Sequence fingerprints of enzyme specificities from the glycoside hydrolase family GH57

Abstract

The glycoside hydrolase family 57 (GH57) contains five well-established enzyme specificities: α-amylase, amylopullulanase, branching enzyme, 4-α-glucanotransferase and α-galactosidase. Around 700 GH57 members originate from Bacteria and Archaea, a substantial number being produced by thermophiles. An intriguing feature of family GH57 is that only slightly more than 2 % of its members (i.e., less than 20 enzymes) have already been biochemically characterized. The main goal of the present bioinformatics study was to retrieve from databases, and analyze in detail, sequences having clear features of the five GH57 enzyme specificities mentioned above. Of the 367 GH57 sequences, 56 were evaluated as α-amylases, 99 as amylopullulanases, 158 as branching enzymes, 46 as 4-α-glucanotransferases and 8 as α-galactosidases. Based on the analysis of collected sequences, sequence logos were created for each specificity and unique sequence features were identified within the logos. These features were proposed to define the so-called sequence fingerprints of GH57 enzyme specificities. Domain arrangements characteristic of the individual enzyme specificities as well as evolutionary relationships within the family GH57 are also discussed. The results of this study could find use in rational protein design of family GH57 amylolytic enzymes and also in the possibility of assigning a GH57 specificity to a hypothetical GH57 member prior to its biochemical characterization.

An extremely thermostable amylopullulanase from Staphylothermus marinus displays both pullulan- and cyclodextrin-degrading activities

“…1) and the last CSR-5 with the important residues S503, D504, and W507 (Zona et al 2004) was after the 2nd α-helix of the three-helix bundle (Janeček and Blesák 2011). These structural characteristics of SMApu also accorded with the sequence logo of amylopullulanase very well (Blesák and Janeček 2012).…”

“…In the further study, the catalytic properties of the β-strand region-deleted mutant should be investigated. And the amino acid residues of the active center of SMApu, which were identified according to the solved 3-D structures of T. litoralis (Imamura et al 2003) 4-α-glucanotransferase and Thermococcus kodakaraensis branching enzyme (Santos et al 2011), should be further confirmed by the analysis of its crystal structure since these amino acid residues played important roles in the dual enzyme activities of DT4αGT and TMAmyC (Blesák and Janeček 2012).…”

Complete Genome of the Starch-Degrading MyxobacteriaSandaracinus amylolyticusDSM 53668T

“…However, only two of the catalytic residues, viz. , the nucleophile on strand β4 and the proton donor on strand β7 are conserved (Blesak and Janecek 2012). Irrespective of these differences, GH13, and GH57 both employ the same retaining mechanism of action (Janecek and Kuchtova 2012) .…”

Membrane-bound amylopullulanase is essential for starch metabolism of Sulfolobus acidocaldarius DSM639

“…The third and fourth regions contain the catalytic nucleophile and the acid/base catalyst, respectively. It has been known that amylopullulanase is one of the GH57 family thermostable enzymes from extremophiles, which exhibit α-amylase, 4-α-glucanotransferase, amylopullulanase, α-galactosidase, and branching enzyme depending on the enzyme specificities (Blesák and Janeček 2012). Recently, the crystal structure of GH57-type branching enzyme from Thermus thermophilus revealed that the structural characteristics which contained a (β/α) 7 -barrel and the succeeding α-helical region was essential for correct functioning of this family (Palomo et al 2011).…”