3L2M

X-ray Crystallographic Analysis of Pig Pancreatic Alpha-Amylase with Alpha-cyclodextrin

Summary for 3L2M

• Entry DOI: 10.2210/pdb3l2m/pdb
• Related: 3L2L
• Related PRD ID: PRD_900015
• Descriptor: Pancreatic alpha-amylase, Cyclohexakis-(1-4)-(alpha-D-glucopyranose), CALCIUM ION, ... (5 entities in total)
• Functional Keywords: catalytic domain, carbohydrate binding module, alpha-cyclodextrin, carbohydrate metabolism, glycoprotein, glycosidase, metal-binding, pyrrolidone carboxylic acid, secreted, hydrolase
• Biological source: Sus scrofa (pig)
• Total number of polymer chains: 1
• Total formula weight: 58487.89

Authors

Larson, S.B.,Day, J.S.,McPherson, A. (deposition date: 2009-12-15, release date: 2010-04-14, Last modification date: 2024-10-16)

Primary citation

Larson, S.B.,Day, J.S.,McPherson, A.
X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin.
Biochemistry, 49:3101-3115, 2010

PubMed Abstract: Further refinement of the model using maximum likelihood procedures and reevaluation of the native electron density map has shown that crystals of pig pancreatic alpha-amylase, whose structure we reported more than 15 years ago, in fact contain a substantial amount of carbohydrate. The carbohydrate fragments are the products of glycogen digestion carried out as an essential step of the protein's purification procedure. In particular, the substrate-binding cleft contains a limit dextrin of six glucose residues, one of which contains both alpha-(1,4) and alpha-(1,6) linkages to contiguous residues. The disaccharide in the original model, shared between two amylase molecules in the crystal lattice, but also occupying a portion of the substrate-binding cleft, is now seen to be a tetrasaccharide. There are, in addition, several other probable monosaccharide binding sites. Furthermore, we have further reviewed our X-ray diffraction analysis of alpha-amylase complexed with alpha-cyclodextrin. alpha-Amylase binds three cyclodextrin molecules. Glucose residues of two of the rings superimpose upon the limit dextrin and the tetrasaccharide. The limit dextrin superimposes in large part upon linear oligosaccharide inhibitors visualized by other investigators. By comprehensive integration of these complexes we have constructed a model for the binding of polysaccharides having the helical character known to be present in natural substrates such as starch and glycogen.

PubMed: 20222716
DOI: 10.1021/bi902183w

Experimental method

X-RAY DIFFRACTION (1.97 Å)