PDBsum entry 3l2l

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Hydrolase PDB id
Protein chain
496 a.a. *
Waters ×607
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: X-ray crystallographic analysis of pig pancreatic alpha-amyl limit dextrin and oligosaccharide
Structure: Pancreatic alpha-amylase. Chain: a. Fragment: residues 16-511. Synonym: pa, 1,4-alpha-d-glucan glucanohydrolase. Ec:
Source: Sus scrofa. Pig. Organism_taxid: 9823. Other_details: pancreas
2.11Å     R-factor:   0.119     R-free:   0.157
Authors: S.B.Larson,J.S.Day,A.Mcpherson
Key ref: S.B.Larson et al. (2010). X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin. Biochemistry, 49, 3101-3115. PubMed id: 20222716
15-Dec-09     Release date:   14-Apr-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00690  (AMYP_PIG) -  Pancreatic alpha-amylase
511 a.a.
496 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Alpha-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     8 terms  


Biochemistry 49:3101-3115 (2010)
PubMed id: 20222716  
X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin.
S.B.Larson, J.S.Day, A.McPherson.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22184476 J.R.Luft, N.M.Furlani, R.E.Nemoyer, E.J.Penna, J.R.Wolfley, M.E.Snell, S.A.Potter, and E.H.Snell (2010).
Crystal cookery - using high-throughput technologies and the grocery store as a teaching tool.
  J Appl Crystallogr, 43, 1189-1207.  
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