4O8P: Crystal Structure Of Stharaf62a, A Gh62 Family Alpha-l- Arabinofuranosidase From Streptomyces Thermoviolaceus, Bound To Xylotetraose

Xylan debranching enzymes facilitate the complete hydrolysis of xylan and can be used to alter xylan chemistry. Herein, the GH62 family alpha-l-arabinofuranosidase from Streptomyces thermoviolaceus (SthAbf62A) was shown to have a half-life of 60 min at 60 degrees C, and ability to cleave alpha-1,3 l-arabinofuranose (l-Araf ) from singly-substituted xylopyranosyl (Xylp) backbone residues in wheat arabinoxylan; low activity towards arabinan as well as 4-nitrophenyl alpha-l-arabinofuranoside was also detected. After selectively removing alpha-1,3 l-Araf substituents from di-substituted Xylp residues present in wheat arabinoxylan, SthAbf62A could also cleave the remaining alpha-1,2 l-Araf substituents, confirming the ability of SthAbf62A to remove alpha-l-Araf residues that are (1-->2) and (1-->3) linked to mono-substituted beta-d-Xylp sugars. Three-dimensional structures of SthAbf62A and its complex with xylotetraose and l-arabinose confirmed a five-bladed beta-propeller fold and revealed a molecular Velcro in blade V between the beta1 and beta21 strands, a disulfide bond between Cys 27 and Cys 297, 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 beta propeller, which stabilized the arabinofuranosyl substituent through several hydrogen-bonding and hydrophobic interactions. The predicted catalytic amino acids were oriented towards 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 which is open at both ends and comprises multiple binding subsites above and flanking the l-arabinose binding pocket.
PDB ID: 4O8PDownload
MMDB ID: 121160
PDB Deposition Date: 2013/12/28
Updated in MMDB: 2014/07
Experimental Method:
x-ray diffraction
Resolution: 1.56  Å
Source Organism:
Similar Structures:
Biological Unit for 4O8P: monomeric; determined by author and by software (PISA)
Molecular Components in 4O8P
Label Count Molecule
Protein (1 molecule)
Molecule annotation
Chemicals (8 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB