scholarly journals Factor G Utilizes a Carbohydrate-Binding Cleft That Is Conserved between Horseshoe Crab and Bacteria for the Recognition of β-1,3-d-Glucans

2009 ◽  
Vol 183 (6) ◽  
pp. 3810-3818 ◽  
Author(s):  
Yuki Ueda ◽  
Shuhei Ohwada ◽  
Yoshito Abe ◽  
Toshio Shibata ◽  
Manabu Iijima ◽  
...  
Keyword(s):  
Horseshoe Crab ◽  
Carbohydrate Binding ◽  
Binding Cleft ◽  
Factor G

scholarly journals Deamidation and glycation of a Bacillus licheniformis α-amylase during industrial fermentation can improve detergent wash performance

Amylase ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 38-49
Author(s):  
Connie Pontoppidan ◽  
Svend G. Kaasgaard ◽  
Carsten P. Sønksen ◽  
Carsten Andersen ◽  
Birte Svensson
Keyword(s):  
Bacillus Licheniformis ◽  
Mutational Analysis ◽  
Peptide Mapping ◽  
Substrate Binding ◽  
Carbohydrate Binding ◽  
Surface Binding ◽  
Lysine Residues ◽  
Tandem Mass Spectrometric ◽  
Binding Cleft ◽  
Household Detergents

Abstract The industrial thermostable Bacillus licheniformis α-amylase (BLA) has wide applications, including in household detergents, and efforts to improve its performance are continuously ongoing. BLA during the industrial production is deamidated and glycated resulting in multiple forms with different isoelectric points. Forty modified positions were identified by tandem mass spectrometric peptide mapping of BLA forms separated by isoelectric focusing. These modified 12 asparagine, 9 glutamine, 8 arginine and 11 lysine residues are mostly situated on the enzyme surface and several belong to regions involved in stability, activity and carbohydrate binding. Eight residues presumed to interact with starch at the active site and surface binding sites (SBSs) were subjected to mutational analysis. Five mutants mimicking deamidation (N→D, Q→E) at the substrate binding cleft showed moderate to no effect on thermostability and k cat and K M for maltoheptaose and amylose. Notably, the mutations improved laundry wash efficiency in detergents at pH 8.5 and 10.0. Replacing three reducing sugar reactive side chains (K→M, R→L) at a distant substrate binding region and two SBSs enhanced wash performance especially in liquid detergent at pH 8.5, slightly improved enzymatic activity and maintained thermostability. Wash performance was most improved (5-fold) for the N265D mutant near substrate binding subsite +3.

scholarly journals Spatially remote motifs cooperatively affect substrate preference of a ruminal GH26-type endo-β-1,4-mannanase

2020 ◽  
Vol 295 (15) ◽  
pp. 5012-5021 ◽  
Author(s):  
Fernanda Mandelli ◽  
Mariana Abrahão Bueno de Morais ◽  
Evandro Antonio de Lima ◽  
Leane Oliveira ◽  
Gabriela Felix Persinoti ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Substrate Binding ◽  
Substrate Recognition ◽  
Systematic Investigation ◽  
Substrate Preference ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
Binding Cleft ◽  
Aromatic Cluster ◽  
Shed Light

β-Mannanases from the glycoside hydrolase 26 (GH26) family are retaining hydrolases that are active on complex heteromannans and whose genes are abundant in rumen metagenomes and metatranscriptomes. These enzymes can exhibit distinct modes of substrate recognition and are often fused to carbohydrate-binding modules (CBMs), resulting in a molecular puzzle of mechanisms governing substrate preference and mode of action that has not yet been pieced together. In this study, we recovered a novel GH26 enzyme with a CBM35 module linked to its N terminus (CrMan26) from a cattle rumen metatranscriptome. CrMan26 exhibited a preference for galactomannan as substrate and the crystal structure of the full-length protein at 1.85 Å resolution revealed a unique orientation of the ancillary domain relative to the catalytic interface, strategically positioning a surface aromatic cluster of the ancillary domain as an extension of the substrate-binding cleft, contributing to galactomannan preference. Moreover, systematic investigation of nonconserved residues in the catalytic interface unveiled that residues Tyr195 (−3 subsite) and Trp234 (−5 subsite) from distal negative subsites have a key role in galactomannan preference. These results indicate a novel and complex mechanism for substrate recognition involving spatially remote motifs, distal negative subsites from the catalytic domain, and a surface-associated aromatic cluster from the ancillary domain. These findings expand our molecular understanding of the mechanisms of substrate binding and recognition in the GH26 family and shed light on how some CBMs and their respective orientation can contribute to substrate preference.

scholarly journals The substrate/product-binding modes of a novel GH120 β-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485

2012 ◽  
Vol 448 (3) ◽  
pp. 401-407 ◽  
Author(s):  
Chun-Hsiang Huang ◽  
Yu Sun ◽  
Tzu-Ping Ko ◽  
Chun-Chi Chen ◽  
Yingying Zheng ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Product Inhibition ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Binding Modes ◽  
Glycosyl Hydrolases ◽  
Core Domain ◽  
Thermoanaerobacterium Saccharolyticum ◽  
Cazy Database ◽  
Binding Cleft

Xylan-1,4-β-xylosidase (β-xylosidase) hydrolyses xylo-oligomers at their non-reducing ends into individual xylose units. Recently, XylC, a β-xylosidase from Thermoanaerobacterium saccharolyticum JW/SL-YS485, was found to be structurally different from corresponding glycosyl hydrolases in the CAZy database (http://www.cazy.org/), and was subsequently classified as the first member of a novel family of glycoside hydrolases (GH120). In the present paper, we report three crystal structures of XylC in complex with Tris, xylobiose and xylose at 1.48–2.05 Å (1 Å=0.1 nm) resolution. XylC assembles into a tetramer, and each monomer comprises two distinct domains. The core domain is a right-handed parallel β-helix (residues 1–75 and 201–638) and the flanking region (residues 76–200) folds into a β-sandwich domain. The enzyme contains an open carbohydrate-binding cleft, allowing accommodation of longer xylo-oligosaccharides. On the basis of the crystal structures and in agreement with previous kinetic data, we propose that XylC cleaves the glycosidic bond by the retaining mechanism using two acidic residues Asp382 (nucleophile) and Glu405 (general acid/base). In addition to the active site, nine other xylose-binding sites were consistently observed in each of the four monomers, providing a possible reason for the high tolerance of product inhibition.

scholarly journals Purified Horseshoe Crab Factor G

1995 ◽  
Vol 270 (2) ◽  
pp. 892-897 ◽  
Author(s):  
Tatsushi Muta ◽  
Noriaki Seki ◽  
Yoshie Takaki ◽  
Ryuji Hashimoto ◽  
Toshio Oda ◽  
...  
Keyword(s):  
Horseshoe Crab ◽  
Factor G

Horseshoe Crab Factor G: A New Heterodimeric Serine Protease Zymogen Sensitive to (1→3)-β-D-Glucan

1996 ◽  
pp. 79-85 ◽  
Author(s):  
Tatsushi Muta ◽  
Noriaki Seki ◽  
Yoshie Takaki ◽  
Ryuji Hashimoto ◽  
Toshio Oda ◽  
...  
Keyword(s):  
Serine Protease ◽  
Horseshoe Crab ◽  
Factor G

Carbohydrate-binding architecture of the multi-modular α-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces α-1,6-glucosyl-α-glucosaccharides from starch

2017 ◽  
Vol 474 (16) ◽  
pp. 2763-2778 ◽  
Author(s):  
Zui Fujimoto ◽  
Nobuhiro Suzuki ◽  
Naomi Kishine ◽  
Hitomi Ichinose ◽  
Mitsuru Momma ◽  
...  
Keyword(s):  
Binding Pocket ◽  
Binding Mode ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Surface Binding ◽  
Glucose Binding ◽  
Carbohydrate Binding Modules ◽  
Paenibacillus Sp ◽  
Binding Cleft ◽  
Catalytic Cleft

Paenibacillus sp. 598K α-1,6-glucosyltransferase (Ps6TG31A), a member of glycoside hydrolase family 31, catalyzes exo-α-glucohydrolysis and transglucosylation and produces α-1,6-glucosyl-α-glucosaccharides from α-glucan via its disproportionation activity. The crystal structure of Ps6TG31A was determined by an anomalous dispersion method using a terbium derivative. The monomeric Ps6TG31A consisted of one catalytic (β/α)8-barrel domain and six small domains, one on the N-terminal and five on the C-terminal side. The structures of the enzyme complexed with maltohexaose, isomaltohexaose, and acarbose demonstrated that the ligands were observed in the catalytic cleft and the sugar-binding sites of four β-domains. The catalytic site was structured by a glucose-binding pocket and an aglycon-binding cleft built by two sidewalls. The bound acarbose was located with its non-reducing end pseudosugar docked in the pocket, and the other moieties along one sidewall serving three subsites for the α-1,4-glucan. The bound isomaltooligosaccharide was found on the opposite sidewall, which provided the space for the acceptor molecule to be positioned for attack of the catalytic intermediate covalent complex during transglucosylation. The N-terminal domain recognized the α-1,4-glucan in a surface-binding mode. Two of the five C-terminal domains belong to the carbohydrate-binding modules family 35 and one to family 61. The sugar complex structures indicated that the first family 35 module preferred α-1,6-glucan, whereas the second family 35 module and family 61 module preferred α-1,4-glucan. Ps6TG31A appears to have enhanced transglucosylation activity facilitated by its carbohydrate-binding modules and substrate-binding cleft that positions the substrate and acceptor sugar for the transglucosylation.

scholarly journals Duplicated Binding Sites for (1→3)-β-d-Glucan in the Horseshoe Crab Coagulation Factor G

2002 ◽  
Vol 277 (16) ◽  
pp. 14281-14287 ◽  
Author(s):  
Yoshie Takaki ◽  
Noriaki Seki ◽  
Shun-ichiro Kawabata ◽  
Sadaaki Iwanaga ◽  
Tatsushi Muta
Keyword(s):  
Binding Sites ◽  
Horseshoe Crab ◽  
Coagulation Factor ◽  
Factor G

Effects on sialic acid recognition of amino acid mutations in the carbohydrate-binding cleft of the rotavirus spike protein

Glycobiology ◽  
2008 ◽  
Vol 19 (3) ◽  
pp. 194-200 ◽  
Author(s):  
Mark J. Kraschnefski ◽  
Andrea Bugarcic ◽  
Fiona E. Fleming ◽  
Xing Yu ◽  
Mark von Itzstein ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Amino Acid ◽  
Spike Protein ◽  
Carbohydrate Binding ◽  
Amino Acid Mutations ◽  
Binding Cleft
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