PDBsum entry 1esw

Transferase

PDB id: 1esw

Contents

Protein chain

500 a.a. *

Ligands

GLC-GLC-AC1 ×2

EDO ×2

Waters ×603

* Residue conservation analysis

References listed in PDB file

Key reference

Title

X-Ray structure of acarbose bound to amylomaltase from thermus aquaticus. Implications for the synthesis of large cyclic glucans.

Authors

I.Przylas, Y.Terada, K.Fujii, T.Takaha, W.Saenger, N.Sträter.

Ref.

Eur J Biochem, 2000, 267, 6903-6913. [Ref: ]

PubMed id

11082203

Abstract

As a member of the alpha-amylase superfamily of enzymes, amylomaltase catalyzes either the transglycosylation from one alpha-1,4 glucan to another or an intramolecular cyclization. The latter reaction is typical for cyclodextrin glucanotransferases. In contrast to these enzymes, amylomaltase catalyzes the formation of cyclic glucans with a degree of polymerization larger than 22. To characterize the factors that determine the size of the synthesized cycloamyloses, we have analyzed the X-ray structure of amylomaltase from Thermus aquaticus in complex with the inhibitor acarbose, a maltotetraose derivative, at 1.9 A resolution. Two acarbose molecules are bound to the enzyme, one in the active site groove at subsite -3 to +1 and a second one approximately 14 A away from the nonreducing end of the acarbose bound to the catalytic site. The inhibitor bound to the catalytic site occupies subsites -3 to +1. Unlike the situation in other enzymes of the alpha-amylase family, the inhibitor is not processed and the inhibitory cyclitol ring of acarbose, which mimicks the half chair conformation of the transition state, does not bind to catalytic subsite -1. The minimum ring size of cycloamyloses produced by this enzyme is proposed to be determined by the distance of the specific substrate binding sites at the active site and near Tyr54 and by the size of the 460s loop. The 250s loop might be involved in binding of the substrate at the reducing end of the scissile bond.

Figure 1.
Fig. 1 Molecular structure of acarbose and atom numbering for glucose. (A) The hydroxyl group at C1 is termed O4' if it is connected to another glucose. (B) Arrows mark the four differences between maltotetraose and acarbose: the C6-hydroxyl group of glucose B is absent. The O-glycosidic bond between units A and B is replaced by an N-glycosidic bond. In glucose unit A the O5 oxygen is substituted by a carbon atom (C7) and a double bond is introduced between C5 and C7.

Figure 4.
Fig. 4. Binding mode of acarbose to amylomaltase. (A) Acarbose bound to the active site cleft and (B) acarbose near Tyr54. Oxygen atoms are shaded grey and nitrogen atoms black. Hydrogen bonding interactions are shown by dashed lines and the interatomic distance is given. (A) and (B) were prepared using LIGPLOT [55]. (C) Superposition of selected active site residues of the amylomaltase–acarbose complex (carbon atoms colored yellow) and a mutant Bacillus circulans CGTase bound to a maltononaose substrate (PDB entry 1cxk [45]). Only the glucan residues bound to subsites -1 and +1 are shown (programs MOLSCRIPT [52] and RASTER3D [53]).

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2000, 267, 6903-6913) copyright 2000.