Identification of the acid/base catalyst of a glycoside hydrolase family 3 (GH3) β-glucosidase from Aspergillus niger ASKU28

2013 ◽  
Vol 1830 (3) ◽  
pp. 2739-2749 ◽  
Author(s):  
Preeyanuch Thongpoo ◽  
Lauren S. McKee ◽  
Ana Catarina Araújo ◽  
Prachumporn T. Kongsaeree ◽  
Harry Brumer
Keyword(s):  
Aspergillus Niger ◽  
Glycoside Hydrolase ◽  
Glycoside Hydrolase Family ◽  
Base Catalyst ◽  
Acid Base ◽  
Hydrolase Family

scholarly journals Biochemical characterization of a glycoside hydrolase family 43 β-D-galactofuranosidase from the fungus Aspergillus niger

2021 ◽  
Author(s):  
Gregory S Bulmer ◽  
Fang Wei Yuen ◽  
Naimah Begum ◽  
Bethan S Jones ◽  
Sabine S Flitsch ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Glycoside Hydrolase ◽  
Biochemical Characterization ◽  
Maximum Activity ◽  
Glycoside Hydrolase Family ◽  
Enzyme Specificity ◽  
Fungal Enzymes ◽  
Glycoside Hydrolase Family 43 ◽  
Hydrolase Family

β-D-Galactofuranose (Galf) and its polysaccharides are found in bacteria, fungi and protozoa but do not occur in mammalian tissues, and thus represent a specific target for anti-pathogenic drugs. Understanding the enzymatic degradation of these polysaccharides is therefore of great interest, but the identity of fungal enzymes with exclusively galactofuranosidase activity has so far remained elusive. Here we describe the identification and characterization of a galactofuranosidase from the industrially important fungus Aspergillus niger. Phylogenetic analysis of glycoside hydrolase family 43 subfamily 34 (GH43_34) members revealed the occurrence of three distinct clusters and, by comparison with specificities of characterized bacterial members, suggested a basis for prediction of enzyme specificity. Using this rationale, in tandem with molecular docking, we identified a putative β-D-galactofuranosidase from A. niger which was recombinantly expressed in Escherichia coli. The Galf-specific hydrolase, encoded by xynD demonstrates maximum activity at pH 5, 25 °C towards 4-Nitrophenyl-β-galactofuranoside (pNP-βGalf), with a Km of 17.9 ± 1.9 mM and Vmax of 70.6 ± 5.3 μmol min-1. The characterization of this first fungal GH43 galactofuranosidase offers further molecular insight into the degradation of Galf-containing structures and may inform clinical treatments against fungal pathogens.

Crystal Structure of Aspergillus niger Isopullulanase, a Member of Glycoside Hydrolase Family 49

2008 ◽  
Vol 376 (1) ◽  
pp. 210-220 ◽  
Author(s):  
Masahiro Mizuno ◽  
Atsushi Koide ◽  
Akihiro Yamamura ◽  
Hiromi Akeboshi ◽  
Hiromi Yoshida ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Aspergillus Niger ◽  
Glycoside Hydrolase ◽  
Glycoside Hydrolase Family ◽  
Hydrolase Family

scholarly journals Biochemical characterization of Aspergillus niger CfcI, a glycoside hydrolase family 18 chitinase that releases monomers during substrate hydrolysis

Microbiology ◽  
2012 ◽  
Vol 158 (8) ◽  
pp. 2168-2179 ◽  
Author(s):  
Jolanda M. van Munster ◽  
Rachel M. van der Kaaij ◽  
Lubbert Dijkhuizen ◽  
Marc J. E. C. van der Maarel
Keyword(s):  
Aspergillus Niger ◽  
Glycoside Hydrolase ◽  
Biochemical Characterization ◽  
Glycoside Hydrolase Family ◽  
Hydrolase Family ◽  
Substrate Hydrolysis

The Pseudomonas cellulosa glycoside hydrolase family 51 arabinofuranosidase exhibits wide substrate specificity

2001 ◽  
Vol 358 (3) ◽  
pp. 607-614 ◽  
Author(s):  
Marie-Helene BEYLOT ◽  
Vincent A. McKIE ◽  
Alphons G. J. VORAGEN ◽  
Chantal H. L. DOESWIJK-VORAGEN ◽  
Harry J. GILBERT
Keyword(s):  
Substrate Specificity ◽  
Glycoside Hydrolase ◽  
Genomic Dna ◽  
Biochemical Properties ◽  
Glycoside Hydrolase Family ◽  
Acid Base ◽  
Membrane Bound ◽  
Hydrolase Family ◽  
Glycoside Hydrolase Family 51 ◽  
Wide Substrate Specificity

To investigate the mechanism by which Pseudomonas cellulosa releases arabinose from polysaccharides and oligosaccharides, a gene library of P. cellulosa genomic DNA was screened for 4-methylumbelliferyl-α-l-arabinofuranosidase (MUAase) activity. A single MUAase gene (abf51A) was isolated, which encoded a non-modular glycoside hydrolase family (GH) 51 arabinofuranosidase (Abf51A) of 57000Da. The substrate specificity of the Abf51A showed that it preferentially removed α1,2- and α1,3-linked arabinofuranose side chains from either arabinan or arabinoxylan, and hydrolysed α1,5-linked arabino-oligosaccharides, although at a much lower rate. The activity of Abf51A against arabinoxylan was similar to a GH62 arabinofuranosidase encoded by a P. cellulosa gene. Glu-194 and Glu-321 of Abf51A are conserved in GH51 enzymes, and it has been suggested that these amino acids comprise the key catalytic acid/base and nucleophile residues, respectively. To evaluate this hypothesis the biochemical properties of E194A and E321A mutants of Abf51A were evaluated. The data were consistent with the view that Glu-194 and Glu-321 comprise the key catalytic residues of Abf51A. These data, in conjunction with the results presented in the accompanying paper [Beylot, Emami, McKie, Gilbert and Pell (2001) Biochem. J. 358, 599–605], indicate that P. cellulosa expresses a membrane-bound GH51 arabinofuranosidase that plays a pivotal role in releasing arabinose from a range of polysaccharides and oligosaccharides.

Xylanases of glycoside hydrolase family 30 – An overview

2021 ◽  
Vol 47 ◽  
pp. 107704
Author(s):  
Vladimír Puchart ◽  
Katarína Šuchová ◽  
Peter Biely
Keyword(s):  
Glycoside Hydrolase ◽  
Glycoside Hydrolase Family ◽  
Hydrolase Family ◽  
Glycoside Hydrolase Family 30

scholarly journals Modeled 3D-Structures of Proteobacterial Transglycosylases from Glycoside Hydrolase Family 17 Give Insight in Ligand Interactions Explaining Differences in Transglycosylation Products

2021 ◽  
Vol 11 (9) ◽  
pp. 4048
Author(s):  
Javier A. Linares-Pastén ◽  
Lilja Björk Jonsdottir ◽  
Gudmundur O. Hreggvidsson ◽  
Olafur H. Fridjonsson ◽  
Hildegard Watzlawick ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Ligand Docking ◽  
Glycoside Hydrolase Family ◽  
Ligand Interactions ◽  
Tim Barrel ◽  
Branching Point ◽  
The Difference ◽  
Dynamics Simulations ◽  
And Function ◽  
Hydrolase Family

The structures of glycoside hydrolase family 17 (GH17) catalytic modules from modular proteins in the ndvB loci in Pseudomonas aeruginosa (Glt1), P. putida (Glt3) and Bradyrhizobium diazoefficiens (previously B. japonicum) (Glt20) were modeled to shed light on reported differences between these homologous transglycosylases concerning substrate size, preferred cleavage site (from reducing end (Glt20: DP2 product) or non-reducing end (Glt1, Glt3: DP4 products)), branching (Glt20) and linkage formed (1,3-linkage in Glt1, Glt3 and 1,6-linkage in Glt20). Hybrid models were built and stability of the resulting TIM-barrel structures was supported by molecular dynamics simulations. Catalytic amino acids were identified by superimposition of GH17 structures, and function was verified by mutagenesis using Glt20 as template (i.e., E120 and E209). Ligand docking revealed six putative subsites (−4, −3, −2, −1, +1 and +2), and the conserved interacting residues suggest substrate binding in the same orientation in all three transglycosylases, despite release of the donor oligosaccharide product from either the reducing (Glt20) or non-reducing end (Glt1, Gl3). Subsites +1 and +2 are most conserved and the difference in release is likely due to changes in loop structures, leading to loss of hydrogen bonds in Glt20. Substrate docking in Glt20 indicate that presence of covalently bound donor in glycone subsites −4 to −1 creates space to accommodate acceptor oligosaccharide in alternative subsites in the catalytic cleft, promoting a branching point and formation of a 1,6-linkage. The minimum donor size of DP5, can be explained assuming preferred binding of DP4 substrates in subsite −4 to −1, preventing catalysis.

scholarly journals Understanding the Polymerization Mechanism of Glycoside-Hydrolase Family 70 Glucansucrases

2006 ◽  
Vol 281 (42) ◽  
pp. 31254-31267
Author(s):  
Claire Moulis ◽  
Gilles Joucla ◽  
David Harrison ◽  
Emeline Fabre ◽  
Gabrielle Potocki-Veronese ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Glycoside Hydrolase Family ◽  
Polymerization Mechanism ◽  
Hydrolase Family
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