title: Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16.
abstract: The recent division of the large glycoside hydrolase family 43 (GH43) into subfamilies offers a renewed opportunity to develop structure-function studies aimed at clarifying the molecular determinants of substrate specificity in carbohydrate-degrading enzymes. α-L-Arabinofuranosidases (EC 3.2.1.55) remove arabinose side chains from heteropolysaccharides such as xylan and arabinan. However, there is some evidence suggesting that arabinofuranosidases are substrate-specific, being unable to display a debranching activity on different polysaccharides. Here, the structure of Clostridium thermocellum arabinofuranosidase 43A (CtAbf43A), which has been shown to act in the removal of arabinose side chains from arabinoxylan but not from pectic arabinan, is reported. CtAbf43A belongs to GH43 subfamily 16, the members of which have a restricted capacity to attack xylans. The crystal structure of CtAbf43A comprises a five-bladed β-propeller fold typical of GH43 enzymes. CtAbf43A displays a highly compact architecture compatible with its high thermostability. Analysis of CtAbf43A along with the other member of GH43 subfamily 16 with known structure, the Bacillus subtilis arabinofuranosidase BsAXH-m2,3, suggests that the specificity of subfamily 16 for arabinoxylan is conferred by a long surface substrate-binding cleft that is complementary to the xylan backbone. The lack of a curved-shaped carbohydrate-interacting platform precludes GH43 subfamily 16 enzymes from interacting with the nonlinear arabinan scaffold and therefore from deconstructing this polysaccharide.
authors.affiliation: Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India.
authors.forename: Arun
authors.initials: A
authors.lastname: Goyal
authors.affiliation: Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411 007, India.
authors.forename: Shadab
authors.initials: S
authors.lastname: Ahmed
authors.affiliation: Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India.
authors.forename: Kedar
authors.initials: K
authors.lastname: Sharma
authors.affiliation: Qiagen Aarhus, Silkeborgvej 2, 8000 Aarhus C, Denmark.
authors.forename: Vikas
authors.initials: V
authors.lastname: Gupta
authors.affiliation: CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1360-477 Lisbon, Portugal.
authors.forename: Pedro
authors.initials: P
authors.lastname: Bule
authors.affiliation: CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1360-477 Lisbon, Portugal.
authors.forename: Victor D
authors.initials: VD
authors.lastname: Alves
authors.affiliation: CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1360-477 Lisbon, Portugal.
authors.forename: Carlos M G A
authors.initials: CM
authors.lastname: Fontes
authors.affiliation: CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1360-477 Lisbon, Portugal.
authors.forename: Shabir
authors.initials: S
authors.lastname: Najmudin
mesh_terms: D000595:Amino Acid Sequence; D048013:Acetivibrio thermocellus / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D018360:Crystallography, X-Ray; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D010368:Pectins / Q000378:metabolism; D011487:Protein Conformation; D016415:Sequence Alignment; D013379:Substrate Specificity; D014990:Xylans / Q000378:metabolism
chemical_list: D014990:Xylans; D010368:Pectins; C085118:arabinoxylan; D006026:Glycoside Hydrolases; C019713:alpha-N-arabinofuranosidase
keywords: CAZymes; Clostridium thermocellum; arabinofuranosidases; arabinoxylan; glycoside hydrolase family 43; pectin; xylan; α-l-arabinofuranosidase