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Volumn 7, Issue 5, 1997, Pages 637-644

Structural and sequence-based classification of glycoside hydrolases

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOSIDASE; OLIGOSACCHARIDE; POLYSACCHARIDE;

EID: 0030733350     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80072-3     Document Type: Article
Times cited : (1463)

References (62)
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    • The latest paper in the sequence classification trilogy of glycosyl hydrolases. These three papers [8,9,10] present the rationale and details of the classification of glycoside hydrolases based on amino acid sequence similarities. In this paper, almost 60 families are described, together with details of the 'clan' grouping of structurally related families. The sequence classification has been implemented on the web at URL: http//www.expasy.ch/cgi-bin/list?glycosid.text. of special interest
    • Henrissat B, Bairoch A. Updating the sequence-based classification of glycosyl hydrolases. Biochem J. 316:1996;695-696 The latest paper in the sequence classification trilogy of glycosyl hydrolases. These three papers [8,9,10] present the rationale and details of the classification of glycoside hydrolases based on amino acid sequence similarities. In this paper, almost 60 families are described, together with details of the 'clan' grouping of structurally related families. The sequence classification has been implemented on the web at URL: http//www.expasy.ch/cgi-bin/list?glycosid.text. of special interest.
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    • The crystal structures of Sinapis alba myrosinase and of a covalent glycosyl - enzyme intermediate provide insights into the substrate recognition and active-site machinery of an S-glycosidase
    • The first structure determination for an S-glycosidase. In addition to the native structure, the authors describe the trapping of the covalent glycosyl - enzyme intermediate, via the elegant synthesis and utilisation of a 2-fluorothioglucoside. This enzyme displays a striking sequence and structural similarity with an O-glycosidase from Family 1, the cyanogenic β-glucosidase from Trifolium repens. Both enzymes are involved in plant defence systems, suggesting a close evolutionary link. of outstanding interest
    • Burmeister WP, Cottaz S, Driguez H, Palmieri S, Henrissat B. The crystal structures of Sinapis alba myrosinase and of a covalent glycosyl - enzyme intermediate provide insights into the substrate recognition and active-site machinery of an S-glycosidase. Structure. 5:1997;663-675 The first structure determination for an S-glycosidase. In addition to the native structure, the authors describe the trapping of the covalent glycosyl - enzyme intermediate, via the elegant synthesis and utilisation of a 2-fluorothioglucoside. This enzyme displays a striking sequence and structural similarity with an O-glycosidase from Family 1, the cyanogenic β-glucosidase from Trifolium repens. Both enzymes are involved in plant defence systems, suggesting a close evolutionary link. of outstanding interest.
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    • Many systems for the nomenclature of sugar-binding subsites in carbohydrate-metabolising enzymes exist. In this paper, these various schemes are outlined and compared. The authors recommend that the structural biology community adopts the -n to +n subsite nomenclature that is widely used by enzymologists. Enzymatic cleavage takes place between subsites -1 and +1, with subsites labelled +1, +2 to +n towards the reducing end of the sugar and -1, -2, to -n towards the nonreducing end. The advantage of this system is that it allows the comparison both of different enzymes and different complexes of similar enzymes. The description and comparison of the subsites of the various disaccharidases, and exo or endo polysaccharidases thus becomes simple and consistent. of special interest
    • Davies GJ, Wilson KS, Henrissat B. Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem J. 321:1997;557-559 Many systems for the nomenclature of sugar-binding subsites in carbohydrate-metabolising enzymes exist. In this paper, these various schemes are outlined and compared. The authors recommend that the structural biology community adopts the -n to +n subsite nomenclature that is widely used by enzymologists. Enzymatic cleavage takes place between subsites -1 and +1, with subsites labelled +1, +2 to +n towards the reducing end of the sugar and -1, -2, to -n towards the nonreducing end. The advantage of this system is that it allows the comparison both of different enzymes and different complexes of similar enzymes. The description and comparison of the subsites of the various disaccharidases, and exo or endo polysaccharidases thus becomes simple and consistent. of special interest.
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    • This and the preceding paper by Sulzenbacher et al. [19] describe the first endoglucanase structure from Family 7. The active site is located in a long substrate-binding groove as is typical for an endo-acting hydrolase. The corresponding cellobiohydrolase from this family, CBH I, has its substrate binding surface within a tunnel, implying a processive mechanism. The authors describe the use of a nonhydrolysable thio-oligosaccharide, which binds with a skew-boat conformation in the active site, resulting in an axial leaving-group orientation. This conformation brings catalytic benefit as it opens up the C-1 atom for nucleophilic attack, is closer to the reaction transition state and provides beneficial stereoelectronics. of special interest
    • Sulzenbacher G, Schülein M, Davies GJ. Structures of the endoglucanase I from Fusarium oxysporum: native, cellobiose and 3,4-epoxybutyl β-D-cellobioside inhibited forms at 2.3 Å resolution. Biochemistry. 36:1997;5902-5911 This and the preceding paper by Sulzenbacher et al. [19] describe the first endoglucanase structure from Family 7. The active site is located in a long substrate-binding groove as is typical for an endo-acting hydrolase. The corresponding cellobiohydrolase from this family, CBH I, has its substrate binding surface within a tunnel, implying a processive mechanism. The authors describe the use of a nonhydrolysable thio-oligosaccharide, which binds with a skew-boat conformation in the active site, resulting in an axial leaving-group orientation. This conformation brings catalytic benefit as it opens up the C-1 atom for nucleophilic attack, is closer to the reaction transition state and provides beneficial stereoelectronics. of special interest.
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    • Modern developments in molecular replacement
    • A review of the most recent developments in structure solution using molecular replacement. Of particular interest to those working on glycoside hydrolases is the review of current computer programs and methodologies for molecular replacement, plus the descriptions of molecular replacement utilising search models with low sequence similarity to the target structure. As more and more structural representatives from the glycoside hydrolase families become known, molecular replacement utilising the family-derived information is likely to become an important research tool. of special interest
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    • 8 domain which displays sequence similarity to the catalytic domain of the Family 20 human hexosaminidases. Inherited genetic defects in the human hexosaminidases are responsible for a number of disease conditions. The authors have been able to utilise this structure and the sequence relationships within this family to define the structural basis of the pathogenic mutations that underlie Tay - Sachs and Sandhoff diseases. In addition, the chitobiose complex of this structure presents strong evidence in favour of anchimeric (substrate-assisted) catalysis by retaining N-acetyl-glucosamine hydrolases. of outstanding interest.
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    • Crystallographic observation of a covalent catalytic intermediate in a β-glycosidase
    • The first direct crystallographic observation of a trapped covalent glycosyl - enzyme intermediate. The majority of β-retaining enzymes perform catalysis by a double-displacement reaction mechanism in which a covalent glycosyl - enzyme intermediate is formed and subsequently rehydrolysed via oxocarbenium-ion-like transition states, as can be demonstrated by many means - in particular, by secondary kinetic isotope effects. In this case, the covalent glycosyl - enzyme intermediate is trapped on-enzyme via the use of 2-fluoro sugars, permitting a full crystallographic analysis of the complex. of outstanding interest
    • White A, Tull D, Johns K, Withers SG, Rose DR. Crystallographic observation of a covalent catalytic intermediate in a β-glycosidase. Nat Struct Biol. 3:1996;149-154 The first direct crystallographic observation of a trapped covalent glycosyl - enzyme intermediate. The majority of β-retaining enzymes perform catalysis by a double-displacement reaction mechanism in which a covalent glycosyl - enzyme intermediate is formed and subsequently rehydrolysed via oxocarbenium-ion-like transition states, as can be demonstrated by many means - in particular, by secondary kinetic isotope effects. In this case, the covalent glycosyl - enzyme intermediate is trapped on-enzyme via the use of 2-fluoro sugars, permitting a full crystallographic analysis of the complex. of outstanding interest.
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* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.