Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose

Abstract

The structures of isomaltase from Saccharomyces cerevisiae and in complex with maltose were determined at resolutions of 1.30 and 1.60 Å, respectively. Isomaltase contains three domains, namely, A, B, and C. Domain A consists of the (β/α)8‐barrel common to glycoside hydrolase family 13. However, the folding of domain C is rarely seen in other glycoside hydrolase family 13 enzymes. An electron density corresponding to a nonreducing end glucose residue was observed in the active site of isomaltase in complex with maltose; however, only incomplete density was observed for the reducing end. The active site pocket contains two water chains. One water chain is a water path from the bottom of the pocket to the surface of the protein, and may act as a water drain during substrate binding. The other water chain, which consists of six water molecules, is located near the catalytic residues Glu277 and Asp352. These water molecules may act as a reservoir that provides water for subsequent hydrolytic events. The best substrate for oligo‐1,6‐glucosidase is isomaltotriose; other, longer‐chain, oligosaccharides are also good substrates. However, isomaltase shows the highest activity towards isomaltose and very little activity towards longer oligosaccharides. This is because the entrance to the active site pocket of isomaltose is severely narrowed by Tyr158, His280, and loop 310–315, and because the isomaltase pocket is shallower than that of other oligo‐1,6‐glucosidases. These features of the isomaltase active site pocket prevent isomalto‐oligosaccharides from binding to the active site effectively.

On the Assessment of Structural Protein Models with ROSETTA-Design and HMMer: Value, Potential and Limitations

“…The correction of this problem and the use of molecular dynamics simulations led to a well refined and reliable model with a good Rd.HMM score. A few months later (when the paper was in press) the 3D-structure of a close homologue (isomaltase) was released (Yamamoto et al, 2010). The Xray data corroborated the model quality, as the model core backbone has an rmsd of 1.81 Å form the experimental data.…”

“…This last procedure is only recommended if your HMMer score is positive and has good statistical significance, for otherwise, the structural inaccuracy of the Rd.HMMs becomes a serious issue. f. Comparative modeling has been extended thanks to methods able to find templates with low sequence homology to the target (Wallace et al, 2005;Karplus, 2009 (Brindis et al, 2011), with the X-ray solved structure of its homologue, the yeast isomaltase (Yamamoto et al, 2010). The isomaltase is shown as blue cartoons and the -glucosidase cartoons are colored according to the amino acid rmsd from isomaltase, ranging from very low (blue) to intermediate (white) to high (red).…”

Docking Sulochrin and Its Derivative as α-Glucosidase Inhibitors of <i>Saccharomyces cerevisiae</i>

“…The target used in this study was the amino acid sequence of S. cerevisiae α-glucosidase MAL12 with 584 amino acids and obtained from SwissProt (code P53341). The template used in this study was the crystal structure of S. cerevisiae oligo-1,6-glucosidase which was obtained from the PDB (PDBID 3A4A) with resolution 1.60 Å and 589 amino acids [16]. The selection of target and template are based on the sequence similarity their amino acids.…”

“…Oligo-1,6-glucosidase has amino acid residues which responsible for the break the glycosidic bond. These residues are His112, Asp215, Glu277, His351 and Asp352 [16]. The presence of these residues makes the crystal structure is suitable to be used as template in the homology process.…”

SCREENING OF Α-Glucosidase INHIBITORS FROM TERMINALIA CATAPPA L. FRUITS USING MOLECULAR DOCKING METHOD AND IN VITRO TEST

“…The Plot calculation was done with PROCHECK program. The active site was defined as 8 amino acid residues: Asp69, His112, Arg213, Asp215, Glu277, His351, Asp352 and Arg442 [12].…”