PDBsum entry 1g9h

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Hydrolase PDB id
Protein chain
448 a.a. *
Waters ×274
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Ternary complex between psychrophilic alpha-amylase, comii (pseudo tri-saccharide from bayer) and tris (2-amino-2- hydroxymethyl-propane-1,3-diol)
Structure: Alpha-amylase. Chain: a. Other_details: complexed with tri-saccharide and tris
Source: Pseudoalteromonas haloplanktis. Organism_taxid: 228. Strain: a23
1.80Å     R-factor:   0.168     R-free:   0.201
Authors: N.Aghajari,M.Roth,R.Haser
Key ref:
N.Aghajari et al. (2002). Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase. Biochemistry, 41, 4273-4280. PubMed id: 11914073 DOI: 10.1021/bi0160516
23-Nov-00     Release date:   26-Jun-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P29957  (AMY_PSEHA) -  Alpha-amylase
669 a.a.
448 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  


DOI no: 10.1021/bi0160516 Biochemistry 41:4273-4280 (2002)
PubMed id: 11914073  
Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase.
N.Aghajari, M.Roth, R.Haser.
The psychrophilic Pseudoalteromonas haloplanctis alpha-amylase is shown to form ternary complexes with two alpha-amylase inhibitors present in the active site region, namely, a molecule of Tris and a trisaccharide inhibitor or heptasaccharide inhibitor, respectively. The crystal structures of these complexes have been determined by X-ray crystallography to 1.80 and 1.74 A resolution, respectively. In both cases, the prebound inhibitor Tris is expelled from the active site by the incoming oligosaccharide inhibitor substrate analogue, but stays linked to it, forming well-defined ternary complexes with the enzyme. These results illustrate competition in the crystalline state between two inhibitors, an oligosaccharide substrate analogue and a Tris molecule, bound at the same time in the active site region. Taken together, these structures show that the enzyme performs transglycosylation in the complex with the pseudotetrasaccharide acarbose (confirmed by a mutant structure), leading to a well-defined heptasaccharide, considered as a more potent inhibitor. Furthermore, the substrate-induced ordering of water molecules within a channel highlights a possible pathway used for hydrolysis of starch and related poly- and oligosaccharides.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21426903 L.C.Tsai, C.H.Hsiao, W.Y.Liu, L.M.Yin, and L.F.Shyur (2011).
Structural basis for the inhibition of 1,3-1,4-β-d-glucanase by noncompetitive calcium ion and competitive Tris inhibitors.
  Biochem Biophys Res Commun, 407, 593-598.  
20812985 K.Yamamoto, H.Miyake, M.Kusunoki, and S.Osaki (2010).
Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose.
  FEBS J, 277, 4205-4214.
PDB codes: 3a4a 3aj7
18951544 B.Khemakhem, M.B.Ali, N.Aghajari, M.Juy, R.Haser, and S.Bejar (2009).
Engineering of the alpha-amylase from Geobacillus stearothermophilus US100 for detergent incorporation.
  Biotechnol Bioeng, 102, 380-389.  
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.  
18552192 J.Y.Damián-Almazo, A.Moreno, A.López-Munguía, X.Soberón, F.González-Muñoz, and G.Saab-Rincón (2008).
Enhancement of the alcoholytic activity of alpha-amylase AmyA from Thermotoga maritima MSB8 (DSM 3109) by site-directed mutagenesis.
  Appl Environ Microbiol, 74, 5168-5177.  
17039546 N.Nagano, T.Noguchi, and Y.Akiyama (2007).
Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.
  Proteins, 66, 147-159.  
15681870 G.J.Davies, A.M.Brzozowski, Z.Dauter, M.D.Rasmussen, T.V.Borchert, and K.S.Wilson (2005).
Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution.
  Acta Crystallogr D Biol Crystallogr, 61, 190-193.
PDB code: 1w9x
16030022 X.Robert, R.Haser, H.Mori, B.Svensson, and N.Aghajari (2005).
Oligosaccharide binding to barley alpha-amylase 1.
  J Biol Chem, 280, 32968-32978.
PDB codes: 1rp8 1rp9 1rpk
  16233714 A.Hoyoux, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.L.Huston, J.C.Marx, G.Sonan, Y.Zeng, G.Feller, and C.Gerday (2004).
Extreme catalysts from low-temperature environments.
  J Biosci Bioeng, 98, 317-330.  
15182367 N.Ramasubbu, C.Ragunath, P.J.Mishra, L.M.Thomas, G.Gyémánt, and L.Kandra (2004).
Human salivary alpha-amylase Trp58 situated at subsite -2 is critical for enzyme activity.
  Eur J Biochem, 271, 2517-2529.
PDB codes: 1jxj 1nm9
15274914 S.B.Gabelli, M.A.Bianchet, H.F.Azurmendi, Z.Xia, V.Sarawat, A.S.Mildvan, and L.M.Amzel (2004).
Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.
  Structure, 12, 927-935.
PDB code: 1rya
12482867 A.Linden, O.Mayans, W.Meyer-Klaucke, G.Antranikian, and M.Wilmanns (2003).
Differential regulation of a hyperthermophilic alpha-amylase with a novel (Ca,Zn) two-metal center by zinc.
  J Biol Chem, 278, 9875-9884.
PDB codes: 1mwo 1mxd 1mxg
12492486 H.Leemhuis, B.W.Dijkstra, and L.Dijkhuizen (2003).
Thermoanaerobacterium thermosulfurigenes cyclodextrin glycosyltransferase.
  Eur J Biochem, 270, 155-162.  
14617662 M.Kagawa, Z.Fujimoto, M.Momma, K.Takase, and H.Mizuno (2003).
Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose.
  J Bacteriol, 185, 6981-6984.
PDB code: 1ua7
12021442 N.Aghajari, G.Feller, C.Gerday, and R.Haser (2002).
Structural basis of alpha-amylase activation by chloride.
  Protein Sci, 11, 1435-1441.
PDB codes: 1jd7 1jd9 1l0p
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.