1997
DOI: 10.1002/(sici)1097-0134(199706)28:2<162::aid-prot5>3.0.co;2-h
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Automated docking of glucosyl disaccharides in the glucoamylase active site

Abstract: To better understand the molecular basis of glucomylase selectivity, low-energy conformers of glucosyl disaccharides obtained from relaxed-residue conformational mapping were flexibly docked into the glucoamylase active site using AutoDock 2.2. This procedure ensures that significant conformational space is searched and can produce bound structures comparable to those obtained by protein crystallography. alpha-Linked glucosyl disaccharides except alpha,alpha-trehalose dock easily into the active site while exc… Show more

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Cited by 19 publications
(5 citation statements)
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“…The pocket broadens out above the catalytic residues, and this would explain not only why a range of disaccharides can be hydrolyzed by the enzyme (2, 3), but the broadening above the catalytic residues would also allow the limited movement of an incoming 4-NPG molecule that would be necessary for the formation of (1,3)-, (1,4)-, and (1,6)-linked transglycosylation products (Table III). It is not clear why the non-reducing rather than the reducing end of the substrate is oriented at the bottom of the pocket, but this is presumably related to interactions of the enzyme with key hydroxyl groups of the non-reducing terminal residue (43). Again, the Glu 445 residue at the very bottom of the pocket might be involved in , and family 17 (C).…”
Section: Discussionmentioning
confidence: 99%
“…The pocket broadens out above the catalytic residues, and this would explain not only why a range of disaccharides can be hydrolyzed by the enzyme (2, 3), but the broadening above the catalytic residues would also allow the limited movement of an incoming 4-NPG molecule that would be necessary for the formation of (1,3)-, (1,4)-, and (1,6)-linked transglycosylation products (Table III). It is not clear why the non-reducing rather than the reducing end of the substrate is oriented at the bottom of the pocket, but this is presumably related to interactions of the enzyme with key hydroxyl groups of the non-reducing terminal residue (43). Again, the Glu 445 residue at the very bottom of the pocket might be involved in , and family 17 (C).…”
Section: Discussionmentioning
confidence: 99%
“…This allows optimal and suboptimal structures of enzyme–ligand complexes, including those not previously obtained by X‐ray diffraction or nuclear magnetic resonance (NMR), to be estimated. AutoDock has been a valuable tool for better understanding the structure and function of glucoamylase,28–31 β‐amylase,32, 33 surfactant protein D,34 and α‐1,2‐mannosidase 35. In addition, we have modified AutoDock parameters to more closely estimate the free energy of binding of carbohydrates to proteins 36.…”
Section: Introductionmentioning
confidence: 99%
“…Even though the absence of most authentic standards makes the identification of most products except those linked by ␣-(1 → 6) glycosidic bonds somewhat tentative, it seems likely that GA can form not only every possible ␣-glycosidic bond between two glucose molecules but also every such bond between a nonreducing glucosyl residue and myo-inositol and potentially between the former and lyxose, ribose, and xylose also. Computational studies simulating the docking in the GA active site of the disaccharide products tentatively identified here, such as the docking studies already conducted with all 11 glucosyl disaccharides (Coutinho et al, 1997b), should allow their more certain identification.…”
Section: Discussionmentioning
confidence: 95%