PDBsum entry 1p6w

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Hydrolase PDB id
Protein chain
404 a.a. *
_CA ×4
Waters ×641
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of barley alpha-amylase isozyme 1 (amy1) in complex with the substrate analogue, methyl 4i,4ii,4iii- tri-thiomaltotetraoside (thio-dp4)
Structure: Protein (alpha-amylase type a 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:   0.170     R-free:   0.216
Authors: X.Robert,R.Haser,N.Aghajari
Key ref:
X.Robert et al. (2003). The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs. Structure, 11, 973-984. PubMed id: 12906828 DOI: 10.1016/S0969-2126(03)00151-5
30-Apr-03     Release date:   14-Oct-03    
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   2 terms 
  Biochemical function     catalytic activity     7 terms  


DOI no: 10.1016/S0969-2126(03)00151-5 Structure 11:973-984 (2003)
PubMed id: 12906828  
The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
X.Robert, R.Haser, T.E.Gottschalk, F.Ratajczak, H.Driguez, B.Svensson, N.Aghajari.
Though the three-dimensional structures of barley alpha-amylase isozymes AMY1 and AMY2 are very similar, they differ remarkably from each other in their affinity for Ca(2+) and when interacting with substrate analogs. A surface site recognizing maltooligosaccharides, not earlier reported for other alpha-amylases and probably associated with the different activity of AMY1 and AMY2 toward starch granules, has been identified. It is located in the C-terminal part of the enzyme and, thus, highlights a potential role of domain C. In order to scrutinize the possible biological significance of this domain in alpha-amylases, a thorough comparison of their three-dimensional structures was conducted. An additional role for an earlier-identified starch granule binding surface site is proposed, and a new calcium ion is reported.
  Selected figure(s)  
Figure 4.
Figure 4. Substrate Analogs(A) Chemical structure of the thio-DP4 substrate analog.(B) Chemical structure of acarbose. Rings are labeled as referred to in the text. Rings A and B constitute the acarviosine unit, which is a-1,4 linked to a maltose unit (rings C and D).(C) Schematic representation of interactions in the domain C sugar tongs site, between AMY1 and thio-DP4. The substrate analog is shown in ball and stick in purple. AMY1 ligand side chains, orange. Carbon atoms, black; oxygen, red; nitrogen, blue; sulphur, yellow. Direct hydrogen bonds between the protein and thio-DP4, dashed green lines (lengths in ); hydrophobic contacts, dashed red lines. This figure was generated with the program Ligplot (Wallace et al., 1995).
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 973-984) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20552260 E.Hostinová, S.Janecek, and J.Gasperík (2010).
Gene sequence, bioinformatics and enzymatic characterization of alpha-amylase from Saccharomycopsis fibuligera KZ.
  Protein J, 29, 355-364.  
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.  
19338387 C.Montanier, V.A.Money, V.M.Pires, J.E.Flint, B.A.Pinheiro, A.Goyal, J.A.Prates, A.Izumi, H.Stålbrand, C.Morland, A.Cartmell, K.Kolenova, E.Topakas, E.J.Dodson, D.N.Bolam, G.J.Davies, C.M.Fontes, and H.J.Gilbert (2009).
The active site of a carbohydrate esterase displays divergent catalytic and noncatalytic binding functions.
  PLoS Biol, 7, e71.
PDB codes: 2w9x 2waa 2wab 2wao
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.  
17690769 E.C.Stanca-Kaposta, D.P.Gamblin, J.Screen, B.Liu, L.C.Snoek, B.G.Davis, and J.P.Simons (2007).
Carbohydrate molecular recognition: a spectroscopic investigation of carbohydrate-aromatic interactions.
  Phys Chem Chem Phys, 9, 4444-4451.  
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
17597061 S.Ravaud, X.Robert, H.Watzlawick, R.Haser, R.Mattes, and N.Aghajari (2007).
Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization.
  J Biol Chem, 282, 28126-28136.
PDB codes: 1zja 2pwd 2pwe 2pwf 2pwg 2pwh
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
15657043 B.C.Bønsager, P.K.Nielsen, M.Abou Hachem, K.Fukuda, M.Praetorius-Ibba, and B.Svensson (2005).
Mutational analysis of target enzyme recognition of the beta-trefoil fold barley alpha-amylase/subtilisin inhibitor.
  J Biol Chem, 280, 14855-14864.  
15809849 K.M.Polakova, L.Kucera, D.A.Laurie, K.Vaculova, and J.Ovesna (2005).
Coding region single nucleotide polymorphism in the barley low-pI, alpha-amylase gene Amy32b.
  Theor Appl Genet, 110, 1499-1504.  
16262690 M.Machovic, B.Svensson, E.A.MacGregor, and S.Janecek (2005).
A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21.
  FEBS J, 272, 5497-5513.  
15062085 J.Allouch, W.Helbert, B.Henrissat, and M.Czjzek (2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
  Structure, 12, 623-632.
PDB code: 1urx
15004011 J.L.Henshaw, D.N.Bolam, V.M.Pires, M.Czjzek, B.Henrissat, L.M.Ferreira, C.M.Fontes, and H.J.Gilbert (2004).
The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities.
  J Biol Chem, 279, 21552-21559.  
14660599 K.S.Bak-Jensen, G.André, T.E.Gottschalk, G.Paës, V.Tran, and B.Svensson (2004).
Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley alpha-amylase 1.
  J Biol Chem, 279, 10093-10102.  
12906821 J.H.Geiger (2003).
Sugar tongs get a grip on the starch granule in barley alpha-amylase 1.
  Structure, 11, 903-904.  
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.