A QM/MM study of the catalytic mechanism of alpha-1,4-glucan lyase from the red seaweed Gracilariopsis lemaneiformis

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	A QM/MM study of the catalytic mechanism of alpha-1,4-glucan lyase from the red seaweed Gracilariopsis lemaneiformis
	Su, Hao ; Dong, Lihua ; Liu, Yongjun
	2014
发表期刊	RSC ADVANCES ; Su, H; Dong, LH; Liu, YJ.A QM/MM study of the catalytic mechanism of alpha-1,4-glucan lyase from the red seaweed Gracilariopsis lemaneiformis,RSC ADVANCES,2014,4(97):54398
摘要	alpha-1,4-Glucan lyase (GLase, EC 4.2.2.13), a unique glycoside hydrolase family member, specifically cleaves the alpha-1,4-glucosidic linkages in glycogen, starch and malto-oligosaccharides to produce 1,5-anhydro-D-fructose from the non-reducing end. Previous studies have proved that GLase belongs to the retaining glycoside lyase, and the catalytic reaction contains both the glycosylation and deglycosylation/elimination steps, in which a covalent glycosyl-enzyme intermediate is involved. On the basis of the newly reported crystal structure of GLase (2X2I) and the speculated mechanism, the whole catalytic cycle of GLase has been studied by using a QM/MM method. Calculation results indicate that the whole catalytic cycle contains five elementary steps. Firstly, the aspartic acid residue D665 acts as an acid to protonate the glycoside oxygen, which is concerted with the cleavage of the glycoside bond. Then, the residue D553 functions as the nucleophile to attack the anomeric carbon to form the glycosyl-enzyme intermediate. Different from the retaining alpha-glucosidases whose glycosylation is a typical concerted process, the glycosylation process of glycosidic lyase follows a stepwise mechanism. For the deglycosylation/elimination step, two cases with or without the maltotriose group in the active site were considered. The departure of the maltotriose can facilitate the proceeding of this process. The deprotonated aspartic acid residue D553 further acts as a catalytic base to abstract the C2-proton of the glucosyl residue. The proton abstraction in the deglycosylation/elimination step is calculated to be the rate-limiting step of the whole catalytic reaction, which corresponds to the energy barriers of 20.69 and 18.53 kcal mol(-1) for both of the two cases.; alpha-1,4-Glucan lyase (GLase, EC 4.2.2.13), a unique glycoside hydrolase family member, specifically cleaves the alpha-1,4-glucosidic linkages in glycogen, starch and malto-oligosaccharides to produce 1,5-anhydro-D-fructose from the non-reducing end. Previous studies have proved that GLase belongs to the retaining glycoside lyase, and the catalytic reaction contains both the glycosylation and deglycosylation/elimination steps, in which a covalent glycosyl-enzyme intermediate is involved. On the basis of the newly reported crystal structure of GLase (2X2I) and the speculated mechanism, the whole catalytic cycle of GLase has been studied by using a QM/MM method. Calculation results indicate that the whole catalytic cycle contains five elementary steps. Firstly, the aspartic acid residue D665 acts as an acid to protonate the glycoside oxygen, which is concerted with the cleavage of the glycoside bond. Then, the residue D553 functions as the nucleophile to attack the anomeric carbon to form the glycosyl-enzyme intermediate. Different from the retaining alpha-glucosidases whose glycosylation is a typical concerted process, the glycosylation process of glycosidic lyase follows a stepwise mechanism. For the deglycosylation/elimination step, two cases with or without the maltotriose group in the active site were considered. The departure of the maltotriose can facilitate the proceeding of this process. The deprotonated aspartic acid residue D553 further acts as a catalytic base to abstract the C2-proton of the glucosyl residue. The proton abstraction in the deglycosylation/elimination step is calculated to be the rate-limiting step of the whole catalytic reaction, which corresponds to the energy barriers of 20.69 and 18.53 kcal mol(-1) for both of the two cases.
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/37417
专题	中国科学院西北高原生物研究所
推荐引用方式 GB/T 7714	Su, Hao,Dong, Lihua,Liu, Yongjun. A QM/MM study of the catalytic mechanism of alpha-1,4-glucan lyase from the red seaweed Gracilariopsis lemaneiformis[J]. RSC ADVANCES, Su, H; Dong, LH; Liu, YJ.A QM/MM study of the catalytic mechanism of alpha-1,4-glucan lyase from the red seaweed Gracilariopsis lemaneiformis,RSC ADVANCES,2014,4(97):54398,2014.
APA	Su, Hao,Dong, Lihua,&Liu, Yongjun.(2014).A QM/MM study of the catalytic mechanism of alpha-1,4-glucan lyase from the red seaweed Gracilariopsis lemaneiformis.RSC ADVANCES.
MLA	Su, Hao,et al."A QM/MM study of the catalytic mechanism of alpha-1,4-glucan lyase from the red seaweed Gracilariopsis lemaneiformis".RSC ADVANCES (2014).