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Score: 10.00
Title: Characterization of beta-glucosidase from a strain of Penicillium purpurogenum KJS506 .
Journal: Appl Microbiol Biotechnol Year: 2010 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub20043150 Accession (PMID): 20043150
Abstract: A novel beta-glucosidase ( BGL ) -producing strain was isolated and identified as Penicillium purpurogenum KJS506 based on its morphology and internal transcribed spacer ( ITS ) rDNA gene sequence . When rice straw and corn steep powder were used as carbon and nitrogen sources , respectively , the maximal BGL activity of 12 . 3 U ml ( -1 ) , one of the highest levels among BGL-producing microorganisms was observed . The optimum temperature and pH for BGL production were 32 degrees C and 4 , respectively . An extracellular BGL was purified to homogeneity by sequential chromatography of P purpurogenum culture supernatants , and the purified BGL showed higher activity ( V ( max ) = 934 U mg protein ( -1 ) ) than most BGLs from other sources . The complete ORF of bgl3 was cloned from P purpurogenum by a modified thermal asymmetric interlaced polymerase chain reaction . The bgl3 gene consists of a 2 , 571-bp ORF and encodes a putative protein containing 856 amino acids with a calculated molecular mass of 89 , 624 Da . The putative gene product was identified as a member of glycoside hydrolase family 3 . The present results should contribute to improved industrial production of BGL by P purpurogenum KJS506 .
Matching Sentences:
[ Sen. 4, subscore: 3.00 ]: An extracellular BGL was purified to homogeneity by sequential chromatography of P purpurogenum culture supernatants , and the purified BGL showed higher activity ( V ( max ) = 934 U mg protein ( -1 ) ) than most BGLs from other sources .
[ Sen. 2, subscore: 2.00 ]: When rice straw and corn steep powder were used as carbon and nitrogen sources , respectively , the maximal BGL activity of 12 . 3 U ml ( -1 ) , one of the highest levels among BGL-producing microorganisms was observed .
[ Sen. 1, subscore: 1.00 ]: A novel beta-glucosidase ( BGL ) -producing strain was isolated and identified as Penicillium purpurogenum KJS506 based on its morphology and internal transcribed spacer ( ITS ) rDNA gene sequence .
[ Sen. 3, subscore: 1.00 ]: The optimum temperature and pH for BGL production were 32 degrees C and 4 , respectively .
[ Sen. 5, subscore: 1.00 ]: The complete ORF of bgl3 was cloned from P purpurogenum by a modified thermal asymmetric interlaced polymerase chain reaction .
[ Sen. 6, subscore: 1.00 ]: The bgl3 gene consists of a 2 , 571-bp ORF and encodes a putative protein containing 856 amino acids with a calculated molecular mass of 89 , 624 Da .
[ Sen. 8, subscore: 1.00 ]: The present results should contribute to improved industrial production of BGL by P purpurogenum KJS506 .
Score: 7.00
Title: Rice BGlu1 glycosynthase and wild type transglycosylation activities distinguished by cyclophellitol inhibition .
Journal: Carbohydr Res Year: 2012 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub22418094 Accession (PMID): 22418094
Abstract: The rice BGlu1 beta-D-glucosidase nucleophile mutant E386G is a glycosynthase that catalyzes the synthesis of cellooligosaccharides from alpha-d-glucopyranosyl fluoride ( GlcF ) donor and p-nitrophenyl ( pNP ) cellobioside ( Glc2-pNP ) or cello-oligosaccharide acceptors . When activity with other donors and acceptors was tested , the initial enzyme preparation cleaved pNP-beta-D-glucopyranoside ( Glc-pNP ) and pNP-beta-D-fucopyranoside ( Fuc-pNP ) to pNP and glucose and fucose , suggesting contamination with wild type BGlu1 beta-glucosidase . The products from reaction of GlcF and Fuc-pNP included Fuc-beta- ( 1-->3 ) -Fuc-pNP , Glc-beta- ( 1-->3 ) -Fuc-pNP , and Fuc-beta- ( 1-->4 ) -Glc-beta- ( 1-->3 ) -Fuc-pNP , suggesting the presence of both wild type BGlu1 and its glycosynthase . Inhibition of the BGlu1 beta-glucosidase activity within this preparation by cyclophellitol confirmed that the E386G glycosynthase preparation was contaminated with wild type BGlu1 . Rice BGlu1 E386G-2 , generated from a new construct designed to minimize back-mutation , showed glycosynthase activity without wild type hydrolytic or transglycosylation activity . E386G-2 catalyzed transfer of glycosyl residues from GlcF , alpha-L-arabinosyl fluoride , alpha-D-fucosyl fluoride , alpha-D-galactosyl fluoride , alpha-D-mannosyl fluoride , and alpha-D-xylosyl fluoride donors to Glc2-pNP acceptor . The synthetic products from the reactions of alpha-fucosyl fluoride and alpha-mannosyl fluoride donors were confirmed to result from addition of a beta- ( 1-->4 ) -linked glycosyl residue . Moreover , the E386G glycosynthase transferred glucose from GlcF donor to glucose , cellobiose , Glc-pNP , Fuc-pNP , pNP-beta-D-galactopyranoside , and pNP-beta-D-xylopyranoside acceptors , but little to pNP-beta-D-mannopyranoside . Production of longer oligosaccharides occurred most readily on acceptors with an equatorial 4-OH . Elimination of wild type contamination thereby allowed a clear assessment of BGlu1 E386G glycosynthase catalytic abilities .
Matching Sentences:
[ Sen. 4, subscore: 2.00 ]: Inhibition of the BGlu1 beta-glucosidase activity within this preparation by cyclophellitol confirmed that the E386G glycosynthase preparation was contaminated with wild type BGlu1 .
[ Sen. 1, subscore: 1.00 ]: The rice BGlu1 beta-D-glucosidase nucleophile mutant E386G is a glycosynthase that catalyzes the synthesis of cellooligosaccharides from alpha-d-glucopyranosyl fluoride ( GlcF ) donor and p-nitrophenyl ( pNP ) cellobioside ( Glc2-pNP ) or cello-oligosaccharide acceptors .
[ Sen. 2, subscore: 1.00 ]: When activity with other donors and acceptors was tested , the initial enzyme preparation cleaved pNP-beta-D-glucopyranoside ( Glc-pNP ) and pNP-beta-D-fucopyranoside ( Fuc-pNP ) to pNP and glucose and fucose , suggesting contamination with wild type BGlu1 beta-glucosidase .
[ Sen. 3, subscore: 1.00 ]: The products from reaction of GlcF and Fuc-pNP included Fuc-beta- ( 1-->3 ) -Fuc-pNP , Glc-beta- ( 1-->3 ) -Fuc-pNP , and Fuc-beta- ( 1-->4 ) -Glc-beta- ( 1-->3 ) -Fuc-pNP , suggesting the presence of both wild type BGlu1 and its glycosynthase .
[ Sen. 5, subscore: 1.00 ]: Rice BGlu1 E386G-2 , generated from a new construct designed to minimize back-mutation , showed glycosynthase activity without wild type hydrolytic or transglycosylation activity .
[ Sen. 10, subscore: 1.00 ]: Elimination of wild type contamination thereby allowed a clear assessment of BGlu1 E386G glycosynthase catalytic abilities .
Score: 6.00
Title: Complex arrangement of dispersed repeated DNA sequences in Oryza officinalis .
Journal: Genome Year: 1996 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub8851805 Accession (PMID): 8851805
Abstract: A 525-bp BglII fragment was isolated from Oryza officinalis DNA ( accession W1278 ) and shown to correspond to a new dispersed repetitive DNA sequence with specificity restricted to a subset of the wild rice with a C genome . The sequence of the fragment was determined but it does not correspond to any sequence already present in databases . It contains several imperfect palindromes . Larger genomic clones ( 12-18 kbp ) were isolated and all contain sequences homologous to the BglII element . Analysis of these clones confirms that the BglII element is dispersed in the O officinalis genome . From one genomic clone , the sequences adjacent to the BglII element were subcloned and used as probes to demonstrate that the sequences flanking the BglII element are variable in different genomic clones and that some of them are also dispersed repetitive sequences . The genomic specificity of two of these dispersed repeats was evaluated and shown to be different from that of the initial BglII element . This analysis revealed a complex arrangement of various dispersed repeated sequences .
Matching Sentences:
[ Sen. 6, subscore: 2.00 ]: From one genomic clone , the sequences adjacent to the BglII element were subcloned and used as probes to demonstrate that the sequences flanking the BglII element are variable in different genomic clones and that some of them are also dispersed repetitive sequences .
[ Sen. 1, subscore: 1.00 ]: A 525-bp BglII fragment was isolated from Oryza officinalis DNA ( accession W1278 ) and shown to correspond to a new dispersed repetitive DNA sequence with specificity restricted to a subset of the wild rice with a C genome .
[ Sen. 4, subscore: 1.00 ]: Larger genomic clones ( 12-18 kbp ) were isolated and all contain sequences homologous to the BglII element .
[ Sen. 5, subscore: 1.00 ]: Analysis of these clones confirms that the BglII element is dispersed in the O officinalis genome .
[ Sen. 7, subscore: 1.00 ]: The genomic specificity of two of these dispersed repeats was evaluated and shown to be different from that of the initial BglII element .
Score: 5.00
Title: Expression of thermostable bacterial beta-glucosidase ( BglB ) in transgenic tobacco plants .
Journal: Bioresour Technol Year: 2010 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub20427180 Accession (PMID): 20427180
Abstract: Transgenic tobacco plants expressing the hyperthermostable beta-glucosidase BglB of Thermotoga maritima were generated with the goal of cost-effective production of the enzyme for the application in bioconversion of lignocellulosic biomass . The enzyme was targeted to the cytosol and chloroplasts , where it accumulated to level of 4 . 5% and 5 . 8% of total soluble protein , respectively . The optimal temperature and pH of the plant-expressed BglB was 80 degrees C and 4 . 5 , respectively . BglB activity was preserved in leaves after lyophilization , but decreased by over 70% with drying at room temperature . When BglB was synergistically supplied in a 1% ( w/v ) rice straw with Cel5A for efficient cellulase conversion , a 37% increase in glucose was observed . This report demonstrates the potential of utilizing transgenic tobacco for mass production of BglB .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Transgenic tobacco plants expressing the hyperthermostable beta-glucosidase BglB of Thermotoga maritima were generated with the goal of cost-effective production of the enzyme for the application in bioconversion of lignocellulosic biomass .
[ Sen. 3, subscore: 1.00 ]: The optimal temperature and pH of the plant-expressed BglB was 80 degrees C and 4 . 5 , respectively .
[ Sen. 4, subscore: 1.00 ]: BglB activity was preserved in leaves after lyophilization , but decreased by over 70% with drying at room temperature .
[ Sen. 5, subscore: 1.00 ]: When BglB was synergistically supplied in a 1% ( w/v ) rice straw with Cel5A for efficient cellulase conversion , a 37% increase in glucose was observed .
[ Sen. 6, subscore: 1.00 ]: This report demonstrates the potential of utilizing transgenic tobacco for mass production of BglB .
Score: 4.00
Title: Purification , crystallization and preliminary X-ray analysis of rice BGlu1 beta-glucosidase with and without 2-deoxy-2-fluoro-beta-D-glucoside .
Journal: Acta Crystallograph . Sect . F Struct . Biol . Cryst Commun . Year: 2006 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub16880561 Accession (PMID): 16880561
Abstract: Rice ( Oryza sativa ) BGlu1 beta-glucosidase was expressed in Escherichia coli with N-terminal thioredoxin and hexahistidine tags and purified by immobilized metal-affinity chromatography ( IMAC ) . After removal of the N-terminal tags , cation-exchange and S-200 gel-filtration chromatography yielded a 50 kDa BGlu1 with >95% purity . The free enzyme and a complex with 2 , 4-dinitrophenyl-2-deoxy-2-fluoro-beta-D-glucopyranoside inhibitor were crystallized by microbatch and hanging-drop vapour diffusion . Small tetragonal crystals of BGlu1 with and without inhibitor grew in 18% ( w/v ) PEG 8000 with 0 . 1 M sodium cacodylate pH 6 . 5 and 0 . 2 M zinc acetate . Crystals of BGlu1 with inhibitor were streak-seeded into 23% ( w/v ) PEG MME 5000 , 0 . 2 M ammonium sulfate , 0 . 1 M MES pH 6 . 7 to yield larger crystals . Crystals with and without inhibitor diffracted to 2 . 15 and 2 . 75 angstroms resolution , respectively , and had isomorphous orthorhombic unit cells belonging to space group P2 ( 1 ) 2 ( 1 ) 2 ( 1 ) .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Rice ( Oryza sativa ) BGlu1 beta-glucosidase was expressed in Escherichia coli with N-terminal thioredoxin and hexahistidine tags and purified by immobilized metal-affinity chromatography ( IMAC ) .
[ Sen. 2, subscore: 1.00 ]: After removal of the N-terminal tags , cation-exchange and S-200 gel-filtration chromatography yielded a 50 kDa BGlu1 with >95% purity .
[ Sen. 4, subscore: 1.00 ]: Small tetragonal crystals of BGlu1 with and without inhibitor grew in 18% ( w/v ) PEG 8000 with 0 . 1 M sodium cacodylate pH 6 . 5 and 0 . 2 M zinc acetate .
[ Sen. 5, subscore: 1.00 ]: Crystals of BGlu1 with inhibitor were streak-seeded into 23% ( w/v ) PEG MME 5000 , 0 . 2 M ammonium sulfate , 0 . 1 M MES pH 6 . 7 to yield larger crystals .
Score: 4.00
Title: Enzymatic synthesis of cello-oligosaccharides by rice BGlu1 { beta } -glucosidase glycosynthase mutants .
Journal: Year: 2007 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub17405771 Accession (PMID): 17405771
Abstract: Rice ( BGlu1 ) beta-glucosidase is a glycosyl hydrolase family 1 enzyme that acts as an exoglucanase on beta- ( 1 , 4 ) - and short beta- ( 1 , 3 ) -linked gluco-oligosaccharides . Mutations of BGlu1 beta-glucosidase at glutamate residue 414 of its natural precursor destroyed the enzymes catalytic activity , but the enzyme could be rescued in the presence of the anionic nucleophiles formate and azide , which verifies that this residue is the catalytic nucleophile . The catalytic activities of three candidate mutants , E414G , E414S , and E414A , in the presence of the nucleophiles were compared . The E414G mutant had approximately 25 and 1400-fold higher catalytic efficiency than E414A and E414S , respectively . All three mutants could catalyze the synthesis of mixed length oligosaccharides by transglucosylation , when alpha-glucosyl fluoride was used as donor and pNP-cellobioside as acceptor . The E414G mutant gave the fastest transglucosylation rate , which was approximately 3 and 19 fold faster than E414S and E414A , respectively , and gave yields of up to 70-80 % insoluble products with a donor : acceptor ratio of 5 : 1 . ( 13 ) C-NMR , methylation analysis and electrospray ionization mass spectrometry showed that the insoluble products were beta- ( 1 , 4 ) -linked oligomers with a degree of polymerization ( DP ) of 5 to at least 11 . The BGlu1 E414G glycosynthase was found to prefer longer chain length oligosaccharides that occupy at least three sugar residue binding subsites as acceptors for productive transglucosylation . This is the first report of a beta-glucansynthase derived from an exoglycosidase that can produce long chain cello-oligosaccharides , which likely reflects the extended oligosaccharide binding site of rice BGlu1 beta-glucosidase .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Rice ( BGlu1 ) beta-glucosidase is a glycosyl hydrolase family 1 enzyme that acts as an exoglucanase on beta- ( 1 , 4 ) - and short beta- ( 1 , 3 ) -linked gluco-oligosaccharides .
[ Sen. 2, subscore: 1.00 ]: Mutations of BGlu1 beta-glucosidase at glutamate residue 414 of its natural precursor destroyed the enzymes catalytic activity , but the enzyme could be rescued in the presence of the anionic nucleophiles formate and azide , which verifies that this residue is the catalytic nucleophile .
[ Sen. 8, subscore: 1.00 ]: The BGlu1 E414G glycosynthase was found to prefer longer chain length oligosaccharides that occupy at least three sugar residue binding subsites as acceptors for productive transglucosylation .
[ Sen. 9, subscore: 1.00 ]: This is the first report of a beta-glucansynthase derived from an exoglycosidase that can produce long chain cello-oligosaccharides , which likely reflects the extended oligosaccharide binding site of rice BGlu1 beta-glucosidase .
Score: 3.00
Title: Beta-glucosidase , exo-beta-glucanase and pyridoxine transglucosylase activities of rice BGlu1 .
Journal: Biochem . J Year: 2004 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub14692878 Accession (PMID): 14692878
Abstract: The bglu1 cDNA for a beta-glucosidase cloned from rice ( Oryza sativa L ) seedlings was expressed as a soluble and active protein in Escherichia coli and designated BGlu1 . This enzyme hydrolysed beta-1 , 4-linked oligosaccharides with increasing catalytic efficiency ( kcat/Km ) values as the DP ( degree of polymerization ) increased from 2 to 6 . In contrast , hydrolysis of beta-1 , 3-linked oligosaccharides decreased from DP 2 to 3 , and polymers with a DP greater than 3 were not hydrolysed . The enzyme also hydrolysed p -nitrophenyl beta-D-glycosides and some natural glucosides but with lower catalytic efficiency than beta-linked oligosaccharides . Pyridoxine 5-O-beta-D-glucoside was the most efficiently hydrolysed natural glycoside tested . BGlu1 also had high transglucosylation activity towards pyridoxine , producing pyridoxine 5-O-beta-D-glucopyranoside in the presence of the glucose donor p-nitrophenyl beta-D-glucoside .
Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: The bglu1 cDNA for a beta-glucosidase cloned from rice ( Oryza sativa L ) seedlings was expressed as a soluble and active protein in Escherichia coli and designated BGlu1 .
[ Sen. 6, subscore: 1.00 ]: BGlu1 also had high transglucosylation activity towards pyridoxine , producing pyridoxine 5-O-beta-D-glucopyranoside in the presence of the glucose donor p-nitrophenyl beta-D-glucoside .
Score: 3.00
Title: Structural insights into rice BGlu1 beta-glucosidase oligosaccharide hydrolysis and transglycosylation .
Journal: J Mol Biol Year: 2008 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18308333 Accession (PMID): 18308333
Abstract: The structures of rice BGlu1 beta-glucosidase , a plant beta-glucosidase active in hydrolyzing cell wall-derived oligosaccharides , and its covalent intermediate with 2-deoxy-2-fluoroglucoside have been solved at 2 . 2 A and 1 . 55 A resolution , respectively . The structures were similar to the known structures of other glycosyl hydrolase family 1 ( GH1 ) beta-glucosidases , but showed several differences in the loops around the active site , which lead to an open active site with a narrow slot at the bottom , compatible with the hydrolysis of long beta-1 , 4-linked oligosaccharides . Though this active site structure is somewhat similar to that of the Paenibacillus polymyxa beta-glucosidase B , which hydrolyzes similar oligosaccharides , molecular docking studies indicate that the residues interacting with the substrate beyond the conserved -1 site are completely different , reflecting the independent evolution of plant and microbial GH1 exo-beta-glucanase/beta-glucosidases . The complex with the 2-fluoroglucoside included a glycerol molecule , which appears to be in a position to make a nucleophilic attack on the anomeric carbon in a transglycosylation reaction . The coordination of the hydroxyl groups suggests that sugars are positioned as acceptors for transglycosylation by their interactions with E176 , the catalytic acid/base , and Y131 , which is conserved in barley BGQ60/beta-II beta-glucosidase , that has oligosaccharide hydrolysis and transglycosylation activity similar to rice BGlu1 . As the rice and barley enzymes have different preferences for cellobiose and cellotriose , residues that appeared to interact with docked oligosaccharides were mutated to those of the barley enzyme to see if the relative activities of rice BGlu1 toward these substrates could be changed to those of BGQ60 . Although no single residue appeared to be responsible for these differences , I179 , N190 and N245 did appear to interact with the substrates .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The structures of rice BGlu1 beta-glucosidase , a plant beta-glucosidase active in hydrolyzing cell wall-derived oligosaccharides , and its covalent intermediate with 2-deoxy-2-fluoroglucoside have been solved at 2 . 2 A and 1 . 55 A resolution , respectively .
[ Sen. 5, subscore: 1.00 ]: The coordination of the hydroxyl groups suggests that sugars are positioned as acceptors for transglycosylation by their interactions with E176 , the catalytic acid/base , and Y131 , which is conserved in barley BGQ60/beta-II beta-glucosidase , that has oligosaccharide hydrolysis and transglycosylation activity similar to rice BGlu1 .
[ Sen. 6, subscore: 1.00 ]: As the rice and barley enzymes have different preferences for cellobiose and cellotriose , residues that appeared to interact with docked oligosaccharides were mutated to those of the barley enzyme to see if the relative activities of rice BGlu1 toward these substrates could be changed to those of BGQ60 .
Score: 3.00
Title: The structural basis of oligosaccharide binding by rice BGlu1 beta-glucosidase .
Journal: J Struct Biol Year: 2011 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub20884352 Accession (PMID): 20884352
Abstract: Rice BGlu1 beta-glucosidase is an oligosaccharide exoglucosidase that binds to six beta- ( 1-->4 ) -linked glucosyl residues in its active site cleft . Here , we demonstrate that a BGlu1 E176Q active site mutant can be effectively rescued by small nucleophiles , such as acetate , azide and ascorbate , for hydrolysis of aryl glycosides in a pH-independent manner above pH5 , consistent with the role of E176 as the catalytic acid-base . Cellotriose , cellotetraose , cellopentaose , cellohexaose and laminaribiose are not hydrolyzed by the mutant and instead exhibit competitive inhibition . The structures of the BGlu1 E176Q , its complexes with cellotetraose , cellopentaose and laminaribiose , and its covalent intermediate with 2-deoxy-2-fluoroglucoside were determined at 1 . 65 , 1 . 95 , 1 . 80 , 2 . 80 , and 1 . 90A resolution , respectively . The Q176Nepsilon was found to hydrogen bond to the glycosidic oxygen of the scissile bond , thereby explaining its high activity . The enzyme interacts with cellooligosaccharides through direct hydrogen bonds to the nonreducing terminal glucosyl residue . However , interaction with the other glucosyl residues is predominantly mediated through water molecules , with the exception of a direct hydrogen bond from N245 to glucosyl residue 3 , consistent with the apparent high binding energy at this residue . Hydrophobic interactions with the aromatic sidechain of W358 appear to orient glucosyl residues 2 and 3 , while Y341 orients glucosyl residues 4 and 5 . In contrast , laminaribiose has its second glucosyl residue positioned to allow direct hydrogen bonding between its O2 and Q176 Oepsilon and O1 and N245 . These are the first GH1 glycoside hydrolase family structures to show oligosaccharide binding in the hydrolytic configuration .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Rice BGlu1 beta-glucosidase is an oligosaccharide exoglucosidase that binds to six beta- ( 1-->4 ) -linked glucosyl residues in its active site cleft .
[ Sen. 2, subscore: 1.00 ]: Here , we demonstrate that a BGlu1 E176Q active site mutant can be effectively rescued by small nucleophiles , such as acetate , azide and ascorbate , for hydrolysis of aryl glycosides in a pH-independent manner above pH5 , consistent with the role of E176 as the catalytic acid-base .
[ Sen. 4, subscore: 1.00 ]: The structures of the BGlu1 E176Q , its complexes with cellotetraose , cellopentaose and laminaribiose , and its covalent intermediate with 2-deoxy-2-fluoroglucoside were determined at 1 . 65 , 1 . 95 , 1 . 80 , 2 . 80 , and 1 . 90A resolution , respectively .
Score: 3.00
Title: The rice bright green leaf ( bgl ) locus encodes OsRopGEF10 , which activates the development of small cuticular papillae on leaf surfaces .
Journal: Plant Mol Biol Year: 2011 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub22038138 Accession (PMID): 22038138
Abstract: Development of specialized epidermal cells and structures plays a key role in plant tolerance to biotic and abiotic stresses . In the paddy field , the bright green leaf ( bgl ) mutants of rice ( Oryza sativa ) exhibit a luminous green color that is clearly distinguishable from the normal green of wild-type plants . Transmission and scanning electron microscopy revealed that small cuticular papillae ( or small papillae ; SP ) , nipple-like structures , are absent on the adaxial and abaxial leaf surfaces of bgl mutants , leading to more direct reflection and less diffusion of green light . Map-based cloning revealed that the bgl locus encodes OsRopGEF10 , one of eleven OsRopGEFs in rice . RopGEFs ( guanine nucleotide exchange factors for Rop ) activate Rop/Rac GTPases , acting as molecular switches in eukaryotic signal transduction by replacing the bound GDP ( inactive form ) with GTP ( active form ) in response to external or internal cues . In agreement with the timing of SP initiation on the leaf epidermis , OsRopGEF10 is most strongly expressed in newly developing leaves before emergence from the leaf sheath . In yeast two-hybrid assays , OsRopGEF10 interacts with OsRac1 , one of seven OsRac proteins ; consistent with this , both proteins are localized in the plasma membrane . These results suggest that OsRopGEF10 activates OsRac1 to turn on the molecular signaling pathway for SP development . Together , our findings provide new insights into the molecular genetic mechanism of SP formation during early leaf morphogenesis .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: In the paddy field , the bright green leaf ( bgl ) mutants of rice ( Oryza sativa ) exhibit a luminous green color that is clearly distinguishable from the normal green of wild-type plants .
[ Sen. 3, subscore: 1.00 ]: Transmission and scanning electron microscopy revealed that small cuticular papillae ( or small papillae ; SP ) , nipple-like structures , are absent on the adaxial and abaxial leaf surfaces of bgl mutants , leading to more direct reflection and less diffusion of green light .
[ Sen. 4, subscore: 1.00 ]: Map-based cloning revealed that the bgl locus encodes OsRopGEF10 , one of eleven OsRopGEFs in rice .
Score: 3.00
Title: The role of the oligosaccharide binding cleft of rice BGlu1 in hydrolysis of cellooligosaccharides and in their synthesis by rice BGlu1 glycosynthase .
Journal: Protein Sci Year: 2012 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub22238157 Accession (PMID): 22238157
Abstract: Rice BGlu1 beta-glucosidase nucleophile mutant E386G is a glycosynthase that can synthesize p-nitrophenyl ( pNP ) -cellooligosaccharides of up to 11 residues . The X-ray crystal structures of the E386G glycosynthase with and without alpha-glucosyl fluoride were solved and the alpha-glucosyl fluoride complex was found to contain an ordered water molecule near the position of the nucleophile of the BGlu1 native structure , which is likely to stabilize the departing fluoride . The structures of E386G glycosynthase in complexes with cellotetraose and cellopentaose confirmed that the side chains of N245 , S334 , and Y341 interact with glucosyl residues in cellooligosaccharide binding subsites +2 , +3 , and +4 . Mutants in which these residues were replaced in BGlu1 beta-glucosidase hydrolyzed cellotetraose and cellopentaose with k ( cat ) /K ( m ) values similar to those of the wild type enzyme . However , the Y341A , Y341L , and N245V mutants of the E386G glycosynthase synthesize shorter pNP-cellooligosaccharides than do the E386G glycosynthase and its S334A mutant , suggesting that Y341 and N245 play important roles in the synthesis of long oligosaccharides . X-ray structural studies revealed that cellotetraose binds to the Y341A mutant of the glycosynthase in a very different , alternative mode not seen in complexes with the E386G glycosynthase , possibly explaining the similar hydrolysis , but poorer synthesis of longer oligosaccharides by Y341 mutants .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Rice BGlu1 beta-glucosidase nucleophile mutant E386G is a glycosynthase that can synthesize p-nitrophenyl ( pNP ) -cellooligosaccharides of up to 11 residues .
[ Sen. 2, subscore: 1.00 ]: The X-ray crystal structures of the E386G glycosynthase with and without alpha-glucosyl fluoride were solved and the alpha-glucosyl fluoride complex was found to contain an ordered water molecule near the position of the nucleophile of the BGlu1 native structure , which is likely to stabilize the departing fluoride .
[ Sen. 4, subscore: 1.00 ]: Mutants in which these residues were replaced in BGlu1 beta-glucosidase hydrolyzed cellotetraose and cellopentaose with k ( cat ) /K ( m ) values similar to those of the wild type enzyme .
Score: 2.00
Title: QM/MM studies on the glycosylation mechanism of rice BGlu1 beta-glucosidase .
Journal: J Mol Graph Model Year: 2011 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub21802967 Accession (PMID): 21802967
Abstract: The quantum-mechanical/molecular-mechanical ( QM/MM ) method was used to study the glycosylation mechanism of rice BGlu1 beta-glucosidase in complex with laminaribiose . The calculation results reveal that the glycosylation step experiences a concerted process from the reactant to the glycosyl-enzyme complex with an activation barrier of 15 . 7 kcal/mol , in which an oxocarbenium cation-like transition state ( TS ) is formed . At the TS , the terminal saccharide residue planarizes toward the half-chair conformation , and the glycosidic bond cleavage is promoted by the attacks of proton donor ( E176 ) on glycosidic oxygen and nucleophilic residue ( E386 ) on the anomeric carbon of laminaribiose . Both the nucleophilic glutamate ( E386 ) and acid/base catalyst ( E176 ) establish shorter hydrogen bridges with the C-hydroxyl groups of sugar ring , which play an important role in the catalytic reaction of rice BGlu1 beta-glucosidase .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: The quantum-mechanical/molecular-mechanical ( QM/MM ) method was used to study the glycosylation mechanism of rice BGlu1 beta-glucosidase in complex with laminaribiose .
[ Sen. 4, subscore: 1.00 ]: Both the nucleophilic glutamate ( E386 ) and acid/base catalyst ( E176 ) establish shorter hydrogen bridges with the C-hydroxyl groups of sugar ring , which play an important role in the catalytic reaction of rice BGlu1 beta-glucosidase .
Score: 2.00
Title: The role of the oligosaccharide binding cleft of rice BGlu1 in hydrolysis of cellooligosaccharides and in their synthesis by rice BGlu1 glycosynthase .
Journal: Protein Sci Year: 2012 Type: MEDLINE
Literature: oryza Field: title Doc ID: pub22238157 Accession (PMID): 22238157
Abstract: Rice BGlu1 beta-glucosidase nucleophile mutant E386G is a glycosynthase that can synthesize p-nitrophenyl ( pNP ) -cellooligosaccharides of up to 11 residues . The X-ray crystal structures of the E386G glycosynthase with and without alpha-glucosyl fluoride were solved and the alpha-glucosyl fluoride complex was found to contain an ordered water molecule near the position of the nucleophile of the BGlu1 native structure , which is likely to stabilize the departing fluoride . The structures of E386G glycosynthase in complexes with cellotetraose and cellopentaose confirmed that the side chains of N245 , S334 , and Y341 interact with glucosyl residues in cellooligosaccharide binding subsites +2 , +3 , and +4 . Mutants in which these residues were replaced in BGlu1 beta-glucosidase hydrolyzed cellotetraose and cellopentaose with k ( cat ) /K ( m ) values similar to those of the wild type enzyme . However , the Y341A , Y341L , and N245V mutants of the E386G glycosynthase synthesize shorter pNP-cellooligosaccharides than do the E386G glycosynthase and its S334A mutant , suggesting that Y341 and N245 play important roles in the synthesis of long oligosaccharides . X-ray structural studies revealed that cellotetraose binds to the Y341A mutant of the glycosynthase in a very different , alternative mode not seen in complexes with the E386G glycosynthase , possibly explaining the similar hydrolysis , but poorer synthesis of longer oligosaccharides by Y341 mutants .
Matching Sentences:
[ Sen. 1, subscore: 2.00 ]: The role of the oligosaccharide binding cleft of rice BGlu1 in hydrolysis of cellooligosaccharides and in their synthesis by rice BGlu1 glycosynthase .
Score: 1.00
Title: A telomeric avirulence gene determines efficacy for the rice blast resistance gene Pi-ta .
Journal: Plant Cell Year: 2000 Type: ARTICLE
Literature: oryza Field: abstract Doc ID: pub11090206 Accession (PMID): 11090206
Abstract: Genetic mapping showed that the rice blast avirulence gene AVR-Pita is tightly linked to a telomere on chromosome 3 in the plant pathogenic fungus Magnaporthe grisea . AVR-Pita corresponds in gene-for-gene fashion to the disease resistance ( R ) gene Pi-ta . Analysis of spontaneous avr-pita ( - ) mutants indicated that the gene is located in a telomeric 6 . 5-kb BglII restriction fragment . Cloning and DNA sequencing led to the identification of a candidate gene with features typical of metalloproteases . This gene is located entirely within the most distal 1 . 5 kb of the chromosome . When introduced into virulent rice pathogens , the cloned gene specifically confers avirulence toward rice cultivars that contain Pi-ta . Frequent spontaneous loss of AVR-Pita appears to be the result of its telomeric location . Diverse mutations in AVR-Pita , including point mutations , insertions , and deletions , permit the fungus to avoid triggering resistance responses mediated by Pi-ta . A point mutation in the protease consensus sequence abolishes the AVR-Pita avirulence function .
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[ Sen. 3, subscore: 1.00 ]: Analysis of spontaneous avr-pita ( - ) mutants indicated that the gene is located in a telomeric 6 . 5-kb BglII restriction fragment .
Score: 1.00
Title: A thermotolerant beta-glucosidase isolated from an endophytic fungi , Periconia sp . , with a possible use for biomass conversion to sugars .
Journal: Protein Expr Purif Year: 2009 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub18602476 Accession (PMID): 18602476
Abstract: A fungal strain , BCC2871 ( Periconia sp . ) , was found to produce a thermotolerant beta-glucosidase , BGL I , with high potential for application in biomass conversion . The full-length gene encoding the target enzyme was identified and cloned into Pichia pastoris KM71 . Similar to the native enzyme produced by BCC2871 , the recombinant beta-glucosidase showed optimal temperature at 70 degrees C and optimal pH of 5 and 6 . The enzyme continued to exhibit high activity even after long incubation at high temperature , retaining almost 60% of maximal activity after 1 . 5h at 70 degrees C It was also stable under basic conditions , retaining almost 100% of maximal activity after incubation for 2h at pH8 . The enzyme has high activity towards cellobiose and other synthetic substrates containing glycosyl groups as well as cellulosic activity toward carboxymethylcellulose . Thermostability of the enzyme was improved remarkably in the presence of cellobiose , glucose , or sucrose . This beta-glucosidase was able to hydrolyze rice straw into simple sugars . The addition of this beta-glucosidase to the rice straw hydrolysis reaction containing a commercial cellulase , Celluclast 1 . 5L ( Novozyme , Denmark ) resulted in increase of reducing sugars being released compared to the hydrolysis without the beta-glucosidase . This enzyme is a candidate for applications that convert lignocellulosic biomass to biofuels and chemicals .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: A fungal strain , BCC2871 ( Periconia sp . ) , was found to produce a thermotolerant beta-glucosidase , BGL I , with high potential for application in biomass conversion .
Score: 1.00
Title: [ Screening , identifying of cellulose-decomposing strain L-06 and its enzyme-producing conditions ]
Journal: Sheng Wu Gong Cheng Xue Bao Year: 2008 Type: In-Process
Literature: oryza Field: abstract Doc ID: pub18808002 Accession (PMID): 18808002
Abstract: Cellulases are relatively costly enzymes that are sold in large volumes for use in different industrial applications , and a significant reduction in cost will be important for their commercial use in biorefineries . The production of cellulase is a major factor in the hydrolysis of cellulosic materials . Hence it is essential to make the process economically viable . A strain ( L-06 ) with high cellulase activity was screened from rice straw compost and classified as Penicillium decumbens by the analysis of its morphology and 18S rRNA gene sequences . Different conditions of liquid fermentation medium including nitrogen source , carbon source , surfactant , temperature , initial pH , inoculation quantity for the production of cellulase had been studied . The maximal beta-1 , 4-glucosidase ( BGL ) activity was 1662 u/mL which is 1 . 49 times of the previous and the maximal exo-beta-1 , 4-glucanases ( CBH ) activity was 2770 u/mL which is 1 . 36 times of the previous , cultured in the optimal condition for three days . And the maximal endo-beta-1 , 4-glucanases ( EG ) activity was 18064 u/mL which is 1 . 87 times of the previous and the maximal filter paper enzyme ( FPase ) activity was 4035 u/mL which is 1 . 47 times of the previous , cultured in the optimal condition for four days . In the optimization experiments , the EG and CBH in the culture condition ( pH10 ) maintained 70% and 43% activity . In the culture condition ( 50 degrees C ) EG and CBH maintained 59% and 68% activity , which showed heat and alkali resistant characteristics .
Matching Sentences:
[ Sen. 6, subscore: 1.00 ]: The maximal beta-1 , 4-glucosidase ( BGL ) activity was 1662 u/mL which is 1 . 49 times of the previous and the maximal exo-beta-1 , 4-glucanases ( CBH ) activity was 2770 u/mL which is 1 . 36 times of the previous , cultured in the optimal condition for three days .
Score: 1.00
Title: Enhanced saccharification of alkali-treated rice straw by cellulase from Trametes hirsuta and statistical optimization of hydrolysis conditions by RSM .
Journal: Bioresour Technol Year: 2009 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub19540109 Accession (PMID): 19540109
Abstract: A white rot fungus , identified as Trametes hirsuta based on morphological and phylogenetic analysis , was found to contain efficient cellulose degrading enzymes . The strain showed maximum endoglucanase ( EG ) , cellobiohydrolase ( CBH ) and beta-glucosidase ( BGL ) activities of 55 , 0 . 28 and 5 . 0 U/mg-protein , respectively . Rice straw was found to be a potentially good substrate for growth of T hirsuta for cellulase production . Statistical experimental design was used to optimize hydrolysis parameters such as pH , temperature , and concentrations of substrates and enzymes to achieve the highest saccharification yield . Enzyme concentration was identified as the limiting factor for saccharification of rice straw . A maximum saccharification rate of 88% was obtained at an enzyme concentration of 37 . 5 FPU/g-substrate after optimization of the hydrolysis parameters . The results of a confirmation experiment under the optimum conditions agreed well with model predictions . T hirsuta may be a good choice for the production of reducing sugars from cellulosic biomass .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The strain showed maximum endoglucanase ( EG ) , cellobiohydrolase ( CBH ) and beta-glucosidase ( BGL ) activities of 55 , 0 . 28 and 5 . 0 U/mg-protein , respectively .
Score: 1.00
Title: Structural and enzymatic characterization of Os3BGlu6 , a rice beta-glucosidase hydrolyzing hydrophobic glycosides and ( 1->3 ) - and ( 1->2 ) -linked disaccharides .
Journal: Plant Physiol Year: 2009 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub19587102 Accession (PMID): 19587102
Abstract: Glycoside hydrolase family 1 ( GH1 ) beta-glucosidases play roles in many processes in plants , such as chemical defense , alkaloid metabolism , hydrolysis of cell wall-derived oligosaccharides , phytohormone regulation , and lignification . However , the functions of most of the 34 GH1 gene products in rice ( Oryza sativa ) are unknown . Os3BGlu6 , a rice beta-glucosidase representing a previously uncharacterized phylogenetic cluster of GH1 , was produced in recombinant Escherichia coli . Os3BGlu6 hydrolyzed p-nitrophenyl ( pNP ) -beta-d-fucoside ( k ( cat ) /K ( m ) = 67 mm ( -1 ) s ( -1 ) ) , pNP-beta-d-glucoside ( k ( cat ) /K ( m ) = 6 . 2 mm ( -1 ) s ( -1 ) ) , and pNP-beta-d-galactoside ( k ( cat ) /K ( m ) = 1 . 6 mm ( -1 ) s ( -1 ) ) efficiently but had little activity toward other pNP glycosides . It also had high activity toward n-octyl-beta-d-glucoside and beta- ( 1-->3 ) - and beta- ( 1-->2 ) -linked disaccharides and was able to hydrolyze apigenin beta-glucoside and several other natural glycosides . Crystal structures of Os3BGlu6 and its complexes with a covalent intermediate , 2-deoxy-2-fluoroglucoside , and a nonhydrolyzable substrate analog , n-octyl-beta-d-thioglucopyranoside , were solved at 1 . 83 , 1 . 81 , and 1 . 80 A resolution , respectively . The position of the covalently trapped 2-F-glucosyl residue in the enzyme was similar to that in a 2-F-glucosyl intermediate complex of Os3BGlu7 ( rice BGlu1 ) . The side chain of methionine-251 in the mouth of the active site appeared to block the binding of extended beta- ( 1-->4 ) -linked oligosaccharides and interact with the hydrophobic aglycone of n-octyl-beta-d-thioglucopyranoside . This correlates with the preference of Os3BGlu6 for short oligosaccharides and hydrophobic glycosides .
Matching Sentences:
[ Sen. 7, subscore: 1.00 ]: The position of the covalently trapped 2-F-glucosyl residue in the enzyme was similar to that in a 2-F-glucosyl intermediate complex of Os3BGlu7 ( rice BGlu1 ) .
Score: 1.00
Title: Conversion of woody biomass into fermentable sugars by cellulase from Agaricus arvensis .
Journal: Bioresour Technol Year: 2010 Type: MEDLINE
Literature: oryza Field: abstract Doc ID: pub20609581 Accession (PMID): 20609581
Abstract: Agaricus arvensis , a newly isolated basidiomycetous fungus , was found to secrete efficient cellulases . The strain produced the highest endoglucanase ( EG ) , cellobiohydrolase ( CBH ) and beta-glucosidase ( BGL ) activities of 0 . 3 , 3 . 2 and 8U/mg-protein , respectively , with rice straw as the carbon source . Saccharification of the woody biomass with A arvensis cellulase as the enzyme source released a high level of fermentable sugars . Enzymatic hydrolysis of the poplar biomass was optimized using the response surface methodology in order to study the influence of the variables ( pH , temperature , cellulases concentration and substrate concentration ) . The enzyme and substrate concentrations were identified as the limiting factors for the saccharification of poplar wood biomass . A total reducing sugar level of 29g/L ( 293mg/g-substrate ) was obtained at an enzyme concentration of 65FPU/g-substrate after optimization of the hydrolysis parameters . The model validation showed a good agreement between the experimental results and the predicted responses . A arvensis could be a good candidate for the production of reducing sugars from a cellulosic biomass .
Matching Sentences:
[ Sen. 2, subscore: 1.00 ]: The strain produced the highest endoglucanase ( EG ) , cellobiohydrolase ( CBH ) and beta-glucosidase ( BGL ) activities of 0 . 3 , 3 . 2 and 8U/mg-protein , respectively , with rice straw as the carbon source .
Score: 1.00
Title: Beta-glucosidase , exo-beta-glucanase and pyridoxine transglucosylase activities of rice BGlu1 .
Journal: Biochem . J Year: 2004 Type: ARTICLE
Literature: oryza Field: title Doc ID: pub14692878 Accession (PMID): 14692878
Abstract: The bglu1 cDNA for a beta-glucosidase cloned from rice ( Oryza sativa L ) seedlings was expressed as a soluble and active protein in Escherichia coli and designated BGlu1 . This enzyme hydrolysed beta-1 , 4-linked oligosaccharides with increasing catalytic efficiency ( kcat/Km ) values as the DP ( degree of polymerization ) increased from 2 to 6 . In contrast , hydrolysis of beta-1 , 3-linked oligosaccharides decreased from DP 2 to 3 , and polymers with a DP greater than 3 were not hydrolysed . The enzyme also hydrolysed p -nitrophenyl beta-D-glycosides and some natural glucosides but with lower catalytic efficiency than beta-linked oligosaccharides . Pyridoxine 5-O-beta-D-glucoside was the most efficiently hydrolysed natural glycoside tested . BGlu1 also had high transglucosylation activity towards pyridoxine , producing pyridoxine 5-O-beta-D-glucopyranoside in the presence of the glucose donor p-nitrophenyl beta-D-glucoside .
Matching Sentences:
[ Sen. 1, subscore: 1.00 ]: Beta-glucosidase , exo-beta-glucanase and pyridoxine transglucosylase activities of rice BGlu1 .
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