cd11326

Alpha amylase catalytic domain found in glycogen debranching enzymes

CDD entry
Member databaseCDD
CDD typedomain
Short nameAmyAc_Glg_debranch
SetAmyAc_family

Description

Debranching enzymes facilitate the breakdown of glycogen through glucosyltransferase and glucosidase activity. These activities are performed by a single enzyme in mammals, yeast, and some bacteria, but by two distinct enzymes in Escherichia coli and other bacteria. Debranching enzymes perform two activities: 4-alpha-D-glucanotransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). 4-alpha-D-glucanotransferase catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. In Escherichia coli, GlgX is the debranching enzyme and malQ is the 4-alpha-glucanotransferase. TreX, an archaeal glycogen-debranching enzyme has dual activities like mammals and yeast, but is structurally similar to GlgX. TreX exists in two oligomeric states, a dimer and tetramer. Isoamylase (EC 3.2.1.68) is one of the starch-debranching enzymes that catalyzes the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen and their beta-limit dextrins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.
[5, 1, 4, 8, 6, 3, 7, 2]

References

1.Structural insight into the bifunctional mechanism of the glycogen-debranching enzyme TreX from the archaeon Sulfolobus solfataricus. Woo EJ, Lee S, Cha H, Park JT, Yoon SM, Song HN, Park KH. J. Biol. Chem. 283, 28641-8, (2008). View articlePMID: 18703518

2.alpha-Amylase family: molecular biology and evolution. Janecek S. Prog. Biophys. Mol. Biol. 67, 67-97, (1997). PMID: 9401418

3.Properties and applications of starch-converting enzymes of the alpha-amylase family. van der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L. J. Biotechnol. 94, 137-55, (2002). View articlePMID: 11796168

4.Identification of the sequence motif of glycoside hydrolase 13 family members. Kumar V. Bioinformation 6, 61-3, (2011). PMID: 21544166

5.Structural rationale for the short branched substrate specificity of the glycogen debranching enzyme GlgX. Song HN, Jung TY, Park JT, Park BC, Myung PK, Boos W, Woo EJ, Park KH. Proteins 78, 1847-55, (2010). PMID: 20187119

6.The concept of the alpha-amylase family: structural similarity and common catalytic mechanism. Kuriki T, Imanaka T. J. Biosci. Bioeng. 87, 557-65, (1999). PMID: 16232518

7.Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. MacGregor EA, Janecek S, Svensson B. Biochim. Biophys. Acta 1546, 1-20, (2001). View articlePMID: 11257505

8.Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Stam MR, Danchin EG, Rancurel C, Coutinho PM, Henrissat B. Protein Eng. Des. Sel. 19, 555-62, (2006). View articlePMID: 17085431

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