Crystal Structure of an Essential Enzyme in Seed Starch Degradation: Barley Limit Dextrinase in Complex with Cyclodextrins

Allelic variation at a single gene increases food value in a drought-tolerant staple cereal

“…It has been proposed that the N-terminal domain, although poorly defined functionally, forms one-half of a pore, leading to the catalytic region in HvLD. In vivo support for this function, however, is lacking at present in cereals 25 . Identification of the variant SbPUL-GD allele type will allow further biochemical studies of sorghum pullulanase and may shed insight into the function of the N-terminal domain.…”

“…Superimposing our sorghum gene models onto the Hordeum vulgare limit dextrinase (HvLD) three-dimensional structure revealed that these residues are solvent exposed and proximal to one another in the folded peptide ( Supplementary Fig. S1) 24,25 . This implies that the SbPUL-RA allele product resembles other cereal pullulanases in these conserved regions both in primary sequence and possibly in peptide chemical properties within the region.…”

Association of Novel Domain in Active Site of Archaic Hyperthermophilic Maltogenic Amylase from Staphylothermus marinus

“…Previously, CBMs were thought to be motifs that are functionally independent from the catalytic domains located distal to the active sites, and it has been proposed that they enhance the interaction between the carbohydrate substrate and protein (52)(53)(54)(55). For many amylolytic enzymes, CBMs were reportedly involved in starch hydrolysis by disrupting the starch granule structure, which allowed for a concentration of catalytic domains on the surface and carbohydrate starch hydrolysis by proximity (56 -59).…”

“…The only exception is represented by the ␤-subunit of AMPK (37), which showed that CBM48 is a separate domain that binds cyclodextrin to increase its binding ability for the glucosyl polymeric structures commonly found in glycogen (62). Despite the wealth of structural information on CBM48 (36,52,55,(63)(64)(65)(66)(67) (for a review, see Ref. 68)), this paper is, to the best of our knowledge, the first to demonstrate that an independent CBM domain folds to interact with the catalytic domain and participates in substrate binding at the active site.…”

Crystal Structure of Barley Limit Dextrinase-Limit Dextrinase Inhibitor (LD-LDI) Complex Reveals Insights into Mechanism and Diversity of Cereal Type Inhibitors

“…However, three short flexible loops in the N-terminal domain of free LD (28) were too flexible to be modeled in LD-LDI as seen also for LD-cyclodextrin complexes (29). The catalytic site residues Asp 473 , Glu 510 , and Asp 642 from free LD and from LD in complex with LDI were essentially superimposable, but two residues at the active site, Phe 553 and Arg 697 , adopted different rotamers in LD-LDI compared with free LD (Fig.…”