PDBsum entry 1rpk

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
Protein chain
404 a.a. *
_CA ×3
Waters ×549
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of barley alpha-amylase isozyme 1 (amy1) in complex with acarbose
Structure: Alpha-amylase type 1 isozyme. Chain: a. Synonym: 1,4-alpha-d-glucan glucanohydrolase, amy1, low pi alpha-amylase. Engineered: yes
Source: Hordeum vulgare. Organism_taxid: 4513. Gene: amy1.1. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
2.00Å     R-factor:   0.180     R-free:   0.231
Authors: X.Robert,R.Haser,N.Aghajari
Key ref:
X.Robert et al. (2005). Oligosaccharide binding to barley alpha-amylase 1. J Biol Chem, 280, 32968-32978. PubMed id: 16030022 DOI: 10.1074/jbc.M505515200
03-Dec-03     Release date:   07-Jun-05    
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 1 residue position (black cross)

 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  


DOI no: 10.1074/jbc.M505515200 J Biol Chem 280:32968-32978 (2005)
PubMed id: 16030022  
Oligosaccharide binding to barley alpha-amylase 1.
X.Robert, R.Haser, H.Mori, B.Svensson, N.Aghajari.
Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) described here give for the first time a thorough insight into the substrate binding by describing residues defining 9 subsites, namely -7 through +2. These structures support that the pseudotetrasaccharide inhibitor acarbose is hydrolyzed by the active enzymes. Moreover, sugar binding was observed to the starch granule-binding site previously determined in barley alpha-amylase isozyme 2 (AMY2), and the sugar binding modes are compared between the two isozymes. The "sugar tongs" surface binding site discovered in the AMY1-thio-DP4 complex is confirmed in the present work. A site that putatively serves as an entrance for the substrate to the active site was proposed at the glycone part of the binding cleft, and the crystal structures of the catalytic nucleophile mutant (AMY1D180A) complexed with acarbose and maltoheptaose, respectively, suggest an additional role for the nucleophile in the stabilization of the Michaelis complex. Furthermore, probable roles are outlined for the surface binding sites. Our data support a model in which the two surface sites in AMY1 can interact with amylose chains in their naturally folded form. Because of the specificities of these two sites, they may locate/orient the enzyme in order to facilitate access to the active site for polysaccharide chains. Moreover, the sugar tongs surface site could also perform the unraveling of amylose chains, with the aid of Tyr-380 acting as "molecular tweezers."
  Selected figure(s)  
Figure 2.
FIGURE 2. A, atoms labeling convention for glucosyl residues and acarbose. The acarviosine unit is constituted by rings A and B, including the amino group valienamine, and are -1,4-linked to rings C and D representing a maltose unit. B, superimposition of residues implicated in the substrate binding in active sites of AMY1 and AMY2 (stereo view). Only residues interacting directly by hydrogen bonds are shown. The complex AMY2-acarbose (4) (Protein Data Bank entry 1BG9 [PDB] ) is presented in blue, AMY1-acarbose (this work, Protein Data Bank entry 1RPK [PDB] ) in red, AMY1-thio-DP4 (28) (Protein Data Bank entry 1P6W [PDB] ) in green, and AMY1[D180A]-acarbose (this work, Protein Data Bank entry 1RP9 [PDB] ) in yellow.
Figure 4.
FIGURE 4. Schematic representation of hydrogen bonding network in the catalytic cleft of the AMY1[D180A]-maltoheptaose complex. Amino acid residues are in rectangles and water molecules in ellipsoids. Catalytic residues are highlighted. Figure was rendered using the ISIS-Draw software.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 32968-32978) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
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.  
18611383 N.M.Koropatkin, E.C.Martens, J.I.Gordon, and T.J.Smith (2008).
Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.
  Structure, 16, 1105-1115.
PDB codes: 3ck7 3ck8 3ck9 3ckb 3ckc
17803687 S.Bozonnet, M.T.Jensen, M.M.Nielsen, N.Aghajari, M.H.Jensen, B.Kramhøft, M.Willemoës, S.Tranier, R.Haser, and B.Svensson (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.
PDB codes: 2qps 2qpu
16649993 J.Sevcík, E.Hostinová, A.Solovicová, J.Gasperík, Z.Dauter, and K.S.Wilson (2006).
Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain.
  FEBS J, 273, 2161-2171.
PDB codes: 2f6d 2fba
16452622 R.Kanai, K.Haga, T.Akiba, K.Yamane, and K.Harata (2006).
Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707.
  Protein Sci, 15, 468-477.
PDB codes: 2d3l 2d3n
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.