Putative role of invariant water molecules in the X-ray structures of family G fungal endoxylanases (original) (raw)
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Proteins: Structure, Function, and Genetics, 1998
Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The openclose movement was characterized by the use of distance difference matrixes and the Hingefind program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a 'hinge-bending' motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII. Proteins 31:434-444, 1998. 1998 Wiley-Liss, Inc.
2003
The Humicola grisea var. thermoidea is known as a good producer of hydrolytic enzymes. The H. grisea endo-1,4-xylanase gene (xyn2) was isolated and its sequence was translated into a predicted protein coding for a xylanase of 23 kDa. A structural model of H. grisea endo-1,4-xylanase (XYN2) was built by homology modeling based on the database search results of related proteins, belonging to Glycoside Hydrolase Family 11 (GH11). The inactive/active conformation transition of the XYN2 model active site is pH sensitive as revealed by independent molecular dynamics simulations at different pH. The active conformation exhibits the common structural-sheet twisted architecture of the GH11. The active site is formed by a large cleft containing the catalytic residues (E84 and E175), and is stabilized by hydrogen bond network involving the Q134, Y75, Y88, W77, and Y169. Additionally, the structural properties described by the model explain the observed thermostability of the XYN2 protein. Acco...
The Humicola grisea var. thermoidea is known as a good producer of hydrolytic enzymes. The H. grisea endo-1,4--xylanase gene (xyn2) was isolated and its sequence was translated into a predicted protein coding for a xylanase of 23 kDa. A structural model of H. grisea endo-1,4--xylanase (XYN2) was built by homology modeling based on the database search results of related proteins, belonging to Glycoside Hydrolase Family 11 (GH11). The inactive/active conformation transition of the XYN2 model active site is pH sensitive as revealed by independent molecular dynamics simulations at different pH. The active conformation exhibits the common structural -sheet twisted architecture of the GH11. The active site is formed by a large cleft containing the catalytic residues (E84 and E175), and is stabilized by hydrogen bond network involving the Q134, Y75, Y88, W77, and Y169. Additionally, the structural properties described by the model explain the observed thermostability of the XYN2 protein. According to our results, the thermostability of XYN2 protein, compared to mesophilic xylanases, can be explained by an additional electrostatic network and extra aromatic exposed residues.
NU. International Journal of Science, 2009
Xylanases hydrolyze the β-1,4-linked xylose backbone of xylans, the major hemicellulosic components of plant cell walls. They are especially useful in paper industry because they decrease the demand for chlorine-based chemicals in the wood pulp delignification process. In this study, 3D structure of Xyn10A, a family 10 xylanase from Bacillus firmus K-1 was generated by homology modeling using X-ray structure of xylanase from Bacillus sp. strain NG-27 as a template. The root mean square deviation (RMSD) of backbone atoms between the X-ray and homology modeled structures was 0.8 Å. Binding of xylopentaose (X 5) to the Xyn10A was investigated using molecular dynamics simulations via comparison the total energy, RMSD of Cα atom and root mean square fluctuation (RMSF) of free and complex forms of Xyn10A. In the reactive Xyn10A-X 5 conformation, in which the two catalytic sites, E149 and E255 are precisely positioned for the catalytic reaction, the-1 sugar moiety of the X 5 adopted a 1 C 4 chair conformation for the Xyn10A. According to the RMSF, 13 amino acid residues in active site of complex form showed more flexibility than those of free form. The result suggested that they may implicate in binding to X 5 at subsites-3 to +2 of substrate-binding site through hydrogen bonding and stacking interactions. Furthermore, the RMSF of X 5 revealed that the substrate binding site of Xyn10A was more specific to three middle xylose moieties than two terminal xylose moieties. The role of sugar moiety interaction with Xyn10A in catalytic mechanism is discussed.
Journal of molecular graphics & modelling, 2017
Xylanase belongs to, Glycoside hydrolase family, playing a major role in xylan degradation. Bacterial and most of the fungal Xylanase, are categorized as true Xylanase belong to GH 10 and GH 11 families. Xylanase is an industrially important enzyme. Most of the research has progressed in the field of isolation, purification and characterization of Xylanases, without giving much emphasis on the interaction of the substrate and the enzyme. To study the structure and ligand interaction, xylanase form Bacillus brevis was modeled, docking studies were performed and ligand interactions were studied. The comparative study gave detailed insight into the conserved amino acids which are involved in ligand interaction and complex stability. The amino acids like Tyrosine, Glutamic acid, Aspartic acid, Aspartate, Arginine play a major role in placing the substrate accurately in the binding cavity; also interact with the ligand for the specific activity. This study clarifies that amino acid Tyros...
Crystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38
Acta crystallographica. Section D, Biological crystallography, 2001
Family 11 endo-beta-1,4-xylanases degrade xylan, the main constituent of plant hemicelluloses, and have many potential uses in biotechnology. The structure of Xyl1, a family 11 endo-xylanase from Streptomyces sp. S38, has been solved. The protein crystallized from ammonium sulfate in the trigonal space group P321, with unit-cell parameters a = b = 71.49, c = 130.30 A, gamma = 120.0 degrees. The structure was solved at 2.0 A by X-ray crystallography using the molecular-replacement method and refined to a final R factor of 18.5% (R(free) = 26.9%). Xyl1 has the overall fold characteristic of family 11 xylanases, with two highly twisted beta-sheets defining a long cleft containing the two catalytic residues Glu87 and Glu177.
Organic & Biomolecular Chemistry, 2009
Molecular dynamics simulations have been performed for non-covalent complexes of phenyl b-xylobioside with the retaining endo-b-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. A trajectory initiated for the wild-type enzyme-substrate complex with the proximal xylose ring bound at the -1 subsite (adjacent to the scissile glycosidic bond) in the 4 C 1 chair conformation shows spontaneous transformation to the 2,5 B boat conformation, and potential of mean force calculations indicate that the boat is~30 kJ mol -1 lower in free energy than the chair. Analogous simulations for the mutant lacking one oxygen atom confirm the key role of Tyr69 in stabilizing the boat in preference to the 4 C 1 chair conformation, with a relative free energy difference of about 20 kJ mol -1 , by donating a hydrogen bond to the endocyclic oxygen of the proximal xylose ring. QM/MM MD simulations for phenyl b-xyloside in water, with and without a propionate/propionic acid pair to mimic the catalytic glutamate/glutamic acid pair of the enzyme, show the 4 C 1 chair to be stable, although a hydrogen bond between the OH group at C2 of xylose and the propionate moiety seems to provide some stabilization for the 2,5 B conformation. Fig. 1 Mechanism of retaining endo-1,4-b-xylanase: catalytic residues are Glu78 and Glu172. (Sugar-ring distortion not shown.) which computational modeling provides a powerful investigative tool. Many modelling studies have confirmed that substrate ring distortion is a common feature among glycosidases. 16-19 Molecular dynamics (MD) simulations have shown that the boat conformation at the -1 subsite is critical in the mechanism of family 18 chitinases, 16 and other studies have demonstrated that the -1 sugar moiety in cellulase Ce16A from Trichoderma reesi adopts a skew-boat conformation. 17 Similarly, modelling 460
Comparative characterization of commercially important xylanase enzymes.
Xylanase is an industrially important enzyme having wide range of applications especially in paper industry. It is crucial to gain an understanding about the structure and functional aspects of various xylanases produced from diverse sources. In this study, a bioinformatics and molecular modeling approach was adopted to explore properties and structure of xylanases. Physico-chemical properties were predicted and prediction of motifs, disulfide bridges and secondary structure was performed for functional characterization. Apart from these analyses, three dimensional structures were constructed and stereo-chemical quality was evaluated by different structure validation tools. Comparative catalytic site analysis and assessment was performed to extract information about the important residues. Asn72 was found to be the common residue in the active sites of the proteins P35809 and Q12603.
We report the crystal structure at 1.59 A Ê and the proposed amino acid sequence of an endo-1,4-b-xylanase (PVX) from the thermophilic fungus Paecilomyces varioti Bainier (PvB), stable up to 75 C. This fungus is attracting clinical attention as a pathogen causing post-surgical infections. Its xylanase, known as a skin-contact allergen, is the ®rst protein from this fungus whose three-dimensional structure has been elucidated. The crystals of PVX conform to the space group P2 1 2 1 2 1 with a 38.76 A Ê , b 54.06 A Ê and c 90.06 A Ê . The structure was solved by molecular replacement techniques using polyalanine coordinates of the Thermomyces lanuginosus xylanase (PDB code 1YNA) and a careful model building based on the amino acid sequence known for two trypsin-digested peptide fragments (17 residues), the sequence and structural alignment of family-11 xylanases and electron density maps. The ®nal re®ned model has 194 amino acid residues and 128 water molecules, with a crystallographic R-factor of 19.07 % and a free R-factor of 21.94 %. The structure belongs to an all-b fold, with two curved b-sheets, forming the cylindrical active-site cleft, and a lone a-helix, as present in other family-11 xylanases. We have carried out a quantitative comparison of the structure and sequence of the present thermophilic xylanase (PVX) with other available native structures of mesophiles and thermophiles, the ®rst such detailed analysis to be carried out on family-11 xylanases. The analysis provides a basis for the rationalisation of the idea that the``hinge'' region is made more compact in thermophiles by the addition of a disulphide bridge between Cys110 and Cys154 and a N-H Á Á ÁO hydrogen bond between Trp159 near the extremity of the lone a-helix and Trp138 on b-strand B8. This work brings out explicitly the presence of the C-H Á Á ÁO and the C-H Á Á Áp type interactions in these enzymes. A complete description of structural stability of these enzymes needs to take account of these weaker interactions.
Structure of xylanase Xys1Δ from Streptomyces halstedii
Acta Crystallographica Section D Biological Crystallography, 2003
Xylanases hydrolyze the -1,4-linked xylose backbone of xylans. They are of increasing interest in the paper and food industries for their pre-bleaching and bio-pulping applications. Such industries demand new xylanases to cover a wider range of cleavage speci®city, activity and stability. The catalytic domain of xylanase Xys1 from Streptomyces halstedii JM8 was expressed, puri®ed and crystallized and native data were collected to 1.78 A Ê resolution with an R merge of 4.4%. The crystals belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 34.05, b = 79.60, c = 87.80 A Ê . The structure was solved by the molecular-replacement method using the structure of the homologue Xyl10A from Streptomyces lividans. In a similar manner to other members of its family, Xys1 folds to form a standard (/) 8 barrel with the two catalytic functions, the acid/base and the nucleophile, at its C-terminal side. The overall structure is described and compared with those of related xylanases.