ABSTRACT
The thermostable endo-1,5-α-L-arabinanase from Bacillus thermodenitrificans TS-3 (ABN-TS) hydrolyzes the α-1,5-L-arabinofuranoside linkages of arabinan. In this study, the crystal structures of inactive ABN-TS mutants, D27A and D147N, were determined in complex with arabino-oligosaccharides. The crystal structures revealed that ABN-TS has at least six subsites in the deep V-shaped cleft formed across one face of the propeller structure. The structural features indicate that substrate recognition is profoundly influenced by the remote subsites as well as by the subsites surrounding the active center. The `open' structure of the substrate-binding cleft of the endo-acting ABN-TS is suitable for the random binding of several sugar units in polymeric substrates.
Subject(s)
Bacillus/chemistry , Glycoside Hydrolases/chemistry , Mutation , Oligosaccharides/chemistry , Polysaccharides/chemistry , Amino Acid Sequence , Bacillus/genetics , Bacillus/metabolism , Crystallization/methods , Crystallography, X-Ray/methods , Glycoside Hydrolases/genetics , Glycoside Hydrolases/metabolism , Mutation/physiology , Oligosaccharides/genetics , Oligosaccharides/metabolism , Polysaccharides/genetics , Polysaccharides/metabolism , Protein Structure, Secondary , Protein Structure, TertiaryABSTRACT
The crystal structure of a thermostable endo-1,5-alpha-L-arabinanase, ABN-TS, from Bacillus thermodenitrificans TS-3 was determined at 1.9 A to an R-factor of 18.3% and an R-free-factor of 22.5%. The enzyme molecule has a five-bladed beta-propeller fold. The substrate-binding cleft formed across one face of the propeller is open on both sides to allow random binding of several sugar units in the polymeric substrate arabinan. The beta-propeller fold is stabilized through a ring closure. ABN-TS exhibits a new closure-mode involving residues in the N-terminal region: Phe7 to Gly21 exhibit hydrogen bonds and hydrophobic interactions with the first and last blades, and Phe4 links the second and third blades through a hydrogen bond and an aromatic stacking interaction, respectively. The role of the N-terminal region in the thermostability was confirmed with a mutant lacking 16 amino acid residues from the N-terminus of ABN-TS.
Subject(s)
Enzyme Stability , Glycoside Hydrolases/chemistry , Bacillus/enzymology , Crystallography, X-Ray , Glycoside Hydrolases/genetics , Hot Temperature , Models, Molecular , Protein Structure, QuaternaryABSTRACT
A thermostable endo-1,5-alpha-L-arabinanase ABN-TS from Bacillus thermodenitrificans TS-3 with a molecular weight of 35 kDa was crystallized by the hanging-drop vapour-diffusion method using sodium citrate as a precipitant. The crystals were loop-mounted in a cryoprotectant solution containing 28%(w/v) sucrose and 1 M sodium citrate pH 6.0 and flash-cooled. Sucrose was selected as the most suitable cryoprotectant. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 40.3, b = 77.8, c = 89.7 angstroms. The calculated VM based on one molecule per asymmetric unit was 2.0 angstroms3 Da(-1). A complete data set from a frozen crystal was collected to 1.9 angstroms resolution using synchrotron radiation at SPring-8. A molecular-replacement solution was obtained using the structure of alpha-arabinanase 43A from Cellvibrio japonicus.
Subject(s)
Bacillus/enzymology , Glycoside Hydrolases/chemistry , X-Ray Diffraction/methods , Cellvibrio/metabolism , Citrates/chemistry , Citrates/pharmacology , Crystallization , Crystallography, X-Ray/methods , Glycerol/chemistry , Kinetics , Sodium Citrate , Sucrose/chemistry , Sucrose/pharmacologyABSTRACT
The thermostable pectate lyase PL 47 from Bacillus sp. TS 47, with a molecular weight of 50 kDa, was crystallized by the hanging-drop vapour-diffusion method using 2-propanol and polyethylene glycol 4000 as precipitants. The crystals belong to the trigonal space group P3(1)21, with unit-cell parameters a = b = 58.8, c = 229.7 A, gamma = 120 degrees. The calculated V(M) based on one molecule per asymmetric unit is 2.30 A(3) Da(-1). A native data set from a frozen crystal was collected to 1.8 A resolution using synchrotron radiation at SPring-8. A molecular-replacement solution was obtained using the structure of pectate lyase from B. subtilis as a model.
Subject(s)
Bacillus/enzymology , Polysaccharide-Lyases/chemistry , Crystallization/methods , Crystallography, X-Ray , Enzyme Stability , Hot Temperature , Polysaccharide-Lyases/genetics , SynchrotronsABSTRACT
The gene that encodes a thermostable endo-arabinase (called ABN-TS) from Bacillus thermodenitrificans TS-3 was cloned, sequenced, and expressed in the mesophilic B. subtilis. The gene contained an open reading frame consists of 939 bp, which encodes 313 amino acids. The deduced amino acid sequence of the enzyme showed 50, 46, and 36% similarity with endo-arabinase from B. subtilis IFO 3134 (PPase-C), Pseudomonas fluorescens (ArbA), and Aspergillus niger (ABNA), respectively. The hydrophobic and acidic amino acids making up ABN-TS outnumbered those in PPase-C. The gene product expressed in B. subtilis, as the host, had substantially the same characteristics, and was stable up to 70 degrees C, and the reaction was optimal around 70 degrees C, as well as native ABN-TS.
Subject(s)
Bacillus/enzymology , Glycoside Hydrolases/genetics , Amino Acid Sequence , Bacillus/genetics , Base Sequence , Cloning, Molecular , Enzyme Stability , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/metabolism , Molecular Sequence Data , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Homology, Amino AcidABSTRACT
A strain of a thermophilic bacterium, tentatively designated Bacillus thermodenitrificans TS-3, with arabinan-degrading activity was isolated. It produced an endo-arabinase (ABN) (EC 3.2.1.99) and two arabinofuranosidases (EC 3.2.1.55) extracellularly when grown at 60 degrees C on a medium containing sugar beet arabinan. The ABN (tentatively called an ABN-TS) was purified 7,417-fold by anion-exchange, hydrophobic, size exclusion, and hydroxyapatite chromatographies. The molecular mass of ABN-TS was 35 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the isoelectric point was pH 4.5. The enzyme was observed to be more thermostable than known ABNs; it had a half-life of 4 h at 75 degrees C. The enzyme had optimal activity at 70 degrees C and pH 6.0. The enzyme had apparent K(m) values of 8.5 and 45 mg/ml and apparent V(max) values of 1.6 and 1.1 mmol/min/mg of protein against debranched arabinan (alpha-1,5-arabinan) and arabinan, respectively. The enzyme had no pectin-releasing activity (protopectinase activity) from sugar beet protopectin, differing from an ABN (protopectinase-C) from mesophilic Bacillus subtilis IFO 3134. The pattern of degradation of debranched arabinan by ABN-TS indicated that the enzyme was an endo-acting enzyme and the main end products were arabinobiose and arabinose. The results of preliminary experiments indicated that the culture filtrate of strain TS-3 is suitable for L-arabinose production from sugar beet pulp at high temperature.
Subject(s)
Bacillus/enzymology , Glycoside Hydrolases , Bacillus/growth & development , Enzyme Stability , Genes, rRNA , Glycoside Hydrolases/chemistry , Glycoside Hydrolases/genetics , Glycoside Hydrolases/isolation & purification , Glycoside Hydrolases/metabolism , Hot Temperature , Kinetics , Molecular Sequence Data , Polysaccharides/metabolism , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Substrate SpecificityABSTRACT
A protopectinase (PPase)-encoding gene, PSE3, from Trichosporon penicillatum was cloned by colony hybridization using two oligonucleotide probes synthesized from the N-terminal amino acid sequences of native PPase SE1 and one peptide from a lysyl endopeptidase digest. Nucleotide sequencing revealed that PSE3 contains an ORF encoding a 367 amino acid protein. Mature PPase SE3 is composed of 340 amino acids and the N-terminus of the ORF appeared to correspond to a signal peptide and a propeptide processed by a KEX2-like proteinase. The deduced amino acid sequence of PSE3 was 65.4, 56.7, 58.1, 61.8 and 48.9% homologous to the polygalacturonases of Aspergillus oryzae, Aspergillus niger, Aspergillus tubigensis, Cochliobolus carbonum and Fusarium moniliforme, respectively. One domain, which might interact with polygalacturonic acid, is highly conserved not only in fungal polygalacturonases but also in bacterial and plant polygalacturonases. PSE3 was expressed in Saccharomyces cerevisiae, but three forms (the mature form, a glycosylated form and an uncharacterized processed form) of PPase SE3 were present among the PSE3 products.