PubMed:21493662 JSONTXT

{"project":"OryzaGP_2022","denotations":[{"id":"T1","span":{"begin":177,"end":178},"obj":"http://identifiers.org/oryzabase.gene/11216"},{"id":"T2","span":{"begin":1283,"end":1294},"obj":"http://identifiers.org/oryzabase.gene/8905"},{"id":"T3","span":{"begin":1436,"end":1447},"obj":"http://identifiers.org/oryzabase.gene/8905"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"sentences","denotations":[{"id":"TextSentencer_T1","span":{"begin":0,"end":124},"obj":"Sentence"},{"id":"TextSentencer_T2","span":{"begin":125,"end":280},"obj":"Sentence"},{"id":"TextSentencer_T3","span":{"begin":281,"end":504},"obj":"Sentence"},{"id":"TextSentencer_T4","span":{"begin":505,"end":655},"obj":"Sentence"},{"id":"TextSentencer_T5","span":{"begin":656,"end":841},"obj":"Sentence"},{"id":"TextSentencer_T6","span":{"begin":842,"end":1042},"obj":"Sentence"},{"id":"TextSentencer_T7","span":{"begin":1043,"end":1295},"obj":"Sentence"},{"id":"TextSentencer_T8","span":{"begin":1296,"end":1448},"obj":"Sentence"},{"id":"T1","span":{"begin":0,"end":124},"obj":"Sentence"},{"id":"T2","span":{"begin":125,"end":280},"obj":"Sentence"},{"id":"T3","span":{"begin":281,"end":504},"obj":"Sentence"},{"id":"T4","span":{"begin":505,"end":655},"obj":"Sentence"},{"id":"T5","span":{"begin":656,"end":841},"obj":"Sentence"},{"id":"T6","span":{"begin":842,"end":1042},"obj":"Sentence"},{"id":"T7","span":{"begin":1043,"end":1295},"obj":"Sentence"},{"id":"T8","span":{"begin":1296,"end":1448},"obj":"Sentence"},{"id":"T1","span":{"begin":0,"end":124},"obj":"Sentence"},{"id":"T2","span":{"begin":125,"end":280},"obj":"Sentence"},{"id":"T3","span":{"begin":281,"end":504},"obj":"Sentence"},{"id":"T4","span":{"begin":505,"end":655},"obj":"Sentence"},{"id":"T5","span":{"begin":656,"end":841},"obj":"Sentence"},{"id":"T6","span":{"begin":842,"end":1042},"obj":"Sentence"},{"id":"T7","span":{"begin":1043,"end":1295},"obj":"Sentence"},{"id":"T8","span":{"begin":1296,"end":1448},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"OryzaGP_2021_v2","denotations":[{"id":"T1","span":{"begin":45,"end":48},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T2","span":{"begin":331,"end":334},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T3","span":{"begin":544,"end":547},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T4","span":{"begin":690,"end":693},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T5","span":{"begin":1092,"end":1095},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T6","span":{"begin":1428,"end":1431},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T93073","span":{"begin":45,"end":48},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T96840","span":{"begin":331,"end":334},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T47010","span":{"begin":544,"end":547},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T39628","span":{"begin":690,"end":693},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T82048","span":{"begin":1092,"end":1095},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T570","span":{"begin":1428,"end":1431},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

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{"project":"OryzaGP_2021","denotations":[{"id":"T1","span":{"begin":25,"end":43},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T2","span":{"begin":45,"end":48},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T3","span":{"begin":311,"end":329},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T4","span":{"begin":331,"end":334},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T5","span":{"begin":544,"end":547},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T6","span":{"begin":690,"end":693},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T7","span":{"begin":1092,"end":1095},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T8","span":{"begin":1283,"end":1294},"obj":"http://identifiers.org/oryzabase.gene/8905"},{"id":"T9","span":{"begin":1428,"end":1431},"obj":"http://identifiers.org/oryzabase.gene/730"},{"id":"T10","span":{"begin":1436,"end":1447},"obj":"http://identifiers.org/oryzabase.gene/8905"},{"id":"T22276","span":{"begin":25,"end":43},"obj":"http://identifiers.org/ricegap/LOC_Os06g51084"},{"id":"T1213","span":{"begin":45,"end":48},"obj":"http://identifiers.org/ricegap/LOC_Os06g51084"},{"id":"T80850","span":{"begin":311,"end":329},"obj":"http://identifiers.org/ricegap/LOC_Os06g51084"},{"id":"T50576","span":{"begin":331,"end":334},"obj":"http://identifiers.org/ricegap/LOC_Os06g51084"},{"id":"T99791","span":{"begin":544,"end":547},"obj":"http://identifiers.org/ricegap/LOC_Os06g51084"},{"id":"T73511","span":{"begin":690,"end":693},"obj":"http://identifiers.org/ricegap/LOC_Os06g51084"},{"id":"T28812","span":{"begin":1092,"end":1095},"obj":"http://identifiers.org/ricegap/LOC_Os06g51084"},{"id":"T86823","span":{"begin":1428,"end":1431},"obj":"http://identifiers.org/ricegap/LOC_Os06g51084"},{"id":"T37879","span":{"begin":25,"end":43},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T55293","span":{"begin":45,"end":48},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T27566","span":{"begin":311,"end":329},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T75723","span":{"begin":331,"end":334},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T44133","span":{"begin":544,"end":547},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T44181","span":{"begin":690,"end":693},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T85707","span":{"begin":1092,"end":1095},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T5622","span":{"begin":1283,"end":1294},"obj":"http://identifiers.org/rapdb.locus/Os04g0164900"},{"id":"T10241","span":{"begin":1428,"end":1431},"obj":"http://identifiers.org/rapdb.locus/Os06g0726400"},{"id":"T55738","span":{"begin":1436,"end":1447},"obj":"http://identifiers.org/rapdb.locus/Os04g0164900"},{"id":"T102","span":{"begin":25,"end":43},"obj":"http://identifiers.org/uniprot/Q01401"},{"id":"T54332","span":{"begin":25,"end":43},"obj":"http://identifiers.org/uniprot/D0TZI4"},{"id":"T4595","span":{"begin":25,"end":43},"obj":"http://identifiers.org/uniprot/A3BFK2"},{"id":"T46561","span":{"begin":45,"end":48},"obj":"http://identifiers.org/uniprot/Q01401"},{"id":"T35393","span":{"begin":45,"end":48},"obj":"http://identifiers.org/uniprot/D0TZI4"},{"id":"T32494","span":{"begin":45,"end":48},"obj":"http://identifiers.org/uniprot/A3BFK2"},{"id":"T65398","span":{"begin":311,"end":329},"obj":"http://identifiers.org/uniprot/Q01401"},{"id":"T96855","span":{"begin":311,"end":329},"obj":"http://identifiers.org/uniprot/D0TZI4"},{"id":"T92159","span":{"begin":311,"end":329},"obj":"http://identifiers.org/uniprot/A3BFK2"},{"id":"T75973","span":{"begin":331,"end":334},"obj":"http://identifiers.org/uniprot/Q01401"},{"id":"T11","span":{"begin":331,"end":334},"obj":"http://identifiers.org/uniprot/D0TZI4"},{"id":"T12","span":{"begin":331,"end":334},"obj":"http://identifiers.org/uniprot/A3BFK2"},{"id":"T13","span":{"begin":544,"end":547},"obj":"http://identifiers.org/uniprot/Q01401"},{"id":"T14","span":{"begin":544,"end":547},"obj":"http://identifiers.org/uniprot/D0TZI4"},{"id":"T15","span":{"begin":544,"end":547},"obj":"http://identifiers.org/uniprot/A3BFK2"},{"id":"T16","span":{"begin":690,"end":693},"obj":"http://identifiers.org/uniprot/Q01401"},{"id":"T17","span":{"begin":690,"end":693},"obj":"http://identifiers.org/uniprot/D0TZI4"},{"id":"T18","span":{"begin":690,"end":693},"obj":"http://identifiers.org/uniprot/A3BFK2"},{"id":"T19","span":{"begin":1092,"end":1095},"obj":"http://identifiers.org/uniprot/Q01401"},{"id":"T20","span":{"begin":1092,"end":1095},"obj":"http://identifiers.org/uniprot/D0TZI4"},{"id":"T21","span":{"begin":1092,"end":1095},"obj":"http://identifiers.org/uniprot/A3BFK2"},{"id":"T22","span":{"begin":1428,"end":1431},"obj":"http://identifiers.org/uniprot/Q01401"},{"id":"T23","span":{"begin":1428,"end":1431},"obj":"http://identifiers.org/uniprot/D0TZI4"},{"id":"T24","span":{"begin":1428,"end":1431},"obj":"http://identifiers.org/uniprot/A3BF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structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"GlycoBiology-PACDB","denotations":[{"id":"_T1","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC002,LEC056,LEC062,LEC069,LEC081,LEC111,LEC133,LEC171,LEC177,LEC187,LEC211,LEC242,LEC252,LEC258,LEC259,LEC260,LEC262,LEC369,LEC377,LEC422,LEC442,LEC448,LEC450,LEC451,LEC454,LEC472,LEC492,LEC620"},{"id":"_T2","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC157,LEC407"},{"id":"_T3","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC754"},{"id":"_T4","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC243,LEC640"},{"id":"_T5","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC295,LEC417"},{"id":"_T6","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC636"},{"id":"_T7","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC244,LEC256,LEC354"},{"id":"_T8","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC054,LEC058,LEC073,LEC082,LEC091,LEC103,LEC109,LEC110,LEC123,LEC158,LEC179,LEC198,LEC205,LEC222,LEC223,LEC224,LEC225,LEC232,LEC298,LEC357,LEC378,LEC383,LEC388,LEC389,LEC397,LEC401,LEC410,LEC452"},{"id":"_T9","span":{"begin":608,"end":624},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC487"},{"id":"_T10","span":{"begin":1261,"end":1282},"obj":"http://acgg.asia/db/diseases/pacdb/lec?ids=LEC136,LEC221,LEC595"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"ICD10","denotations":[{"id":"T1","span":{"begin":1272,"end":1282},"obj":"http://purl.bioontology.org/ontology/ICD10/J18.9"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"GlycoBiology-FMA","denotations":[{"id":"_T1","span":{"begin":25,"end":34},"obj":"FMAID:226027"},{"id":"_T2","span":{"begin":25,"end":34},"obj":"FMAID:226028"},{"id":"_T3","span":{"begin":132,"end":141},"obj":"FMAID:226028"},{"id":"_T4","span":{"begin":132,"end":141},"obj":"FMAID:226027"},{"id":"_T5","span":{"begin":252,"end":258},"obj":"FMAID:226028"},{"id":"_T6","span":{"begin":252,"end":258},"obj":"FMAID:226027"},{"id":"_T7","span":{"begin":259,"end":264},"obj":"FMAID:50596"},{"id":"_T8","span":{"begin":259,"end":264},"obj":"FMAID:146304"},{"id":"_T9","span":{"begin":311,"end":320},"obj":"FMAID:226028"},{"id":"_T10","span":{"begin":311,"end":320},"obj":"FMAID:226027"},{"id":"_T11","span":{"begin":379,"end":386},"obj":"FMAID:242678"},{"id":"_T12","span":{"begin":379,"end":386},"obj":"FMAID:174816"},{"id":"_T13","span":{"begin":379,"end":386},"obj":"FMAID:30328"},{"id":"_T14","span":{"begin":407,"end":414},"obj":"FMAID:104341"},{"id":"_T15","span":{"begin":446,"end":458},"obj":"FMAID:197276"},{"id":"_T16","span":{"begin":446,"end":458},"obj":"FMAID:82737"},{"id":"_T17","span":{"begin":625,"end":633},"obj":"FMAID:82747"},{"id":"_T18","span":{"begin":625,"end":633},"obj":"FMAID:196736"},{"id":"_T19","span":{"begin":774,"end":780},"obj":"FMAID:180723"},{"id":"_T20","span":{"begin":774,"end":780},"obj":"FMAID:75037"},{"id":"_T21","span":{"begin":842,"end":852},"obj":"FMAID:196728"},{"id":"_T22","span":{"begin":842,"end":852},"obj":"FMAID:82739"},{"id":"_T23","span":{"begin":1014,"end":1021},"obj":"FMAID:30328"},{"id":"_T24","span":{"begin":1014,"end":1021},"obj":"FMAID:174816"},{"id":"_T25","span":{"begin":1014,"end":1021},"obj":"FMAID:242678"},{"id":"_T26","span":{"begin":1035,"end":1041},"obj":"FMAID:75037"},{"id":"_T27","span":{"begin":1035,"end":1041},"obj":"FMAID:180723"}],"namespaces":[{"prefix":"FMAID","uri":"http://purl.org/sig/ont/fma/fma"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"uniprot-human","denotations":[{"id":"T1","span":{"begin":25,"end":41},"obj":"http://www.uniprot.org/uniprot/Q04446"},{"id":"T2","span":{"begin":132,"end":148},"obj":"http://www.uniprot.org/uniprot/Q04446"},{"id":"T3","span":{"begin":311,"end":327},"obj":"http://www.uniprot.org/uniprot/Q04446"},{"id":"T4","span":{"begin":175,"end":181},"obj":"http://www.uniprot.org/uniprot/P13674"},{"id":"T5","span":{"begin":222,"end":234},"obj":"http://www.uniprot.org/uniprot/O43451"},{"id":"T6","span":{"begin":222,"end":234},"obj":"http://www.uniprot.org/uniprot/Q2M2H8"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"uniprot-mouse","denotations":[{"id":"T1","span":{"begin":25,"end":41},"obj":"http://www.uniprot.org/uniprot/Q9D6Y9"},{"id":"T2","span":{"begin":132,"end":148},"obj":"http://www.uniprot.org/uniprot/Q9D6Y9"},{"id":"T3","span":{"begin":311,"end":327},"obj":"http://www.uniprot.org/uniprot/Q9D6Y9"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"GlycoBiology-NCBITAXON","denotations":[{"id":"T1","span":{"begin":55,"end":60},"obj":"http://purl.bioontology.org/ontology/NCBITAXON/4527"},{"id":"T2","span":{"begin":55,"end":67},"obj":"http://purl.bioontology.org/ontology/NCBITAXON/4530"},{"id":"T3","span":{"begin":608,"end":619},"obj":"http://purl.bioontology.org/ontology/NCBITAXON/561"},{"id":"T4","span":{"begin":1261,"end":1271},"obj":"http://purl.bioontology.org/ontology/NCBITAXON/415850"},{"id":"T5","span":{"begin":1261,"end":1271},"obj":"http://purl.bioontology.org/ontology/NCBITAXON/570"},{"id":"T6","span":{"begin":1261,"end":1282},"obj":"http://purl.bioontology.org/ontology/NCBITAXON/573"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"GO-BP","denotations":[{"id":"T1","span":{"begin":125,"end":148},"obj":"http://purl.obolibrary.org/obo/GO_0003844"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"GO-MF","denotations":[{"id":"T1","span":{"begin":116,"end":123},"obj":"http://purl.obolibrary.org/obo/GO_0070026"},{"id":"T2","span":{"begin":459,"end":466},"obj":"http://purl.obolibrary.org/obo/GO_0070026"},{"id":"T3","span":{"begin":828,"end":835},"obj":"http://purl.obolibrary.org/obo/GO_0070026"},{"id":"T4","span":{"begin":1157,"end":1164},"obj":"http://purl.obolibrary.org/obo/GO_0070026"},{"id":"T5","span":{"begin":116,"end":123},"obj":"http://purl.obolibrary.org/obo/GO_0003680"},{"id":"T6","span":{"begin":459,"end":466},"obj":"http://purl.obolibrary.org/obo/GO_0003680"},{"id":"T7","span":{"begin":828,"end":835},"obj":"http://purl.obolibrary.org/obo/GO_0003680"},{"id":"T8","span":{"begin":1157,"end":1164},"obj":"http://purl.obolibrary.org/obo/GO_0003680"},{"id":"T9","span":{"begin":116,"end":123},"obj":"http://purl.obolibrary.org/obo/GO_0017091"},{"id":"T10","span":{"begin":459,"end":466},"obj":"http://purl.obolibrary.org/obo/GO_0017091"},{"id":"T11","span":{"begin":828,"end":835},"obj":"http://purl.obolibrary.org/obo/GO_0017091"},{"id":"T12","span":{"begin":1157,"end":1164},"obj":"http://purl.obolibrary.org/obo/GO_0017091"},{"id":"T13","span":{"begin":116,"end":123},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T14","span":{"begin":459,"end":466},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T15","span":{"begin":828,"end":835},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T16","span":{"begin":1157,"end":1164},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T17","span":{"begin":116,"end":131},"obj":"http://purl.obolibrary.org/obo/GO_2001070"},{"id":"T18","span":{"begin":446,"end":466},"obj":"http://purl.obolibrary.org/obo/GO_0030246"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"GO-CC","denotations":[{"id":"T1","span":{"begin":774,"end":780},"obj":"http://purl.obolibrary.org/obo/GO_0097610"},{"id":"T2","span":{"begin":1035,"end":1041},"obj":"http://purl.obolibrary.org/obo/GO_0097610"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"UBERON-AE","denotations":[{"id":"T1","span":{"begin":379,"end":386},"obj":"http://purl.obolibrary.org/obo/UBERON_0012131"},{"id":"T2","span":{"begin":1014,"end":1021},"obj":"http://purl.obolibrary.org/obo/UBERON_0012131"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"Allie","denotations":[{"id":"SS1_21493662_0_0","span":{"begin":25,"end":43},"obj":"expanded"},{"id":"SS2_21493662_0_0","span":{"begin":45,"end":48},"obj":"abbr"},{"id":"SS1_21493662_2_0","span":{"begin":306,"end":329},"obj":"expanded"},{"id":"SS2_21493662_2_0","span":{"begin":331,"end":334},"obj":"abbr"}],"relations":[{"id":"AE1_21493662_0_0","pred":"abbreviatedTo","subj":"SS1_21493662_0_0","obj":"SS2_21493662_0_0"},{"id":"AE1_21493662_2_0","pred":"abbreviatedTo","subj":"SS1_21493662_2_0","obj":"SS2_21493662_2_0"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"performance-test","denotations":[{"id":"PD-UBERON-AE-B_T1","span":{"begin":379,"end":386},"obj":"http://purl.obolibrary.org/obo/UBERON_0012131"},{"id":"PD-UBERON-AE-B_T2","span":{"begin":1014,"end":1021},"obj":"http://purl.obolibrary.org/obo/UBERON_0012131"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"mondo_disease","denotations":[{"id":"T1","span":{"begin":1261,"end":1282},"obj":"Disease"}],"attributes":[{"id":"A1","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0030602"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"Oryza_sentences","blocks":[{"id":"T1","span":{"begin":0,"end":124},"obj":"Sentence"},{"id":"T2","span":{"begin":125,"end":280},"obj":"Sentence"},{"id":"T3","span":{"begin":281,"end":504},"obj":"Sentence"},{"id":"T4","span":{"begin":505,"end":655},"obj":"Sentence"},{"id":"T5","span":{"begin":656,"end":841},"obj":"Sentence"},{"id":"T6","span":{"begin":842,"end":1042},"obj":"Sentence"},{"id":"T7","span":{"begin":1043,"end":1295},"obj":"Sentence"},{"id":"T8","span":{"begin":1296,"end":1448},"obj":"Sentence"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"NCBITAXON","denotations":[{"id":"T1","span":{"begin":55,"end":67},"obj":"OrganismTaxon"},{"id":"T2","span":{"begin":306,"end":310},"obj":"OrganismTaxon"},{"id":"T3","span":{"begin":608,"end":624},"obj":"OrganismTaxon"},{"id":"T4","span":{"begin":764,"end":773},"obj":"OrganismTaxon"},{"id":"T5","span":{"begin":1261,"end":1282},"obj":"OrganismTaxon"}],"attributes":[{"id":"A1","pred":"db_id","subj":"T1","obj":"4530"},{"id":"A2","pred":"db_id","subj":"T2","obj":"4530"},{"id":"A3","pred":"db_id","subj":"T3","obj":"562"},{"id":"A4","pred":"db_id","subj":"T4","obj":"37571"},{"id":"A5","pred":"db_id","subj":"T5","obj":"573"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"Anatomy-UBERON","denotations":[{"id":"T1","span":{"begin":774,"end":780},"obj":"Body_part"},{"id":"T4","span":{"begin":1035,"end":1041},"obj":"Body_part"},{"id":"T7","span":{"begin":1219,"end":1224},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0004704"},{"id":"A2","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0006846"},{"id":"A3","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0014764"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0004704"},{"id":"A5","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0006846"},{"id":"A6","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0014764"},{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0000464"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}

{"project":"HP-phenotype","denotations":[{"id":"T1","span":{"begin":1272,"end":1282},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"HP:0002090"}],"namespaces":[{"prefix":"HP","uri":"http://purl.obolibrary.org/obo/HP_"}],"text":"Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.\nStarch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase."}