3wkx

Structural highlights

3wkx is a 1 chain structure. Full crystallographic information is available from OCA.
Related: 3wkw
Activity: Glucokinase, with EC number 2.7.1.2

Publication Abstract from PubMed

Enzymes acting on beta-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of beta-l-arabinofuranosyl oligosaccharides in plant cells. Recently, a beta-l-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system of hydroxyproline-linked beta-l-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and beta-l-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional beta-sandwich domains, with one beta-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn(2+) coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the beta-l-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.

Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum.,Ito T, Saikawa K, Kim S, Fujita K, Ishiwata A, Kaeothip S, Arakawa T, Wakagi T, Beckham GT, Ito Y, Fushinobu S Biochem Biophys Res Commun. 2014 Apr 25;447(1):32-7. doi:, 10.1016/j.bbrc.2014.03.096. Epub 2014 Mar 27. PMID:24680821^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

1. ↑ Ito T, Saikawa K, Kim S, Fujita K, Ishiwata A, Kaeothip S, Arakawa T, Wakagi T, Beckham GT, Ito Y, Fushinobu S. Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum. Biochem Biophys Res Commun. 2014 Apr 25;447(1):32-7. doi:, 10.1016/j.bbrc.2014.03.096. Epub 2014 Mar 27. PMID:24680821 doi:http://dx.doi.org/10.1016/j.bbrc.2014.03.096