scholarly journals Structural analysis of rice Os4BGlu18 monolignol β-glucosidase

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0241325
Author(s):  
Supaporn Baiya ◽  
Salila Pengthaisong ◽  
Sunan Kitjaruwankul ◽  
James R. Ketudat Cairns
Keyword(s):  
Molecular Docking ◽  
Substrate Specificity ◽  
Disulfide Bonds ◽  
Complex Structure ◽  
Docking Studies ◽  
Structural Basis ◽  
Glycoside Hydrolase Family ◽  
Multiple Sequence ◽  
X Ray Crystallography ◽  
Tim Barrel

Monolignol glucosides are storage forms of monolignols, which are polymerized to lignin to strengthen plant cell walls. The conversion of monolignol glucosides to monolignols is catalyzed by monolignol β-glucosidases. Rice Os4BGlu18 β-glucosidase catalyzes hydrolysis of the monolignol glucosides, coniferin, syringin, and p-coumaryl alcohol glucoside more efficiently than other natural substrates. To understand more clearly the basis for substrate specificity of a monolignol β-glucosidase, the structure of Os4BGlu18 was determined by X-ray crystallography. Crystals of Os4BGlu18 and its complex with δ-gluconolactone diffracted to 1.7 and 2.1 Å resolution, respectively. Two protein molecules were found in the asymmetric unit of the P212121 space group of their isomorphous crystals. The Os4BGlu18 structure exhibited the typical (β/α)8 TIM barrel of glycoside hydrolase family 1 (GH1), but the four variable loops and two disulfide bonds appeared significantly different from other known structures of GH1 β-glucosidases. Molecular docking studies of the Os4BGlu18 structure with monolignol substrate ligands placed the glycone in a similar position to the δ-gluconolactone in the complex structure and revealed the interactions between protein and ligands. Molecular docking, multiple sequence alignment, and homology modeling identified amino acid residues at the aglycone-binding site involved in substrate specificity for monolignol β-glucosides. Thus, the structural basis of substrate recognition and hydrolysis by monolignol β-glucosidases was elucidated.

scholarly journals Structural analysis of rice Os4BGlu18 monolignol β-glucosidase

2020 ◽  
Author(s):  
Supaporn Baiya ◽  
Salila Pengthaisong ◽  
James R. Ketudat Cairns
Keyword(s):  
Molecular Docking ◽  
Substrate Specificity ◽  
Disulfide Bonds ◽  
Complex Structure ◽  
Docking Studies ◽  
Structural Basis ◽  
Glycoside Hydrolase Family ◽  
Multiple Sequence ◽  
X Ray Crystallography ◽  
Tim Barrel

AbstractMonolignol glucosides are storage forms of monolignols, which are polymerized to lignin to strengthen plant cell walls. The conversion of monolignol glucosides to monolignols is catalyzed by monolignol β-glucosidases. Rice Os4BGlu18 β-glucosidase catalyzes hydrolysis of the monolignol glucosides, coniferin, syringin, and p-coumaryl alcohol glucoside more efficiently than other natural substrates. To understand more clearly the basis for substrate specificity of a monolignol β-glucosidase, the structure of Os4BGlu18 was determined by X-ray crystallography. Crystals of Os4BGlu18 and its complex with δ-gluconolactone diffracted to 1.7 and 2.1 Å resolution, respectively. Two protein molecules were found in the asymmetric unit of the P212121 space group of their isomorphous crystals. The Os4BGlu18 structure exhibited the typical (β/α)8 TIM barrel of glycoside hydrolase family 1 (GH1), but the four variable loops and two disulfide bonds appeared significantly different from other known structures of GH1 β-glucosidases. Molecular docking studies of the Os4BGlu18 structure with monolignol substrate ligands placed the glycone in a similar position to the δ-gluconolactone in the complex structure and revealed the interactions between protein and ligands. Molecular docking, multiple sequence alignment, and homology modeling identified amino acid residues at the aglycone-binding site involved in substrate specificity for monolignol β-glucosides. Thus, the structural basis of substrate recognition and hydrolysis by monolignol β-glucosidases was elucidated.

Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32

2017 ◽  
Vol 474 (20) ◽  
pp. 3373-3389 ◽  
Author(s):  
Dong-Dong Meng ◽  
Xi Liu ◽  
Sheng Dong ◽  
Ye-Fei Wang ◽  
Xiao-Qing Ma ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Specificity ◽  
Glycoside Hydrolase ◽  
Complex Structure ◽  
Dynamics Simulation ◽  
Structural Basis ◽  
Glycoside Hydrolase Family ◽  
Substrate Selectivity ◽  
Glucose Residue ◽  
Structural Insights

Glycoside hydrolase (GH) family 5 is one of the largest GH families with various GH activities including lichenase, but the structural basis of the GH5 lichenase activity is still unknown. A novel thermostable lichenase F32EG5 belonging to GH5 was identified from an extremely thermophilic bacterium Caldicellulosiruptor sp. F32. F32EG5 is a bi-functional cellulose and a lichenan-degrading enzyme, and exhibited a high activity on β-1,3-1,4-glucan but side activity on cellulose. Thin-layer chromatography and NMR analyses indicated that F32EG5 cleaved the β-1,4 linkage or the β-1,3 linkage while a 4-O-substitued glucose residue linked to a glucose residue through a β-1,3 linkage, which is completely different from extensively studied GH16 lichenase that catalyses strict endo-hydrolysis of the β-1,4-glycosidic linkage adjacent to a 3-O-substitued glucose residue in the mixed-linked β-glucans. The crystal structure of F32EG5 was determined to 2.8 Å resolution, and the crystal structure of the complex of F32EG5 E193Q mutant and cellotetraose was determined to 1.7 Å resolution, which revealed that the exit subsites of substrate-binding sites contribute to both thermostability and substrate specificity of F32EG5. The sugar chain showed a sharp bend in the complex structure, suggesting that a substrate cleft fitting to the bent sugar chains in lichenan is a common feature of GH5 lichenases. The mechanism of thermostability and substrate selectivity of F32EG5 was further demonstrated by molecular dynamics simulation and site-directed mutagenesis. These results provide biochemical and structural insights into thermostability and substrate selectivity of GH5 lichenases, which have potential in industrial processes.

Homogeneous assay for zearalenone analogues and their docking studies with apo-/holo-estrogen receptors

2019 ◽  
Vol 11 (2) ◽  
pp. 192-199 ◽  
Author(s):  
Jie Zhang ◽  
Wenfu Wu ◽  
Yifan Song ◽  
Ligang Hou ◽  
Tiezhu Li ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Estrogen Receptors ◽  
Docking Studies ◽  
Structural Basis ◽  
Homogeneous Assay

A homogeneous assay was developed for zearalenone analogues and the structural basis of their estrogenicity was demonstrated by molecular docking.

scholarly journals Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity

2016 ◽  
Vol 72 (9) ◽  
pp. 1017-1025 ◽  
Author(s):  
Pavel Mikulecký ◽  
Jirí Zahradník ◽  
Petr Kolenko ◽  
Jiří Černý ◽  
Tatsiana Charnavets ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Disulfide Bonds ◽  
Bioinformatic Analysis ◽  
Structural Features ◽  
Interferon Γ ◽  
Cell Surface Receptor ◽  
Structural Basis ◽  
Human Interferon ◽  
Multiple Sequence ◽  
Surface Receptor

Interferon-γ receptor 2 is a cell-surface receptor that is required for interferon-γ signalling and therefore plays a critical immunoregulatory role in innate and adaptive immunity against viral and also bacterial and protozoal infections. A crystal structure of the extracellular part of human interferon-γ receptor 2 (IFNγR2) was solved by molecular replacement at 1.8 Å resolution. Similar to other class 2 receptors, IFNγR2 has two fibronectin type III domains. The characteristic structural features of IFNγR2 are concentrated in its N-terminal domain: an extensive π–cation motif of stacked residues KWRWRH, a NAG–W–NAG sandwich (where NAG stands forN-acetyl-D-glucosamine) and finally a helix formed by residues 78–85, which is unique among class 2 receptors. Mass spectrometry and mutational analyses showed the importance of N-linked glycosylation to the stability of the protein and confirmed the presence of two disulfide bonds. Structure-based bioinformatic analysis revealed independent evolutionary behaviour of both receptor domains and, together with multiple sequence alignment, identified putative binding sites for interferon-γ and receptor 1, the ligands of IFNγR2.

Characterization of Three Osmotin-Like Proteins from Plumeria rubra and Prospection for Adiponectin Peptidomimetics

2020 ◽  
Vol 27 (7) ◽  
pp. 593-603 ◽  
Author(s):  
Cleverson D.T. de Freitas ◽  
Beatriz C. Nishi ◽  
Camila T.M. do Nascimento ◽  
Maria Z.R. Silva ◽  
Eduardo H.S. Bezerra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Disulfide Bonds ◽  
3D Models ◽  
Docking Studies ◽  
Adiponectin Receptors ◽  
Defense Proteins ◽  
Defensive Role ◽  
Molecular Masses ◽  
Plumeria Rubra

Background: Osmotin-Like Proteins (OLPs) have been purified and characterized from different plant tissues, including latex fluids. Besides its defensive role, tobacco osmotin seems to induce adiponectin-like physiological effects, acting as an agonist. However, molecular information about this agonistic effect on adiponectin receptors has been poorly exploited and other osmotins have not been investigated yet. Objective and Methods: The present study involved the characterization of three OLPs from Plumeria rubra latex and molecular docking studies to evaluate the interaction between them and adiponectin receptors (AdipoR1 and AdipoR2). Results: P. rubra Osmotin-Like Proteins (PrOLPs) exhibited molecular masses from 21 to 25 kDa and isoelectric points ranging from 4.4 to 7.7. The proteins have 16 cysteine residues, which are involved in eight disulfide bonds, conserved in the same positions as other plant OLPs. The threedimensional (3D) models exhibited the three typical domains of OLPs, and molecular docking analysis showed that two PrOLP peptides interacted with two adiponectin receptors similarly to tobacco osmotin peptide. Conclusion: As observed for tobacco osmotin, the latex osmotins of P. rubra exhibited compatible interactions with adiponectin receptors. Therefore, these plant defense proteins (without known counterparts in humans) are potential tools to study modulation of glucose metabolism in type II diabetes, where adiponectin plays a pivotal role in homeostasis.

Molecular Cloning and Structural Insights into pectin lyase proteins from different strains of Fusarium

2020 ◽  
Vol 17 ◽  
Author(s):  
Sangeeta Yadav ◽  
Gautam Anand ◽  
Vinay K Singh ◽  
Dinesh Yadav
Keyword(s):  
Structure Prediction ◽  
Disulfide Bonds ◽  
3D Structure ◽  
Chemical Characterization ◽  
Structural Features ◽  
Docking Studies ◽  
Biochemical Properties ◽  
Pectin Lyase ◽  
Homology Search ◽  
Multiple Sequence

: Pectin lyaseis an industrially important enzymeof pectinase group that degrade pectin polymers forming 4,5-unsaturated oligogalacturonides. Several fugal pectin lyase genes predominately from Aspergillus and Penicillium genera have been reported in the literature. Five pectin lyase genes were cloned from FusariumoxysporumMTCC1755, F.monoliforme var. subglutinansMTCC2015, FusariumavneceumMTCC10572, and FusariumsolaniMTCC3004 using PCR approach. Pectin lyase genes and proteins were subjected to homology search, multiple sequence alignment, motif search, physio-chemical characterization, phylogenetic tree construction, 3D structure prediction and molecular docking. Many conserved amino acids were found at several positions in all the pectin lyase proteins. Phylogenetic analysis of these proteins alongwith other pectinases revealed two major clusters representing members of lyases and hydrolases. In-silico characterization revealed pectin lyase proteins to be highly stable owing to the presence of disulfide bonds in their structure. Molecular weight and pI of these proteins were in the range 14.4 to 25.1 kDa and 4.47-9.39 respectively. Pectin lyase proteins from different Fusariumstrains were very much similar in their structural features and biochemical properties which might be due to their similarity on the primary sequence. Docking studies revealed that electrostatic forces, vander Waal and hydrogen bonds are the major interacting forces between the ligands and the enzyme. This might be accountable for comparatively higher and better activity of pectin lyase against galacturonic acid as compared to α-D-galactopyranuronic acid, galactofuranuronicacid and galactopyranuronate. Aspartate, tyrosine and tryptophan residues in the active site of the enzyme are responsible for ligand binding.

scholarly journals Loop 3 of Fungal Endoglucanases of Glycoside Hydrolase Family 12 Modulates Catalytic Efficiency

2016 ◽  
Vol 83 (6) ◽  
Author(s):  
Hong Yang ◽  
Pengjun Shi ◽  
Yun Liu ◽  
Wei Xia ◽  
Xiaoyu Wang ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Glycoside Hydrolase ◽  
Turnover Rate ◽  
Catalytic Efficiency ◽  
Glycoside Hydrolase Family ◽  
Multiple Sequence ◽  
Content Type ◽  
Hydrogen Bond Interactions ◽  
Wide Range ◽  
Hydrogen Network

ABSTRACT Glycoside hydrolase (GH) family 12 comprises enzymes with a wide range of activities critical for the degradation of lignocellulose. However, the important roles of the loop regions of GH12 enzymes in substrate specificity and catalytic efficiency remain poorly understood. This study examined how the loop 3 region affects the enzymatic properties of GH12 glucanases using NfEG12A from Neosartorya fischeri P1 and EG (PDB 1KS4 ) from Aspergillus niger. Acidophilic and thermophilic NfEG12A had the highest catalytic efficiency (k cat/Km , 3,001 and 263 ml/mg/s toward lichenin and carboxymethyl cellulose sodium [CMC-Na], respectively) known so far. Based on the multiple-sequence alignment and homology modeling, two specific sequences (FN and STTQA) were identified in the loop 3 region of GH12 endoglucanases from fungi. To determine their functions, these sequences were introduced into NfEG12A, or the counterpart sequence STTQA was removed from EG. These modifications had no effects on the optimal pH and temperature or substrate specificity but changed the catalytic efficiency (k cat/Km ) of these enzymes (in descending order, NfEG12A [100%], NfEG12A-FN [140%], and NfEG12A-STTQA [190%]; EG [100%] and EGΔSTTQA [41%]). Molecular docking and dynamic simulation analyses revealed that the longer loop 3 in GH12 may strengthen the hydrogen-bond interactions between the substrate and protein, thereby increasing the turnover rate (k cat). This study provides a new insight to understand the vital roles of loop 3 for GH12 endoglucanases in catalysis. IMPORTANCE Loop structures play critical roles in the substrate specificity and catalytic hydrolysis of GH12 enzymes. Three typical loops exist in these enzymes. Loops 1 and 2 are recognized as the catalytic loops and are closely related to the substrate specificity and catalytic efficiency. Loop 3 locates in the −1 or +1 subsite and varies a lot in amino acid composition, which may play a role in catalysis. In this study, two GH12 glucanases, NfEG12A and EG, which were mutated by introducing or deleting partial loop 3 sequences FN and/or STTQA, were selected to identify the function of loop 3. It revealed that the longer loop 3 of GH12 glucanases may strengthen the hydrogen network interactions between the substrate and protein, consequently increasing the turnover rate (k cat). This study proposes a strategy to increase the catalytic efficiency of GH12 glucanases by improving the hydrogen network between substrates and catalytic loops.

scholarly journals Two distinct mechanisms of transcriptional regulation by the redox sensor YodB

2016 ◽  
Vol 113 (35) ◽  
pp. E5202-E5211 ◽  
Author(s):  
Sang Jae Lee ◽  
In-Gyun Lee ◽  
Ki-Young Lee ◽  
Dong-Gyun Kim ◽  
Hyun-Jong Eun ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Disulfide Bonds ◽  
Structural Changes ◽  
High Specificity ◽  
Redox Balance ◽  
Structural Basis ◽  
X Ray Crystallography ◽  
Redox Sensor ◽  
Regulatory Systems ◽  
Sense And Respond

For bacteria, cysteine thiol groups in proteins are commonly used as thiol-based switches for redox sensing to activate specific detoxification pathways and restore the redox balance. Among the known thiol-based regulatory systems, the MarR/DUF24 family regulators have been reported to sense and respond to reactive electrophilic species, including diamide, quinones, and aldehydes, with high specificity. Here, we report that the prototypical regulator YodB of the MarR/DUF24 family from Bacillus subtilis uses two distinct pathways to regulate transcription in response to two reactive electrophilic species (diamide or methyl-p-benzoquinone), as revealed by X-ray crystallography, NMR spectroscopy, and biochemical experiments. Diamide induces structural changes in the YodB dimer by promoting the formation of disulfide bonds, whereas methyl-p-benzoquinone allows the YodB dimer to be dissociated from DNA, with little effect on the YodB dimer. The results indicate that B. subtilis may discriminate toxic quinones, such as methyl-p-benzoquinone, from diamide to efficiently manage multiple oxidative signals. These results also provide evidence that different thiol-reactive compounds induce dissimilar conformational changes in the regulator to trigger the separate regulation of target DNA. This specific control of YodB is dependent upon the type of thiol-reactive compound present, is linked to its direct transcriptional activity, and is important for the survival of B. subtilis. This study of B. subtilis YodB also provides a structural basis for the relationship that exists between the ligand-induced conformational changes adopted by the protein and its functional switch.

scholarly journals Identification of APOE4 modulators, targeted therapeutic candidates in Coronary Artery Disease, using Molecular Docking studies

2021 ◽  
Author(s):  
Lima Hazarika ◽  
Supriyo Sen ◽  
Akshaykumar Zawar ◽  
Jitesh Doshi
Keyword(s):  
Coronary Artery Disease ◽  
Molecular Docking ◽  
Coronary Artery ◽  
Binding Affinity ◽  
Intramolecular Interaction ◽  
Docking Studies ◽  
Structural Basis ◽  
Molecular Docking Studies ◽  
Artery Disease ◽  
Drug Receptor

AbstractA significant genetic suspect for coronary artery disease is the pathological adaptation of apolipoprotein E4 (APOE4) through intramolecular interaction. With the prevailing evidences on APOE4 genotype and its prevalence in coronary artery disease, the present study has investigated the protein–ligand binding affinity and unveil the receptor binding abilities of different classes of ligands for APOE4 through molecular docking studies. Structural basis of APOE4 involvement in CAD suggests that the intramolecular domain interactions to be a suitable target for therapeutic intervention. Various classes of ligands including known drugs used in the treatment of CAD, fragment-based stabilizers and their similar structures and molecules with known bioactivity against APOE4 were screened for their binding affinity and further investigated for their interactions with APOE4. Computational studies show the benzyl amide derived structures to be useful candidates in modulation of APOE4. The dynamics of the binding analysis can be further achieved with an in-depth understanding of drug-receptor interactions performing molecular dynamic simulation studies.

scholarly journals Synthesis, X-ray crystal structure, Hirshfeld surface analysis, and molecular docking studies of DMSO/H2O solvate of 5-chlorospiro[indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione

2021 ◽  
Vol 12 (4) ◽  
pp. 382-388
Author(s):  
Varun Sharma ◽  
Bubun Banerjee ◽  
Aditi Sharma ◽  
Vivek Kumar Gupta
Keyword(s):  
Crystal Structure ◽  
Molecular Docking ◽  
Direct Method ◽  
Docking Studies ◽  
One Pot ◽  
X Ray ◽  
Molecular Docking Studies ◽  
X Ray Crystallography ◽  
Three Component Reaction ◽  
Inhibition Property

The title compound, 5-chlorospiro[indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione was synthesized via one-pot pseudo three-component reaction between one equivalent of 5-chloroisatin and two equivalents of 4-hydroxycoumarin using mandelic acid as catalyst in aqueous ethanol at 110 °C. The synthesized compound was characterized by FT-IR, 1H NMR, and HRMS techniques. Single crystals were grown for crystal structure determination by using single X-ray crystallography technique. It was found that the crystals are triclinic with space group P-1 and Z = 1. The crystal structure was solved by direct method and refined by full-matrix least-squares procedures to a final R-value of 0.0688 for 6738 observed reflections. The crystal structure was stabilized by elaborate system of O-H···O, N-H···O, and C-H···O interactions with the formation of supramolecular structures. 3D Hirshfeld surfaces and allied 2D fingerprint plots were analyzed for molecular interactions. Molecular docking studies have been performed to get insights into the inhibition property of this molecule for Human topoisomerase IIα.

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