Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2

Ali-Ahmad, Ahmad; Garron, Marie-Line; Zamboni, V.; Lenfant, Nicolas; Nurizzo, Didier; Henrissat, Bernard; Berrin, Jean‐Guy; Bourne, Yves; Vincent, Florence

doi:10.1016/j.jsb.2016.11.004

Cited by 7 publications

(7 citation statements)

References 51 publications

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“…Bacterial glycoside hydrolase family 39 (GH39) members typically act as β-xylosidases (Vocadlo et al, 2002;Czjzek et al, 2005;Corrêa et al, 2012), but recent studies have shown that some GH39 enzymes can be devoid of catalytic activity against small xylose-based substrates (Ali-Ahmad et al, 2017). Instead, such enzymes are polyspecific (Jones et al, 2017) and involved in biofilm formation (Baker et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Exploring the Molecular Basis for Substrate Affinity and Structural Stability in Bacterial GH39 β-Xylosidases

Morais

Polo

Domingues

et al. 2020

Front. Bioeng. Biotechnol.

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The glycoside hydrolase family 39 (GH39) is a functionally expanding family with limited understanding about the molecular basis for substrate specificity and extremophilicity. In this work, we demonstrate the key role of the positive-subsite region in modulating substrate affinity and how the lack of a C-terminal extension impacts on oligomerization and structural stability of some GH39 members. The crystallographic and SAXS structures of a new GH39 member from the phytopathogen Xanthomonas citri support the importance of an extended C-terminal to promote oligomerization as a molecular strategy to enhance thermal stability. Comparative structural analysis along with sitedirected mutagenesis showed that two residues located at the positive-subsite region, Lys166 and Asp167, are critical to substrate affinity and catalytic performance, by inducing local changes in the active site for substrate binding. These findings expand the molecular understanding of the mechanisms involved in substrate recognition and structural stability of the GH39 family, which might be instrumental for biological insights, rational enzyme engineering and utilization in biorefineries.

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Section: Introductionmentioning

confidence: 99%

Exploring the Molecular Basis for Substrate Affinity and Structural Stability in Bacterial GH39 β-Xylosidases

Morais

Polo

Domingues

et al. 2020

Front. Bioeng. Biotechnol.

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“…The substrate-binding groove in CmGH1 was slightly larger than that in XynB and smaller than that in GH39wh2, which could be inferred by different states, as XynB and XynB1 appeared to be a tetramer in solution, whereas CcXynB2, PsIG, and GH39wh2 formed monomers in solution (Yang et al, 2004;Czjzek et al, 2005;Santos et al, 2012;Baker et al, 2015;Ali-Ahmad et al, 2017). In addition, the GH1 family members share (α/β) 8 barrel catalytic domain and use Glu as the catalytic residue, whereas the GH3 family members have no specific catalytic domain and use Glu or His or Asp as catalytic acid-base and nucleophile residue, respectively (Rye and Withers, 2000;Vasella et al, 2002).…”

Section: Discussionmentioning

confidence: 93%

“…The catalytic pocket of GH39 family enzymes, such as PslG and GH39wh2, are surrounded by negative charged residues (Ali-Ahmad et al, 2017). The corresponding area in CmGH1 showed the same predominant negative surface potential cluster (Figure 6).…”

Section: Catalytic Center and Active Sites Of Cmgh1mentioning

confidence: 92%

Structural and Functional Insights Into CmGH1, a Novel GH39 Family β-Glucosidase From Deep-Sea Bacterium

Shen

Huo

et al. 2019

Front. Microbiol.

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Glucosidases play key roles in many diseases and are limiting enzymes during cellulose degradation, which is an important part of global carbon cycle. Here, we identified a novel β-glucosidase, CmGH1, isolated from marine bacterium Croceicoccus marinus E4A9 T . In spite of its high sequence and structural similarity with β-xylosidase family members, CmGH1 had enzymatic activity toward p-nitrophenyl-β-D-glucopyranoside (p-NPG) and cellobiose. The K m and K cat values of CmGH1 toward p-NPG were 0.332 ± 0.038 mM and 2.15 ± 0.081 min −1 , respectively. CmGH1 was tolerant to high concentration salts, detergents, as well as many kinds of organic solvents. The crystal structure of CmGH1 was resolved with a 1.8 Å resolution, which showed that CmGH1 was composed of a canonical (α/β) 8 -barrel catalytic domain and an auxiliary β-sandwich domain. Although no canonical catalytic triad residues were found in CmGH1, structural comparison and mutagenesis analysis suggested that residues Gln157 and Tyr264 of CmGH1 were the active sites. Mutant Q157E significantly increased its hydrolase activity up to 15-fold, whereas Y264E totally abolished its enzymatic activity. These results might provide new insights into understanding the different catalytic mechanism during evolution for β-glucosidases and β-xylosidases.

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“…Previously, GH 39 enzymes were regarded as α- l -iduronidases or β-xylosidases. According to the previous phylogenetic analysis performed by Ali-Ahmad et al, the GH 39 family has four subgroups. In this study, GH 39 enzymes were also classified into four subgroups (Figure ).…”

Section: Resultsmentioning

confidence: 99%

“…The GH 39 member in subgroup IV, PslG from Pseudomonas aeruginosa found in chronic leg ulcers, was found to disrupt biofilm matrix exopolysaccharide in bacteria . GH39wh2 from the human gut bacteria Bacteroides cellulosilyticus was classified in subgroup IV and predicted to harbor endoglycosidase activity . TtGH39, Xln-DT, and JB13GH39, as well as other characterized β-xylosidases, were classified into subgroup II.…”

Section: Resultsmentioning

confidence: 99%

Glycoside Hydrolase Family 39 β-Xylosidases Exhibit β-1,2-Xylosidase Activity for Transformation of Notoginsenosides: A New EC Subsubclass

Zhang

et al. 2019

J. Agric. Food Chem.

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β-1,2-Xylosidase activity has not been recorded as an EC subsubclass. In this study, phylogenetic analysis and multiple sequence alignments revealed that characterized β-xylosidases of glycoside hydrolase family (GH) 39 were classified into the same subgroup with conserved amino acid residue positions participating in substrate recognition. Protein−ligand docking revealed that seven of these positions were probably essential to bind xylose−glucose, which is linked by a β-1,2glycosidic bond. Amino acid residues in five of the seven positions are invariant, while those in two of the seven positions are variable with low frequency. Both the wild-type β-xylosidase rJB13GH39 and its mutants with mutation at the two positions exhibited β-1,2-xylosidase activity, as they hydrolyzed o-nitrophenyl-β-D-xylopyranoside and transformed notoginsenosides R 1 and R 2 to ginsenosides Rg 1 and Rh 1 , respectively. The results suggest that all of these characterized GH 39 β-xylosidases probably show β-1,2-xylosidase activity, which should be assigned an EC number with these β-xylosidases as representatives.

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Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2

Cited by 7 publications

References 51 publications

Exploring the Molecular Basis for Substrate Affinity and Structural Stability in Bacterial GH39 β-Xylosidases

Exploring the Molecular Basis for Substrate Affinity and Structural Stability in Bacterial GH39 β-Xylosidases

Structural and Functional Insights Into CmGH1, a Novel GH39 Family β-Glucosidase From Deep-Sea Bacterium

Glycoside Hydrolase Family 39 β-Xylosidases Exhibit β-1,2-Xylosidase Activity for Transformation of Notoginsenosides: A New EC Subsubclass

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