4O8P

Crystal structure of SthAraf62A, a GH62 family alpha-L-arabinofuranosidase from Streptomyces thermoviolaceus, bound to xylotetraose

Summary for 4O8P

• Entry DOI: 10.2210/pdb4o8p/pdb
• Related: 4O8N 4O8O
• Descriptor: Alpha-L-arabinofuranosidase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: 5-fold beta-propeller, glycosyl hydrolase family 62, gh62, alpha-l-arabinofuranosidase, hydrolase
• Biological source: Streptomyces thermoviolaceus
• Total number of polymer chains: 1
• Total formula weight: 43991.67

Authors

Stogios, P.J.,Wang, W.,Xu, X.,Cui, H.,Master, E.,Savchenko, A. (deposition date: 2013-12-28, release date: 2014-07-02, Last modification date: 2022-08-24)

Primary citation

Wang, W.,Mai-Gisondi, G.,Stogios, P.J.,Kaur, A.,Xu, X.,Cui, H.,Turunen, O.,Savchenko, A.,Master, E.R.
Elucidation of the molecular basis for arabinoxylan-debranching activity of a thermostable family GH62 alpha-l-arabinofuranosidase from Streptomyces thermoviolaceus.
Appl.Environ.Microbiol., 80:5317-5329, 2014

PubMed Abstract: Xylan-debranching enzymes facilitate the complete hydrolysis of xylan and can be used to alter xylan chemistry. Here, the family GH62 α-l-arabinofuranosidase from Streptomyces thermoviolaceus (SthAbf62A) was shown to have a half-life of 60 min at 60°C and the ability to cleave α-1,3 l-arabinofuranose (l-Araf) from singly substituted xylopyranosyl (Xylp) backbone residues in wheat arabinoxylan; low levels of activity on arabinan as well as 4-nitrophenyl α-l-arabinofuranoside were also detected. After selective removal of α-1,3 l-Araf substituents from disubstituted Xylp residues present in wheat arabinoxylan, SthAbf62A could also cleave the remaining α-1,2 l-Araf substituents, confirming the ability of SthAbf62A to remove α-l-Araf residues that are (1→2) and (1→3) linked to monosubstituted β-d-Xylp sugars. Three-dimensional structures of SthAbf62A and its complex with xylotetraose and l-arabinose confirmed a five-bladed β-propeller fold and revealed a molecular Velcro in blade V between the β1 and β21 strands, a disulfide bond between Cys27 and Cys297, and a calcium ion coordinated in the central channel of the fold. The enzyme-arabinose complex structure further revealed a narrow and seemingly rigid l-arabinose binding pocket situated at the center of one side of the β propeller, which stabilized the arabinofuranosyl substituent through several hydrogen-bonding and hydrophobic interactions. The predicted catalytic amino acids were oriented toward this binding pocket, and the catalytic essentiality of Asp53 and Glu213 was confirmed by site-specific mutagenesis. Complex structures with xylotetraose revealed a shallow cleft for xylan backbone binding that is open at both ends and comprises multiple binding subsites above and flanking the l-arabinose binding pocket.

PubMed: 24951792
DOI: 10.1128/AEM.00685-14

Experimental method

X-RAY DIFFRACTION (1.557 Å)