Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases

Harvey, Andrew J.; Hrmová, Mária; Gori, Ross De; Varghese, Joseph

doi:10.1002/1097-0134(20001101)41:2<257::aid-prot100>3.0.co;2-c

Cited by 112 publications

(104 citation statements)

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“…There are Ͼ180 known members of this family, most of which are classified as ␤-D-glucosidases, ␤-D-xylosidases, or N-acetyl ␤-D-glucosaminidases and are of microbial origin (Henrissat, 1991;Harvey et al, 2000; http:// afmb.cnrs-mrs.fr/CAZY/). However, when the sequences Broad-Specificity ␤-D-Glucan Glucohydrolases 1045 derived exclusively from higher plant enzymes are used to generate a phylogenetic tree, two quite distinct groups of enzymes become evident ( Figure 9A).…”

Section: Broad-specificity ␤-D-glucan Glucohydrolases 1043mentioning

confidence: 99%

“…There are Ͼ180 known members of this family, most of which are classified as ␤-D-glucosidases, ␤-D-xylosidases, or N-acetyl ␤-D-glucosaminidases and are of microbial origin (Henrissat, 1991;Harvey et al, 2000; http:// afmb.cnrs-mrs.fr/CAZY/). However, when the sequences The derived 2|F o |-|F c | and |F o |-|F c | Fourier syntheses are contoured at 1.0 and 1.15 for the S-cellobioside and S-laminaribioside moieties, respectively.…”

Section: Figure 5 Bonding Interactions Of Barley ␤-D-glucan Glucohydmentioning

confidence: 99%

“…In view of the structural similarities of the barley and other plant ␤ -D -glucan glucohydrolases (Harvey et al, 2000), the barley enzyme can be used as a model to explain the broad specificity of these enzymes more generally in higher plants. In particular, a structural rationale was sought for the ability of the barley enzyme to hydrolyze the (1 → 2)-, (1 → 3)-, (1 → 4)-, or (1 → 6)-␤ -D -linked disaccharides sophorose, laminaribiose, cellobiose, and gentiobiose (Hrmova and Fincher, 1998).…”

Section: Introductionmentioning

confidence: 99%

“…A 13-Å-deep pocket at the interface of the two domains has been identified as the active site of the enzyme. The catalytic nucleophile of the barley enzyme is amino acid residue Asp-285, and the catalytic acid/base is Glu-491 (Varghese et al, 1999;Harvey et al, 2000;. The crystal structure revealed that a Glc molecule remains tightly bound in the active site pocket and is probably the product of the enzyme-catalyzed reaction that is not released after hydrolysis (Varghese et al, 1999).…”

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Structural Basis for Broad Substrate Specificity in Higher Plant β-d-Glucan Glucohydrolases

et al. 2002

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Family 3 ␤ -D -glucan glucohydrolases are distributed widely in higher plants. The enzymes catalyze the hydrolytic removal of ␤ -D -glucosyl residues from nonreducing termini of a range of ␤ -D -glucans and ␤ -D -oligoglucosides. Their broad specificity can be explained by x-ray crystallographic data obtained from a barley ␤ -D -glucan glucohydrolase in complex with nonhydrolyzable S -glycoside substrate analogs and by molecular modeling of enzyme/substrate complexes. The glucosyl residue that occupies binding subsite ؊ 1 is locked tightly into a fixed position through extensive hydrogen bonding with six amino acid residues near the bottom of an active site pocket. In contrast, the glucosyl residue at subsite ؉ 1 is located between two Trp residues at the entrance of the pocket, where it is constrained less tightly. The relative flexibility of binding at subsite ؉ 1, coupled with the projection of the remainder of bound substrate away from the enzyme's surface, means that the overall active site can accommodate a range of substrates with variable spatial dispositions of adjacent ␤ -D -glucosyl residues. The broad specificity for glycosidic linkage type enables the enzyme to perform diverse functions during plant development. INTRODUCTION␤ -D -Glucan glucohydrolases have been purified and characterized from barley seedlings, maize coleoptiles, soybean cultures, Acacia cells, nasturtium cells, and cultured tobacco cells (Cline and Albersheim, 1981;Nari et al., 1982;Lienart et al., 1986;Labrador and Nevins, 1989;Hrmova et al., 1996;Kotake et al., 1997;Crombie et al., 1998;Kim et al., 2000;Koizumi et al., 2000). They can hydrolyze glycosidic linkages in several ␤ -D -glucans, in ␤ -D -oligoglucosides containing (1 → 2)-, (1 → 3)-, (1 → 4)-, or (1 → 6)-linkages, in aryl ␤ -D -glucosides such as 4 Ј -nitrophenyl ␤ -D -glucopyranoside (4NPGlc), and in some ␤ -D -oligoxyloglucosides (Crombie et al., 1998;Hrmova and Fincher, 1998;Kim et al., 2000). The barley ␤ -D -glucan glucohydrolases also hydrolyze cyanogenic ␤ -D -glucosides, albeit with low activity (M. Hrmova and G.B. Fincher, unpublished data). Single Glc molecules are released from the nonreducing termini of these substrates, with retention of the anomeric configuration (Hrmova et al., 1996). Their broad substrate specificity makes it difficult to assign these higher plant ␤ -D -glucan glucohydrolases to current Enzyme Commission classes; therefore, they have been described variously as ␤ -D -glucan glucohydrolases, (1 → 3)-␤ -D -glucan exohydrolases, and ␤ -D -glucosidases. Nevertheless, they can be classified according to the structural criteria of Henrissat (1991) and fall into the family 3 group of glycoside hydrolases (http://afmb.cnrsmrs.fr/CAZY/).The distribution of the broad-specificity ␤ -D -glucan glucohydrolases in various tissues of monocotyledons and dicotyledons, together with the presence of expressed sequence tags in gymnosperm sequence databases (e.g., Pinus taeda ), suggests that they may play a fundamental role in plant growth and development...

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Section: Broad-specificity ␤-D-glucan Glucohydrolases 1043mentioning

confidence: 99%

“…There are Ͼ180 known members of this family, most of which are classified as ␤-D-glucosidases, ␤-D-xylosidases, or N-acetyl ␤-D-glucosaminidases and are of microbial origin (Henrissat, 1991;Harvey et al, 2000; http:// afmb.cnrs-mrs.fr/CAZY/). However, when the sequences The derived 2|F o |-|F c | and |F o |-|F c | Fourier syntheses are contoured at 1.0 and 1.15 for the S-cellobioside and S-laminaribioside moieties, respectively.…”

Section: Figure 5 Bonding Interactions Of Barley ␤-D-glucan Glucohydmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structural Basis for Broad Substrate Specificity in Higher Plant β-d-Glucan Glucohydrolases

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“…Six BGL genes, whose expression is tested in this study, belong to the GH3 family (Table 1). GH3 family BGLs catalyse the removal of monosaccharide residue, including glucose, from the non-reducing ends of a variety of substrates (Harvey et al, 2000). CC_2227 belongs to the GH9 family that primarily contains endogluconases and some GH9 family members contain a C-terminal carbohydratebinding module (CBM) that makes them processive (Sakon et al, 1997).…”

Section: Discussionmentioning

confidence: 99%

Extracellular gluco-oligosaccharide degradation by Caulobacter crescentus

et al. 2014

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The oligotrophic bacterium Caulobacter crescentus has the ability to metabolize various organic molecules, including plant structural carbohydrates, as a carbon source. The nature of b-glucosidase (BGL)-mediated gluco-oligosaccharide degradation and nutrient transport across the outer membrane in C. crescentus was investigated. All gluco-oligosaccharides tested (up to celloheptose) supported growth in M2 minimal media but not cellulose or CM-cellulose. The periplasmic and outer membrane fractions showed highest BGL activity, but no significant BGL activity was observed in the cytosol or extracellular medium. Cells grown in cellobiose showed expression of specific BGLs and TonB-dependent receptors (TBDRs). Carbonyl cyanide 3-chlorophenylhydrazone lowered the rate of cell growth in cellobiose but not in glucose, indicating potential cellobiose transport into the cell by a proton motive force-dependent process, such as TBDR-dependent transport, and facilitated diffusion of glucose across the outer membrane via specific porins. These results suggest that C. crescentus acquires carbon from cellulose-derived gluco-oligosaccharides found in the environment by extracellular and periplasmic BGL activity and TBDR-mediated transport. This report on extracellular degradation of gluco-oligosaccharides and methods of nutrient acquisition by C. crescentus supports a broader suite of carbohydrate metabolic capabilities suggested by the C. crescentus genome sequence that until now have not been reported.

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Functional Genomics and Structural Biology in the Definition of Gene Function

Hrmová

2009

Plant Genomics

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By mid-2007, the three-dimensional (3D) structures of some 45,000 proteins have been solved, over a period where the linear structures of millions of genes have been defined. Technical challenges associated with X-ray crystallography are being overcome and high-throughput methods both for crystallization of proteins and for solving their 3D structures are under development. The question arises as to how structural biology can be integrated with and adds value to functional genomics programs. Structural biology will assist in the definition of gene function through the identification of the likely function of the protein products of genes. The 3D information allows protein sequences predicted from DNA sequences to be classified into broad groups, according to the overall 'fold', or 3D shape, of the protein. Structural information can be used to predict the preferred substrate of a protein, and thereby greatly enhance the accurate annotation of the corresponding gene. Furthermore, it will enable the effects of amino acid substitutions in enzymes to be better understood with respect to enzyme function and could thereby provide insights into natural variation in genes. If the molecular basis of transcription factor-DNA interactions were defined through precise 3D knowledge of the protein-DNA binding site, it would be possible to predict the effects of base substitutions within the motif on the specificity and/or kinetics of binding. In this chapter, we present specific examples of how structural biology can provide valuable information for functional genomics programs.

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Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases

Cited by 112 publications

References 53 publications

Structural Basis for Broad Substrate Specificity in Higher Plant β-d-Glucan Glucohydrolases

Structural Basis for Broad Substrate Specificity in Higher Plant β-d-Glucan Glucohydrolases

Extracellular gluco-oligosaccharide degradation by Caulobacter crescentus

Functional Genomics and Structural Biology in the Definition of Gene Function

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