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Title: Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum

Abstract

The genome of the thermophilic fungus Scytalidium thermophilum (strain CBS 625.91) harbours a wide range of genes involved in carbohydrate degradation, including three genes, abf62A, abf62B and abf62C, predicted to encode glycoside hydrolase family 62 (GH62) enzymes. Transcriptome analysis showed that only abf62A and abf62C are actively expressed during growth on diverse substrates including straws from barley, alfalfa, triticale and canola. The abf62A and abf62C genes were expressed in Escherichia coli and the resulting recombinant proteins were characterized. Calcium-free crystal structures of Abf62C in apo and xylotriose bound forms were determined to 1.23 and 1.48 Å resolution respectively. Site-directed mutagenesis confirmed Asp55, Asp171 and Glu230 as catalytic triad residues, and revealed the critical role of non-catalytic residues Asp194, Trp229 and Tyr338 in positioning the scissile α-L-arabinofuranoside bond at the catalytic site. Further, the +2R substrate-binding site residues Tyr168 and Asn339, as well as the +2NR residue Tyr226, are involved in accommodating long-chain xylan polymers. Overall, our structural and functional analysis highlights characteristic differences between Abf62A and Abf62C, which represent divergent subgroups in the GH62 family.

Authors:
 [1];  [2];  [1];  [3];  [3];  [1];  [1];  [1];  [4];  [5];  [6]
  1. Univ. of Toronto, ON (Canada). Dept. of Chemical Engineering and Applied Chemistry.
  2. Argonne National Lab. (ANL), Argonne, IL (United States). Structureal Biology Center.
  3. Concordia Univ., Montreal, Quebec (Canada). Centre for Structural and Functional Genomics.
  4. Concordia Univ., Montreal, Quebec (Canada). Centre for Structural and Functional Genomics and Dept. of Chemistry and Biochemistry.
  5. Concordia Univ., Montreal, Quebec (Canada). Centre for Structural and Functional Genomics and Dept. of Biology.
  6. Univ. of Toronto, ON (Canada); Dept. of Chemical Engineering and Applied Chemistry.
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1212712
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Microbial Biotechnology (Online)
Additional Journal Information:
Journal Volume: 8; Journal Issue: 3; Journal ID: ISSN 1751-7915
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES

Citation Formats

Kaur, Amrit Pal, Nocek, Boguslaw P., Xu, Xiaohui, Lowden, Michael J., Leyva, Juan Francisco, Stogios, Peter J., Cui, Hong, Leo, Rosa Di, Powlowski, Justin, Tsang, Adrian, and Savchenko, Alexei. Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum. United States: N. p., 2015. Web. doi:10.1111/1751-7915.12168.
Kaur, Amrit Pal, Nocek, Boguslaw P., Xu, Xiaohui, Lowden, Michael J., Leyva, Juan Francisco, Stogios, Peter J., Cui, Hong, Leo, Rosa Di, Powlowski, Justin, Tsang, Adrian, & Savchenko, Alexei. Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum. United States. https://doi.org/10.1111/1751-7915.12168
Kaur, Amrit Pal, Nocek, Boguslaw P., Xu, Xiaohui, Lowden, Michael J., Leyva, Juan Francisco, Stogios, Peter J., Cui, Hong, Leo, Rosa Di, Powlowski, Justin, Tsang, Adrian, and Savchenko, Alexei. 2015. "Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum". United States. https://doi.org/10.1111/1751-7915.12168. https://www.osti.gov/servlets/purl/1212712.
@article{osti_1212712,
title = {Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum},
author = {Kaur, Amrit Pal and Nocek, Boguslaw P. and Xu, Xiaohui and Lowden, Michael J. and Leyva, Juan Francisco and Stogios, Peter J. and Cui, Hong and Leo, Rosa Di and Powlowski, Justin and Tsang, Adrian and Savchenko, Alexei},
abstractNote = {The genome of the thermophilic fungus Scytalidium thermophilum (strain CBS 625.91) harbours a wide range of genes involved in carbohydrate degradation, including three genes, abf62A, abf62B and abf62C, predicted to encode glycoside hydrolase family 62 (GH62) enzymes. Transcriptome analysis showed that only abf62A and abf62C are actively expressed during growth on diverse substrates including straws from barley, alfalfa, triticale and canola. The abf62A and abf62C genes were expressed in Escherichia coli and the resulting recombinant proteins were characterized. Calcium-free crystal structures of Abf62C in apo and xylotriose bound forms were determined to 1.23 and 1.48 Å resolution respectively. Site-directed mutagenesis confirmed Asp55, Asp171 and Glu230 as catalytic triad residues, and revealed the critical role of non-catalytic residues Asp194, Trp229 and Tyr338 in positioning the scissile α-L-arabinofuranoside bond at the catalytic site. Further, the +2R substrate-binding site residues Tyr168 and Asn339, as well as the +2NR residue Tyr226, are involved in accommodating long-chain xylan polymers. Overall, our structural and functional analysis highlights characteristic differences between Abf62A and Abf62C, which represent divergent subgroups in the GH62 family.},
doi = {10.1111/1751-7915.12168},
url = {https://www.osti.gov/biblio/1212712}, journal = {Microbial Biotechnology (Online)},
issn = {1751-7915},
number = 3,
volume = 8,
place = {United States},
year = {Fri May 01 00:00:00 EDT 2015},
month = {Fri May 01 00:00:00 EDT 2015}
}

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Works referenced in this record:

Activation of a GH43 β-xylosidase by divalent metal cations: Slow binding of divalent metal and high substrate specificity
journal, May 2013


Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
journal, June 2010


Thermostable conidial and mycelial alkaline phosphatases from the thermophilic fungus Scytalidium thermophilum
journal, October 2001


Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997


β-Glucosidase activity from the thermophilic fungus Scytalidium thermophilum is stimulated by glucose and xylose
journal, November 2004


Cloning, sequencing and expression of an α-l-Arabinofuranosidase from Aspergillus sojae
journal, January 2000


Identification of a GH62 α-l-arabinofuranosidase specific for arabinoxylan produced by Penicillium chrysogenum
journal, December 2010


Molecular and biochemical characterization of three GH62 α-l-arabinofuranosidases from the soil deuteromycete Penicillium funiculosum
journal, October 2013


The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results
journal, December 2005


PROCHECK: a program to check the stereochemical quality of protein structures
journal, April 1993


Isolation and Characterization of CcAbf62A, a GH62 α- L -Arabinofuranosidase, from the Basidiomycete Coprinopsis cinerea
journal, February 2011


An approach to multi-copy search in molecular replacement
journal, December 2000


ESPript: analysis of multiple sequence alignments in PostScript
journal, April 1999


Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007


Crystal Structure and Characterization of the Glycoside Hydrolase Family 62 α-l-Arabinofuranosidase from Streptomyces coelicolor
journal, January 2014


Cellulosic Biofuels
journal, June 2009


A comparison of the non-starch carbohydrates in cereal grains
journal, December 1985


Synergy between enzymes from Aspergillus involved in the degradation of plant cell wall polysaccharides
journal, August 2000


Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains
journal, April 2012


Purification and characterization of a (1,4)-?-d-arabinoxylan arabinofuranohydrolase from Aspergillus awamori
journal, September 1991


Feruloylation in Grasses: Current and Future Perspectives
journal, September 2009


Maximum-likelihood density modification
journal, August 2000


Cellvibrio japonicus α-L-arabinanase 43A has a novel five-blade β-propeller fold
journal, August 2002


Divalent metal activation of a GH43 β-xylosidase
journal, February 2013


New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases: Role of calcium in the glycosidase reaction
journal, September 2010


The Structure of an Inverting GH43 β-Xylosidase from Geobacillus stearothermophilus with its Substrate Reveals the Role of the Three Catalytic Residues
journal, May 2006


Structure validation by Cα geometry: ϕ,ψ and Cβ deviation
journal, January 2003


PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010


First Structural Insights into α-l-Arabinofuranosidases from the Two GH62 Glycoside Hydrolase Subfamilies
journal, January 2014


A new bioinformatics analysis tools framework at EMBL-EBI
journal, May 2010


Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
journal, June 2008


Adaptation of the Nelson-Somogyi reducing-sugar assay to a microassay using microtiter plates
journal, November 1989


Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris
journal, October 2011


Mechanistic Strategies for Catalysis Adopted by Evolutionary Distinct Family 43 Arabinanases
journal, January 2014


Ecology of Thermophilic Fungi in Mushroom Compost, with Emphasis on Scytalidium thermophilum and Growth Stimulation of Agaricus bisporus Mycelium
journal, January 1994


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