PDBsum entry 2qps

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protein metals links
Hydrolase PDB id
Protein chain
404 a.a. *
_CA ×3
Waters ×169
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: "Sugar tongs" mutant y380a in complex with acarbose
Structure: Alpha-amylase type a isozyme. Chain: a. Synonym: 1,4-alpha-d- glucan glucanohydrolase, amy1, low pi amylase. Engineered: yes. Mutation: yes
Source: Hordeum vulgare. Organism_taxid: 4513. Gene: amy1.1. Expressed in: pichia pastoris. Expression_system_taxid: 4922
2.20Å     R-factor:   0.240     R-free:   0.305
Authors: N.Aghajari,M.H.Jensen,S.Tranier,R.Haser
Key ref: S.Bozonnet et al. (2007). The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity. FEBS J, 274, 5055-5067. PubMed id: 17803687
25-Jul-07     Release date:   12-Feb-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00693  (AMY1_HORVU) -  Alpha-amylase type A isozyme
438 a.a.
404 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   4 terms 
  Biochemical function     catalytic activity     7 terms  


FEBS J 274:5055-5067 (2007)
PubMed id: 17803687  
The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity.
S.Bozonnet, M.T.Jensen, M.M.Nielsen, N.Aghajari, M.H.Jensen, B.Kramhøft, M.Willemoës, S.Tranier, R.Haser, B.Svensson.
Some starch-degrading enzymes accommodate carbohydrates at sites situated at a certain distance from the active site. In the crystal structure of barley alpha-amylase 1, oligosaccharide is thus bound to the 'sugar tongs' site. This site on the non-catalytic domain C in the C-terminal part of the molecule contains a key residue, Tyr380, which has numerous contacts with the oligosaccharide. The mutant enzymes Y380A and Y380M failed to bind to beta-cyclodextrin-Sepharose, a starch-mimic resin used for alpha-amylase affinity purification. The K(d) for beta-cyclodextrin binding to Y380A and Y380M was 1.4 mm compared to 0.20-0.25 mm for the wild-type, S378P and S378T enzymes. The substitution in the S378P enzyme mimics Pro376 in the barley alpha-amylase 2 isozyme, which in spite of its conserved Tyr378 did not bind oligosaccharide at the 'sugar tongs' in the structure. Crystal structures of both wild-type and S378P enzymes, but not the Y380A enzyme, showed binding of the pseudotetrasaccharide acarbose at the 'sugar tongs' site. The 'sugar tongs' site also contributed importantly to the adsorption to starch granules, as Kd = 0.47 mg.mL(-1) for the wild-type enzyme increased to 5.9 mg.mL(-1) for Y380A, which moreover catalyzed the release of soluble oligosaccharides from starch granules with only 10% of the wild-type activity. beta-cyclodextrin both inhibited binding to and suppressed activity on starch granules for wild-type and S378P enzymes, but did not affect these properties of Y380A, reflecting the functional role of Tyr380. In addition, the Y380A enzyme hydrolyzed amylose with reduced multiple attack, emphasizing that the 'sugar tongs' participates in multivalent binding of polysaccharide substrates.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20192737 S.C.Zeeman, J.Kossmann, and A.M.Smith (2010).
Starch: its metabolism, evolution, and biotechnological modification in plants.
  Annu Rev Plant Biol, 61, 209-234.  
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
18951906 C.Ragunath, S.G.Manuel, V.Venkataraman, H.B.Sait, C.Kasinathan, and N.Ramasubbu (2008).
Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding.
  J Mol Biol, 384, 1232-1248.  
18500431 H.Y.Lin, H.H.Chuang, and F.P.Lin (2008).
Biochemical characterization of engineered amylopullulanase from Thermoanaerobacter ethanolicus 39E-implicating the non-necessity of its 100 C-terminal amino acid residues.
  Extremophiles, 12, 641-650.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.