scholarly journals Crystal structure of inactivated Thermotoga maritima invertase in complex with the trisaccharide substrate raffinose

2006 ◽  
Vol 395 (3) ◽  
pp. 457-462 ◽  
Author(s):  
François Alberto ◽  
Emmanuelle Jordi ◽  
Bernard Henrissat ◽  
Mirjam Czjzek
Keyword(s):  
Crystal Structure ◽  
Catalytic Domain ◽  
Thermotoga Maritima ◽  
Three Dimensional ◽  
Catalytic Efficiency ◽  
Dimensional Structure ◽  
Glycoside Hydrolase Family ◽  
Acid Base ◽  
Hydrolase Family ◽  
Binding Subsites

Thermotoga maritima invertase (β-fructosidase), a member of the glycoside hydrolase family GH-32, readily releases β-D-fructose from sucrose, raffinose and fructan polymers such as inulin. These carbohydrates represent major carbon and energy sources for prokaryotes and eukaryotes. The invertase cleaves β-fructopyranosidic linkages by a double-displacement mechanism, which involves a nucleophilic aspartate and a catalytic glutamic acid acting as a general acid/base. The three-dimensional structure of invertase shows a bimodular enzyme with a five bladed β-propeller catalytic domain linked to a β-sandwich of unknown function. In the present study we report the crystal structure of the inactivated invertase in interaction with the natural substrate molecule α-D-galactopyranosyl-(1,6)-α-D-glucopyranosyl-β-D-fructofuranoside (raffinose) at 1.87 Å (1 Å=0.1 nm) resolution. The structural analysis of the complex reveals the presence of three binding-subsites, which explains why T. maritima invertase exhibits a higher affinity for raffinose than sucrose, but a lower catalytic efficiency with raffinose as substrate than with sucrose.

scholarly journals Crystal structure of GH30-7 endoxylanase C from the filamentous fungus Talaromyces cellulolyticus

2020 ◽  
Vol 76 (8) ◽  
pp. 341-349
Author(s):  
Yusuke Nakamichi ◽  
Tatsuya Fujii ◽  
Masahiro Watanabe ◽  
Akinori Matsushika ◽  
Hiroyuki Inoue
Keyword(s):  
Crystal Structure ◽  
Glucuronic Acid ◽  
Catalytic Domain ◽  
Catalytic Efficiency ◽  
Structural Features ◽  
Hydroxyl Group ◽  
Glycoside Hydrolase Family ◽  
Talaromyces Cellulolyticus ◽  
Cellulose Binding ◽  
Hydrolase Family

GH30-7 endoxylanase C from the cellulolytic fungus Talaromyces cellulolyticus (TcXyn30C) belongs to glycoside hydrolase family 30 subfamily 7, and specifically releases 22-(4-O-methyl-α-D-glucuronosyl)-xylobiose from glucuronoxylan, as well as various arabino-xylooligosaccharides from arabinoxylan. TcXyn30C has a modular structure consisting of a catalytic domain and a C-terminal cellulose-binding module 1 (CBM1). In this study, the crystal structure of a TcXyn30C mutant which lacks the CBM1 domain was determined at 1.65 Å resolution. The structure of the active site of TcXyn30C was compared with that of the bifunctional GH30-7 xylanase B from T. cellulolyticus (TcXyn30B), which exhibits glucuronoxylanase and xylobiohydrolase activities. The results revealed that TcXyn30C has a conserved structural feature for recognizing the 4-O-methyl-α-D-glucuronic acid (MeGlcA) substituent in subsite −2b. Additionally, the results demonstrated that Phe47 contributes significantly to catalysis by TcXyn30C. Phe47 is located in subsite −2b and also near the C-3 hydroxyl group of a xylose residue in subsite −2a. Substitution of Phe47 with an arginine residue caused a remarkable decrease in the catalytic efficiency towards arabinoxylan, suggesting the importance of Phe47 in arabinoxylan hydrolysis. These findings indicate that subsite −2b of TcXyn30C has unique structural features that interact with arabinofuranose and MeGlcA substituents.

The first crystal structure of the peptidase domain of the U32 peptidase family

2015 ◽  
Vol 71 (12) ◽  
pp. 2505-2512 ◽  
Author(s):  
Magdalena Schacherl ◽  
Angelika A. M. Montada ◽  
Elena Brunstein ◽  
Ulrich Baumann
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Quaternary Structure ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Zinc Ion ◽  
Crystal Structure Analysis ◽  
Dimensional Structure ◽  
Sequence Motifs ◽  
Conserved Sequence

The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins fromHelicobacterandSalmonella. The first crystal structure analysis of a U32 catalytic domain fromMethanopyrus kandleri(genemk0906) reveals a modified (βα)8TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to aStrep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.

scholarly journals Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121

2020 ◽  
Author(s):  
Keita Saito ◽  
Alexander Holm Viborg ◽  
Shiho Sakamoto ◽  
Takatoshi Arakawa ◽  
Chihaya Yamada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Glycoside Hydrolase ◽  
Plant Pathogens ◽  
Catalytic Domain ◽  
Bifidobacterium Longum ◽  
Degradation Pathway ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Glycoside Hydrolase Family ◽  
Import System

AbstractEnzymes acting on α-L-arabinofuranosides have been extensively studied; however, the structures and functions of β-L-arabinofuranosidases are not fully understood. Three enzymes and an ABC transporter in a gene cluster of Bifidobacterium longum JCM 1217 constitute a degradation and import system of β-L-arabinooligosaccharides on plant hydroxyproline-rich glycoproteins. An extracellular β-L-arabinobiosidase (HypBA2) belonging to the glycoside hydrolase (GH) family 121 plays a key role in the degradation pathway by releasing β-1,2-linked arabinofuranose disaccharide (β-Ara2) for the specific sugar importer. Here, we present the crystal structure of the catalytic region of HypBA2 as the first three-dimensional structure of GH121 at 1.85 Å resolution. The HypBA2 structure consists of a central catalytic (α/α)6 barrel domain and two flanking (N- and C-terminal) β-sandwich domains. A pocket in the catalytic domain appears to be suitable for accommodating the β-Ara2 disaccharide; this pocket is highly conserved among GH121 proteins. The three acidic residues Glu383, Asp515, and Glu713, located in this pocket, are completely conserved among all ~270 members of GH121; site-directed mutagenesis analysis showed that they are essential for catalytic activity. The active site of HypBA2 was compared with those of GH63 α-glycosidase, GH94 chitobiose phosphorylase, GH142 β-L-arabinofuranosidase, GH78 α-L-rhamnosidase, and GH37 α,α-trehalase. Based on these analyses, we concluded that the three conserved residues are essential for catalysis and substrate binding. β-L-Arabinobiosidase genes in GH121 are mainly found in the genomes of bifidobacteria and Xanthomonas species, suggesting that the cleavage and specific import system for the β-Ara2 disaccharide on plant hydroxyproline-rich glycoproteins are shared in animal gut symbionts and plant pathogens.

scholarly journals High Resolution Crystal Structure of the Catalytic Domain of ADAMTS-5 (Aggrecanase-2)

2007 ◽  
Vol 283 (3) ◽  
pp. 1501-1507 ◽  
Author(s):  
Huey-Sheng Shieh ◽  
Karl J. Mathis ◽  
Jennifer M. Williams ◽  
Robert L. Hills ◽  
Joe F. Wiese ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Direct Role ◽  
Three Dimensional Structure ◽  
High Resolution Structure ◽  
A Disintegrin And Metalloproteinase ◽  
Resolution Structure

Aggrecanase-2 (a disintegrin and metalloproteinase with thrombospondin motifs-5 (ADAMTS-5)), a member of the ADAMTS protein family, is critically involved in arthritic diseases because of its direct role in cleaving the cartilage component aggrecan. The catalytic domain of aggrecanase-2 has been refolded, purified, and crystallized, and its three-dimensional structure determined to 1.4Å resolution in the presence of an inhibitor. A high resolution structure of an ADAMTS/aggrecanase protein provides an opportunity for the development of therapeutics to treat osteoarthritis.

scholarly journals Three-dimensional structures of two heavily N-glycosylatedAspergillussp. family GH3 β-D-glucosidases

2016 ◽  
Vol 72 (2) ◽  
pp. 254-265 ◽  
Author(s):  
Jon Agirre ◽  
Antonio Ariza ◽  
Wendy A. Offen ◽  
Johan P. Turkenburg ◽  
Shirley M. Roberts ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Plant Biomass ◽  
Minimum Energy ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Product Inhibition ◽  
Dimensional Structure ◽  
Glycoside Hydrolase Family ◽  
Major Drawback ◽  
Polysaccharide Monooxygenases

The industrial conversion of cellulosic plant biomass into useful products such as biofuels is a major societal goal. These technologies harness diverse plant degrading enzymes, classical exo- and endo-acting cellulases and, increasingly, cellulose-active lytic polysaccharide monooxygenases, to deconstruct the recalcitrant β-D-linked polysaccharide. A major drawback with this process is that the exo-acting cellobiohydrolases suffer from severe inhibition from their cellobiose product. β-D-Glucosidases are therefore important for liberating glucose from cellobiose and thereby relieving limiting product inhibition. Here, the three-dimensional structures of two industrially important family GH3 β-D-glucosidases fromAspergillus fumigatusandA. oryzae, solved by molecular replacement and refined at 1.95 Å resolution, are reported. Both enzymes, which share 78% sequence identity, display a three-domain structure with the catalytic domain at the interface, as originally shown for barley β-D-glucan exohydrolase, the first three-dimensional structure solved from glycoside hydrolase family GH3. Both enzymes show extensive N-glycosylation, with only a few external sites being truncated to a single GlcNAc molecule. Those glycans N-linked to the core of the structure are identified purely as high-mannose trees, and establish multiple hydrogen bonds between their sugar components and adjacent protein side chains. The extensive glycans pose special problems for crystallographic refinement, and new techniques and protocols were developed especially for this work. These protocols ensured that all of the D-pyranosides in the glycosylation trees were modelled in the preferred minimum-energy4C1chair conformation and should be of general application to refinements of other crystal structures containing O- or N-glycosylation. TheAspergillusGH3 structures, in light of other recent three-dimensional structures, provide insight into fungal β-D-glucosidases and provide a platform on which to inform and inspire new generations of variant enzymes for industrial application.

scholarly journals Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus

2005 ◽  
Vol 390 (1) ◽  
pp. 19-27 ◽  
Author(s):  
Carlos Martínez-Fleites ◽  
Miguel Ortíz-Lombardía ◽  
Tirso Pons ◽  
Nicolas Tarbouriech ◽  
Edward J. Taylor ◽  
...  
Keyword(s):  
Thermotoga Maritima ◽  
Three Dimensional ◽  
Data Bank ◽  
Dimensional Structure ◽  
Glycoside Hydrolase Family ◽  
Gluconacetobacter Diazotrophicus ◽  
Negative Bacterium ◽  
Sucrose Hydrolysis ◽  
Gram Negative ◽  
X Ray Crystallography

The endophytic Gram-negative bacterium Gluconacetobacter diazotrophicus SRT4 secretes a constitutively expressed levansucrase (LsdA, EC 2.4.1.10), which converts sucrose into fructooligosaccharides and levan. The enzyme is included in GH (glycoside hydrolase) family 68 of the sequence-based classification of glycosidases. The three-dimensional structure of LsdA has been determined by X-ray crystallography at a resolution of 2.5 Å (1 Å=0.1 nm). The structure was solved by molecular replacement using the homologous Bacillus subtilis (Bs) levansucrase (Protein Data Bank accession code 1OYG) as a search model. LsdA displays a five-bladed β-propeller architecture, where the catalytic residues that are responsible for sucrose hydrolysis are perfectly superimposable with the equivalent residues of the Bs homologue. The comparison of both structures, the mutagenesis data and the analysis of GH68 family multiple sequences alignment show a strong conservation of the sucrose hydrolytic machinery among levansucrases and also a structural equivalence of the Bs levansucrase Ca2+-binding site to the LsdA Cys339–Cys395 disulphide bridge, suggesting similar fold-stabilizing roles. Despite the strong conservation of the sucrose-recognition site observed in LsdA, Bs levansucrase and GH32 family Thermotoga maritima invertase, structural differences appear around residues involved in the transfructosylation reaction.

Three-Dimensional Structure of an Intact Glycoside Hydrolase Family 15 Glucoamylase fromHypocrea jecorina

Biochemistry ◽  
2008 ◽  
Vol 47 (21) ◽  
pp. 5746-5754 ◽  
Author(s):  
Richard Bott ◽  
Mae Saldajeno ◽  
William Cuevas ◽  
Donald Ward ◽  
Martijn Scheffers ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Glycoside Hydrolase Family ◽  
Three Dimensional Structure ◽  
Hydrolase Family

A new three-dimensional anionic cadmium(II) dicyanamide network

2014 ◽  
Vol 70 (11) ◽  
pp. 1054-1056 ◽  
Author(s):  
Qiang Li ◽  
Hui-Ting Wang
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Unit Cell Volume ◽  
Three Dimensional ◽  
Building Blocks ◽  
The Other ◽  
Dimensional Structure ◽  
Cadmium Nitrate ◽  
Nitrate Tetrahydrate ◽  
Anionic Framework

A new cadmium dicyanamide complex, poly[tetramethylphosphonium [μ-chlorido-di-μ-dicyanamido-κ4N1:N5-cadmium(II)]], [(CH3)4P][Cd(NCNCN)2Cl], was synthesized by the reaction of tetramethylphosphonium chloride, cadmium nitrate tetrahydrate and sodium dicyanamide in aqueous solution. In the crystal structure, each CdIIatom is octahedrally coordinated by four terminal N atoms from four anionic dicyanamide (dca) ligands and by two chloride ligands. The dicyanamide ligands play two different roles in the building up of the structure; one role results in the formation of [Cd(dca)Cl]2building blocks, while the other links the building blocks into a three-dimensional structure. The anionic framework exhibits a solvent-accessible void of 673.8 Å3, amounting to 47.44% of the total unit-cell volume. The cavities in the network are occupied by pairs of tetramethylphosphonium cations.

scholarly journals Crystal structure of 2-benzylamino-4-(4-methoxyphenyl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile

2014 ◽  
Vol 70 (12) ◽  
pp. 525-527 ◽  
Author(s):  
R. A. Nagalakshmi ◽  
J. Suresh ◽  
S. Maharani ◽  
R. Ranjith Kumar ◽  
P. L. Nilantha Lakshman
Keyword(s):  
Crystal Structure ◽  
Pyridine Ring ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Dimensional Structure ◽  
Compound C ◽  
Centroid Distance ◽  
Steric Crowding ◽  
Benzene Rings ◽  
Group A

The title compound, C25H25N3O, comprises a 2-aminopyridine ring fused with a cycloheptane ring, which adopts a chair conformation. The central pyridine ring (r.m.s. deviation = 0.013 Å) carries three substituents,viz.a benzylamino group, a methoxyphenyl ring and a carbonitrile group. The N atom of the carbonitrile group is significantly displaced [by 0.2247 (1) Å] from the plane of the pyridine ring, probably due to steric crowding involving the adjacent substituents. The phenyl and benzene rings are inclined to one another by 58.91 (7)° and to the pyridine ring by 76.68 (7) and 49.80 (6)°, respectively. In the crystal, inversion dimers linked by pairs of N—H...Nnitrilehydrogen bonds generateR22(14) loops. The dimers are linked by C—H...π and slipped parallel π–π interactions [centroid–centroid distance = 3.6532 (3) Å] into a three-dimensional structure.

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