of the networks need very large datasets with labels. This heavy dependence on labeled datasets will seriously restrict the application of networks, because it is very costly to annotate a large number of diffraction patterns. In this article we present our job on the classification of diffraction pattern by weakly supervised algorithms, with the aim of reducing as much as possible the size of the labeled dataset required for training. Our result shows that weakly supervised methods can significantly reduce the need for the number of labeled patterns while achieving comparable accuracy to fully supervised methods.

Cocrystal of Codeine and Cyclopentobarbital

The two-component compound formed by codeine and cyclopentobarbital was produced using grinding techniques and through evaporation from alcoholic solutions. The cocrystal nature of this phase was established unequivocally through single crystal X-ray structure determination. The asymmetric unit contains one formula unit. In the cyclopentobarbital molecule, the cyclopentenyl ring is disordered over two positions related by a rotation of approximately 180° about its C—C bond to the pyrimidine ring. The two NH groups of the cyclopentobarbital molecule form N—H⋯N and N—H⋯O bonds to piperidine and hydroxyl groups, respectively, belonging to different codeine molecules. In addition, the hydroxyl and methoxy groups of neighboring codeine molecules are linked by O—H⋯O interactions, resulting in a H-bonded framework structure of codeine and cyclopentobarbital molecules. The cocrystal was also characterized using thermal analysis, X-ray powder diffraction and IR spectroscopy.

Mallestigite, Pb3Sb(SO4)(AsO4)(OH)6·3H2O, from the type locality – new data, crystal structure, and structural relationships

A report of the supergene mineral mallestigite, Pb3Sb5+(SO4)(AsO4)(OH)6·3H2O, from the type locality Neufinkenstein-Grabanz district, Mallestiger Mittagskogel, Carinthia, Austria, is given in order to close gaps that have been left open since its first description. At the type locality, the dump of an abandoned small copper-lead-zinc mine, the mineral occurs frequently in up to ⁓2 mm long clear colourless idiomorphic hexagonal prisms {100} terminated by the bipyramid {101}. Details of the occurrence, paragenesis, physical properties, a FTIR spectrum and X-ray powder diffraction data are reported. Chemical analysis in a scanning electron microscope in conjunction with a crystal structure analysis gave the empirical formula Pb3.02Sb1.06(SO4)0.96(AsO4)0.97(OH)6·3H2O. An ab-initio crystal structure determination with CCD diffractometer data, MoKα radiation, and a nearly untwinned crystal proved that mallestigite is hexagonal, space group P63, a = 8.9326(4), c = 11.1044(5) Å, V = 767.33(8) Å3, Z = 2, and gave a final R1 = 0.0184 for 1632 independent reflections with I > 2σ(I). Mallestigite belongs to the fleischerite group. The structure is built up from [Sb5+(OH)6]1– octahedra which are linked by triplets of edge-sharing Pb2+ into chains [Pb3Sb(OH)6]5+ extending along a 63 axis. Each three of such chains are bridged by triplets of H2O and by rows of SO42– and AsO43– tetrahedra alternating along a 3-fold axis and showing very different links to the Pb atom. Pb2+ is in a strongly distorted one-sided [9]-coordination by O atoms that makes the structure clearly hemimorphic. Structural relationships to the fleischerite group minerals schaurteite, genplesite, despujolsite and fleischerite as well as to synthetic Ba3Sn4+(SeO4)2(OH)6·3H2O are outlined and changes in the space group symmetry of despujolsite (P6¯\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\overline6$$\\end{document}2c → P63/mmc) and fleischerite (P6¯\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\overline6$$\\end{document}2c → P63) are proposed.

Znucalite, the only known zinc uranyl carbonate: Its crystal structure and environmental implications

Abstract Znucalite is a zinc uranyl-carbonate mineral that was until recently only partially characterized with a formula originally given as Zn12Ca(UO2)(CO3)3(OH)22·4H2O, with an unknown crystal structure and ambiguous symmetry determinations. We have reinvestigated this mineral using three-dimensional electron diffraction (3D ED) and powder X-ray diffraction and revealed for the first time its structural details. Znucalite is unambiguously monoclinic, P21/m, with a = 10.722(2) Å, b = 6.259(1) Å, c = 25.355(1) Å, β = 101.13(1)°, and V = 1669.54(9) Å3. The structure refinement of the 3D ED data using the dynamical approach (Robs = 0.1594 for 3579 observed reflections and 244 parameters) provided the following structure model. Znucalite possesses a layered structure, with a [Zn10(OH)14(CO3)2] double sheet (with Zn2+ both in octahedra and tetrahedra), which is connected to a thick interlayer that hosts U 6+, Ca2+, and H2O molecules. The linkage between structural units and the interlayer occurs via the vertices of ZnO4 tetrahedra protruding from the sheet. In the interlayer, differences in ordering between U and Ca take place and likely cause the difficulties encountered during the attempts to solve the structure. The refined structural formula of znucalite, Zn10Ca0.828[UO2]0.828[CO3]4(OH)15.312(H2O)5.484, corresponds well to the composition obtained from the electron-microprobe analyses, (Zn9.84Al0.16)Σ10.00 Ca0.83(UO2)0.80[(CO3)3.96(SO4)0.04]Σ4.00(OH)15.42(H2O)5.48. Raman spectroscopy evidenced the presence of several non-equivalent CO3 groups, as well as OH and H2O. The U-O bond lengths obtained from the stretching frequencies of UO22+ vibrations are in line with the structural model. A discussion on the environmental importance of znucalite is appended, based on geochemical calculations with an estimate of the solubility product for this mineral.

Phasing neural network: ab initio determination of crystal structures at 2 Å resolution

Phasing neural network: <i>ab initio</i> determination of crystal structures at 2 Å resolution

Game-theoretic crystal structure determination by combining diffraction experiments and ab initio calculations

Game-theoretic crystal structure determination by combining diffraction experiments and <i>ab initio</i> calculations

Discovery of novel cGAS inhibitors based on natural flavonoids

Cyclic GMP-AMP synthase (cGAS) plays an important role in the inflammatory response. It has been reported that aberrant activation of cGAS is associated with a variety of immune-mediated inflammatory disorders. The development of small molecule inhibitors of cGAS has been considered as a promising therapeutic strategy for the diseases. Flavonoids, a typical class of natural products, are known for their anti-inflammatory activities. Although cGAS is closely associated with inflammation, the potential effects of natural flavonoid compounds on cGAS have been rarely studied. Therefore, we screened an in-house natural flavonoid library by pyrophosphatase (PPiase) coupling assay and identified novel cGAS inhibitors baicalein and baicalin. Subsequently, crystal structures of the two natural flavonoids in complex with human cGAS were determined, which provide mechanistic insight into the anti-inflammatory activities of baicalein and baicalin at the molecular level. After that, a virtual screening based on the crystal structures of baicalein and baicalin in complex with human cGAS was performed. As a result, compound C20 was identified to inhibit both human and mouse cGAS with IC50 values of 2.28 and 1.44 μM, respectively, and its detailed interactions with human cGAS were further revealed by the X-ray crystal structure determination. These results demonstrate the potential of natural products used as hits in drug discovery and provide valuable hints for further development of cGAS inhibitors.

Red and Blue-Black Tin Monoxide, SnO: Pitfalls, Challenges, and Helpful Tools in Crystal Structure Determination of Low-Intensity Datasets from Microcrystals

The crystal structures of red and blue-black tin(II) oxide, SnO, have been determined for the first time by single-crystal X-ray diffraction. Blue-black SnO crystallizes in the tetragonal space group P4/nmm, representing a layer structure consisting of the square–pyramidally coordinated tin and slightly distorted tetrahedrally coordinated oxygen atoms, in accordance with previous results. In contrast, red SnO crystallizes in the orthorhombic centrosymmetric space group Pbca rather than in the non-centrosymmetric space group Cmc21, as assumed for a long time. Its layer structure consists of very regular, trigonal–pyramidally coordinated tin atoms as well as trigonal–planar coordinated oxygen atoms. Special care was taken on space group determination, including lattice centering. C-centering could be excluded because of systematic absence violations detected when collecting and processing a primitive triclinic dataset and by generating precession images. In the absence of meaningful extinction conditions resulting from the very small crystal under examination, the structure was initially solved and refined in the triclinic space group P1. Subsequently, the observed atom coordinates were used to reconstruct the actual symmetry skeleton. The various possibilities to identify the correct space group starting from the triclinic solution are demonstrated, and the unique structural features of the crystal structure are visualized.

Synthesis, crystal structure, cytotoxicity, in-detail experimental and computational CT-DNA interaction studies of 2-picolinate Pd(II) and Pt(II) complexes

A new Pd(II) complex of formula [Pd(en)(2-pyc)]+ (where, en is ethylenediamine and 2-pyc is 2-pyridinecarboxylate anion) and its reported Pt(II) analogue, i.e. [Pt(en)(2-pyc)]+ have been made by an improved synthetic procedure, yielding above 80%. They have been characterized by FT-IR, UV-Vis, 1H NMR, 13C NMR, conductivity and elemental analysis. Single crystal structural determination of [Pt(en)(2-pyc)]+ displayed that the Pt(II) cation in this complex coordinated by 2-pyc and en each as five member chelate resulting in slightly distorted square-planar array. The time-dependent spectroscopic analysis of these compounds in aqueous medium demonstrated their structural stabilities. The cytotoxic activities of Pd(II) and Pt(II) complexes, free 2-pyc and carboplatin (as standard drug) were assayed in-vitro against the HCT-116 and MCF-7 as cancerous and MCF 10 A and CCD-841 as normal cell lines. They showed the IC50 order of: carboplatin > 2-pyc > Pt(II) > Pd(II) and lower activities against non-cancerous cells. CT-DNA binding of the Pd(II), Pt(II) and 2-pyc free ligand were explored individually. In this relation, UV-Vis and fluorescence titrations disclosed quenching of CT-DNA absorption and emissions by the compounds via dynamic mechanism and formation of H-bonds and van der Waals forces between them. The interaction was further validated and verified by viscosity measurements and gel electrophoresis. Partition coefficient determination showed that all three compounds have more lipophilicity than cisplatin. Furthermore, docking analysis and molecular dynamics simulation were done to evaluate the nature of interaction between aforementioned compounds and CT-DNA. The finding results demonstrated that these agents interact with CT-DNA via groove binding and were in agreement with experimental results. Communicated by Ramaswamy H. Sarma

Crystal structure determination and DFT analysis of doxorubicin hydrochloride for controlled-release drug formulations

Doxorubicin hydrochloride (DOX) is a widely used chemotherapeutic drug that inhibits the growth of cancer cells. Many DOX-based controlled-release systems have been proposed to reduce toxicity. However, knowledge of its crystal structure is essential for optimizing drug release processes and designing co-crystals or salts with different release properties. Although DOX has been extensively studied, no crystal structure is available in the Cambridge Structural Database or literature. In this work, we determine the crystal structure of DOX using a simulated annealing approach based on powder X-ray diffraction data. We confirm its validation by Rietveld refinement and molecular cohesion by using a molecular geometry check tool. We also use density functional theory to optimize the DOX structure and obtain the minimum energy conformation, H-bond donor/acceptor species, charge localization, and crystal structure parameters. This study provides essential structural information on DOX that can be used to rationalize new modified-release dosage forms and to design co-crystals or salts with different release properties.

First Exclusive Stereo- and Regioselective Preparation of 5-Arylimino-1,3,4-Selenadiazole Derivatives: Synthesis, NMR analysis, and Computational Studies.

Isoselenocyanates are valuable coupling partners required for preparing key chemical intermediates and biologically active molecules in an accelerated and effective way. Likewise, (Z)-2-oxo-N-phenylpropanehydrazonoyl chlorides have been employed in numerous one-step heteroannulation reactions to assemble the structural core of several various kinds of heterocyclic compounds. Here, we describe the inverse electron demand 1,3-dipolar cycloaddition reaction of isoselenocyanates with a variety of substituted (Z)-2-oxo-N-phenylpropanehydrazonoyl chlorides to generate, regioselectively and stereoselectively, a series of 5-arylimino-1,3,4-selenadiazole derivatives comprising a multitude of functional groups on both aryl rings. The synthetic method features gentle room-temperature conditions, wide substrate scope, and good to high reaction yields. The selenadiazoles were separated by gravity filtration in all instances and chemical structures were validated by multinuclear NMR spectroscopy and high accuracy mass spectral measurements. First conclusive molecular structure elucidation of the observed 5-arylimino-selenadiazole regioisomer was verified by single-crystal X-ray diffraction analysis. Crystal-structure measurement was successfully carried out on (Z)-1-(4-(4-iodophenyl)-5-(p-tolylimino)-4,5-dihydro-1,3,4-selenadiazol-2-yl)ethan-1-one and (Z)-1-(5-((4-methoxyphenyl)imino)-4-(4-(methylthio)phenyl)-4,5-dihydro-1,3,4-selenadiazol-2-yl)ethan-1-one. Likewise, the (Z)-geometry of the hydrazonoyl chloride reactant was proven by X-ray diffraction studies. As representative examples, crystal-structure determination was carried out on (Z)-2-oxo-N-phenylpropanehydrazonoyl chloride and (Z)-N-(3,5-bis(trifluoromethyl)phenyl)-2-oxopropanehydrazonoyl chloride. Density functional theory calculations at the B3LYP-D4/def2-TZVP level were conducted to support the noted experimental findings and suggested mechanism.

Composition Based Oxidation State Prediction of Materials Using Deep Learning Language Models.

Oxidation states (OS) are the charges on atoms due to electrons gained or lost upon applying an ionic approximation to their bonds. As a fundamental property, OS has been widely used in charge-neutrality verification, crystal structure determination, and reaction estimation. Currently, only heuristic rules exist for guessing the oxidation states of a given compound with many exceptions. Recent work has developed machine learning models based on heuristic structural features for predicting the oxidation states of metal ions. However, composition-based oxidation state prediction still remains elusive so far, which has significant implications for the discovery of new materials for which the structures have not been determined. This work proposes a novel deep learning-based BERT transformer language model BERTOS for predicting the oxidation states for all elements of inorganic compounds given only their chemical composition. This model achieves 96.82% accuracy for all-element oxidation states prediction benchmarked on the cleaned ICSD dataset and achieves 97.61% accuracy for oxide materials. It is also demonstrated how it can be used to conduct large-scale screening of hypothetical material compositions for materials discovery.

Key roles of β-glucosidase BglA for the catabolism of both laminaribiose and cellobiose in the lignocellulolytic bacterium Clostridium thermocellum

The thermophilic bacterium Clostridium thermocellum efficiently degrades polysaccharides into oligosaccharides. The metabolism of β-1,4-linked cello-oligosaccharides is initiated by three enzymes, i.e., the cellodextrin phosphorylase (Cdp), the cellobiose phosphorylase (Cbp), and the β-glucosidase A (BglA), in C. thermocellum. In comparison, how the oligosaccharides containing other kinds of linkage are utilized is rarely understood. In this study, we found that BglA could hydrolyze the β-1,3-disaccharide laminaribiose with much higher activity than that against the β-1,4-disaccharide cellobiose. The structural basis of the substrate specificity was analyzed by crystal structure determination and molecular docking. Genetic deletions of BglA and Cbp, respectively, and enzymatic analysis of cell extracts demonstrated that BglA is the key enzyme responsible for laminaribiose metabolism. Furthermore, the deletion of BglA can suppress the expression of Cbp and the deletion of Cbp can up-regulate the expression of BglA, indicating that BglA and Cbp have cross-regulation and BglA is also critical for cellobiose metabolism. These insights pave the way for both a fundamental understanding of metabolism and regulation in C. thermocellum and emphasize the importance of the degradation and utilization of polysaccharides containing β-1,3-linked glycosidic bonds in lignocellulose biorefinery.