Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family

Abstract

The α-amylase is a ubiquitous starch hydrolase catalyzing the cleavage of the α-1,4-glucosidic bonds in an endo-fashion. Various α-amylases originating from different taxonomic sources may differ from each other significantly in their exact substrate preference and product profile. Moreover, it also seems to be clear that at least two different amino acid sequences utilizing two different catalytic machineries have evolved to execute the same α-amylolytic specificity. The two have been classified in the Cabohydrate-Active enZyme database, the CAZy, in the glycoside hydrolase (GH) families GH13 and GH57. While the former and the larger α-amylase family GH13 evidently forms the clan GH-H with the families GH70 and GH77, the latter and the smaller α-amylase family GH57 has only been predicted to maybe define a future clan with the family GH119. Sequences and several tens of enzyme specificities found throughout all three kingdoms in many taxa provide an interesting material for evolutionarily oriented studies that have demonstrated remarkable observations. This review emphasizes just the three of them: (1) a close relatedness between the plant and archaeal α-amylases from the family GH13; (2) a common ancestry in the family GH13 of animal heavy chains of heteromeric amino acid transporter rBAT and 4F2 with the microbial α-glucosidases; and (3) the unique sequence features in the primary structures of amylomaltases from the genus Borrelia from the family GH77. Although the three examples cannot represent an exhaustive list of exceptional topics worth to be interested in, they may demonstrate the importance these enzymes possess in the overall scientific context.

New insight in cereal starch degradation: identification and structural characterization of four α-amylases in bread wheat

“…Available amino acid sequences were taken from a few previous bioinformatics studies [5,[26][27][28][29][30] focusing mainly on the α-amylases from subfamilies GH13_6 (29 plant α-amylases accompanied by 2 bacterial representatives) and GH13_7 (10 archaeal and 2 bacterial sources). These 43 sequences, retrieved from the UniProt knowledge database ( [31]; http://www.uniprot.org/), were completed by the consensus protein sequence for each wheat isoform.…”

“…The TaAMY4 amino acid sequence corresponds to a 47.6 kDa protein mass with a theoretical pI of 6, which classified it as high pI α-amylase according to the ExPASy proteomics server [47]. The overall protein structure is representative of the GH13_6 family corresponding to the α-amylase from the plant kingdom (for a review, see [29]) (Figure 1). TaAMY4 presents a secreting peptide (Gly2-Arg24), a main catalytic domain (domain A including the domain B) with a (β/α) 8 -barrel fold (Leu28-Leu376) and a C-terminal domain C adopting an antiparallel β-sheet structure (Arg366-Lys426).…”

“…A difference in distance between amino acid residues between the isoforms is highlighted in yellow in the TaAMY3. but indicative differences within their conserved sequence regions [4,26,29].…”

“…Based on the observed relationships, the members of isoforms TaAMY1 and TaAMY2 may very probably represent high and low pI α-amylase isozymes, respectively, since they are grouped with well-characterized α-amylase isozymes from barley, i.e. TaAMY1 with high pI isozyme representatives previously classified in the original plant subfamily GH13_6 were added together with their prokaryotic counterparts from the most closely related subfamily GH13_7 [26], covering only the α-amylases from archaeons and bacteria [29]. In agreement with the CAZy classification [51], the two GH13 subfamilies are clearly separated from each other.…”

“…The tree is based on the alignment of the sequence segment spanning almost the entire catalytic (β/α) 8 -barrel domain including the domain B. Except for the α-amylases from wheat determined in the present study (each starts with "TaAmy"), all remaining α-amylases classified in the CAZy database within the α-amylase family GH13 were taken according to previous bioinformatics studies [5,[26][27][28][29][30]. They are characterized in the tree by the letter P, B or A for "Plants", "Bacteria" and "Archaea", respectively, the GH13 subfamily number 6 or 7 for subfamilies GH13_6 and GH13_7, respectively [33], the source of origin (the organism) and the accession number from the UniProt database.…”