PhanerochaeteV1, Main, Exploration, bibRecord, 000284

Active site and laminarin binding in glycoside hydrolase family 55.

Identifieur interne : 000284 ( Main/Exploration ); précédent : 000283; suivant : 000285

Active site and laminarin binding in glycoside hydrolase family 55.

Auteurs : Christopher M. Bianchetti [États-Unis] ; Taichi E. Takasuka [Japon] ; Sam Deutsch ; Hannah S. Udell [États-Unis] ; Eric J. Yik [États-Unis] ; Lai F. Bergeman [États-Unis] ; Brian G. Fox [États-Unis]

Source :

The Journal of biological chemistry [ 1083-351X ] ; 2015.

RBID : pubmed:25752603

Descripteurs français

KwdFr :
- Biologie informatique (MeSH), Catalyse (MeSH), Concentration en ions d'hydrogène (MeSH), Cristallographie aux rayons X (MeSH), Domaine catalytique (MeSH), Eau (composition chimique), Escherichia coli (métabolisme), Glucanes (composition chimique), Glycosidases (composition chimique), Hydrolyse (MeSH), Liaison aux protéines (MeSH), Modèles moléculaires (MeSH), Mutagenèse (MeSH), Mutation (MeSH), Phanerochaete (enzymologie), Phylogenèse (MeSH), Polyosides (composition chimique), Protéines bactériennes (composition chimique), Streptomyces (enzymologie).
MESH :
- composition chimique : Eau, Glucanes, Glycosidases, Polyosides, Protéines bactériennes.
- enzymologie : Phanerochaete, Streptomyces.
- métabolisme : Escherichia coli.
- Biologie informatique, Catalyse, Concentration en ions d'hydrogène, Cristallographie aux rayons X, Domaine catalytique, Hydrolyse, Liaison aux protéines, Modèles moléculaires, Mutagenèse, Mutation, Phylogenèse.

English descriptors

KwdEn :
- Bacterial Proteins (chemistry), Catalysis (MeSH), Catalytic Domain (MeSH), Computational Biology (MeSH), Crystallography, X-Ray (MeSH), Escherichia coli (metabolism), Glucans (chemistry), Glycoside Hydrolases (chemistry), Hydrogen-Ion Concentration (MeSH), Hydrolysis (MeSH), Models, Molecular (MeSH), Mutagenesis (MeSH), Mutation (MeSH), Phanerochaete (enzymology), Phylogeny (MeSH), Polysaccharides (chemistry), Protein Binding (MeSH), Streptomyces (enzymology), Water (chemistry).
MESH :
- chemical , chemistry : Bacterial Proteins, Glucans, Glycoside Hydrolases, Polysaccharides, Water.
- enzymology : Phanerochaete, Streptomyces.
- metabolism : Escherichia coli.
- Catalysis, Catalytic Domain, Computational Biology, Crystallography, X-Ray, Hydrogen-Ion Concentration, Hydrolysis, Models, Molecular, Mutagenesis, Mutation, Phylogeny, Protein Binding.

Abstract

The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.

DOI: 10.1074/jbc.M114.623579
PubMed: 25752603
PubMed Central: PMC4424323

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<term>Catalysis (MeSH)</term>
<term>Catalytic Domain (MeSH)</term>
<term>Computational Biology (MeSH)</term>
<term>Crystallography, X-Ray (MeSH)</term>
<term>Escherichia coli (metabolism)</term>
<term>Glucans (chemistry)</term>
<term>Glycoside Hydrolases (chemistry)</term>
<term>Hydrogen-Ion Concentration (MeSH)</term>
<term>Hydrolysis (MeSH)</term>
<term>Models, Molecular (MeSH)</term>
<term>Mutagenesis (MeSH)</term>
<term>Mutation (MeSH)</term>
<term>Phanerochaete (enzymology)</term>
<term>Phylogeny (MeSH)</term>
<term>Polysaccharides (chemistry)</term>
<term>Protein Binding (MeSH)</term>
<term>Streptomyces (enzymology)</term>
<term>Water (chemistry)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Biologie informatique (MeSH)</term>
<term>Catalyse (MeSH)</term>
<term>Concentration en ions d'hydrogène (MeSH)</term>
<term>Cristallographie aux rayons X (MeSH)</term>
<term>Domaine catalytique (MeSH)</term>
<term>Eau (composition chimique)</term>
<term>Escherichia coli (métabolisme)</term>
<term>Glucanes (composition chimique)</term>
<term>Glycosidases (composition chimique)</term>
<term>Hydrolyse (MeSH)</term>
<term>Liaison aux protéines (MeSH)</term>
<term>Modèles moléculaires (MeSH)</term>
<term>Mutagenèse (MeSH)</term>
<term>Mutation (MeSH)</term>
<term>Phanerochaete (enzymologie)</term>
<term>Phylogenèse (MeSH)</term>
<term>Polyosides (composition chimique)</term>
<term>Protéines bactériennes (composition chimique)</term>
<term>Streptomyces (enzymologie)</term>
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<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Bacterial Proteins</term>
<term>Glucans</term>
<term>Glycoside Hydrolases</term>
<term>Polysaccharides</term>
<term>Water</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Eau</term>
<term>Glucanes</term>
<term>Glycosidases</term>
<term>Polyosides</term>
<term>Protéines bactériennes</term>
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<keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Phanerochaete</term>
<term>Streptomyces</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Phanerochaete</term>
<term>Streptomyces</term>
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<term>Crystallography, X-Ray</term>
<term>Hydrogen-Ion Concentration</term>
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<term>Concentration en ions d'hydrogène</term>
<term>Cristallographie aux rayons X</term>
<term>Domaine catalytique</term>
<term>Hydrolyse</term>
<term>Liaison aux protéines</term>
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<front><div type="abstract" xml:lang="en">The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. </div>
</front>
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<Title>The Journal of biological chemistry</Title>
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<ArticleTitle>Active site and laminarin binding in glycoside hydrolase family 55.</ArticleTitle>
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<Abstract><AbstractText>The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. </AbstractText>
<CopyrightInformation>© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.</CopyrightInformation>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bianchetti</LastName>
<ForeName>Christopher M</ForeName>
<Initials>CM</Initials>
<AffiliationInfo><Affiliation>From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, the Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, Wisconsin 54901.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Takasuka</LastName>
<ForeName>Taichi E</ForeName>
<Initials>TE</Initials>
<AffiliationInfo><Affiliation>From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, the Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.</Affiliation>
</AffiliationInfo>
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<ForeName>Eric J</ForeName>
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<AffiliationInfo><Affiliation>the Department of Chemistry and Biochemistry, California State University-Fullerton, Fullerton, California 92831.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Bergeman</LastName>
<ForeName>Lai F</ForeName>
<Initials>LF</Initials>
<AffiliationInfo><Affiliation>From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Fox</LastName>
<ForeName>Brian G</ForeName>
<Initials>BG</Initials>
<AffiliationInfo><Affiliation>From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, bgfox@biochem.wisc.edu.</Affiliation>
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Active site and laminarin binding in glycoside hydrolase family 55.

Active site and laminarin binding in glycoside hydrolase family 55.

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