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Hydrolase PDB id
1w9x
Jmol
Contents
Protein chain
481 a.a. *
Ligands
BGC-GLC-AC1-GLC-
GLC-GLC-AC1
Metals
_CA ×3
_NA
Waters ×290
* Residue conservation analysis
PDB id:
1w9x
Name: Hydrolase
Title: Bacillus halmapalus alpha amylase
Structure: Alpha amylase. Chain: a. Engineered: yes. Other_details: acarbose-derived nonasaccharide
Source: Bacillus halmapalus. Organism_taxid: 79882. Expressed in: bacillus subtilis. Expression_system_taxid: 1423
Resolution:
2.1Å     R-factor:   0.152     R-free:   0.198
Authors: G.J.Davies,A.M.Brzozowski,Z.Dauter,M.D.Rasmussen, T.V.Borchert,K.S.Wilson
Key ref:
G.J.Davies et al. (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. PubMed id: 15681870 DOI: 10.1107/S0907444904027118
Date:
20-Oct-04     Release date:   09-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O82839  (O82839_BACSP) -  Amylase
Seq:
Struc: 		516 a.a.
481 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 66 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1107/S0907444904027118 Acta Crystallogr D Biol Crystallogr 61:190-193 (2005)
PubMed id: 15681870  
 
 
Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution.
G.J.Davies, A.M.Brzozowski, Z.Dauter, M.D.Rasmussen, T.V.Borchert, K.S.Wilson.
 
  ABSTRACT  
 
The enzymatic digestion of starch by alpha-amylases is one of the key biotechnological reactions of recent times. In the search for industrial biocatalysts, the family GH13 alpha-amylase BHA from Bacillus halmapalus has been cloned and expressed. The three-dimensional structure at 2.1 A resolution has been determined in complex with the (pseudo)tetrasaccharide inhibitor acarbose. Acarbose is found bound as a nonasaccharide transglycosylation product spanning the -6 to +3 subsites. Careful inspection of electron density suggests that the bound ligand could not have been formed through successive transglycosylations of acarbose and must also have featured maltose or maltooligosaccharides as an acceptor.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 (a) The covalent glycosyl-enzyme intermediate of a retaining glycosidase is normally intercepted by water. Under some circumstances, it is instead intercepted by another sugar in a transglycosylation reaction; such a mechanism gives rise to the many elongated forms of acarbose seen in amylase structures. (b) The structure of the pseudo-tetrasaccharide inhibitor acarbose. (c) The nonasaccharide observed in BHA (this work) and (d) that previously observed on the BA2 -amylase (Brzozowski et al., 2000[Brzozowski, A. M., Lawson, D. M., Turkenburg, J. P., Bisgaard-Frantzen, H., Svendsen, A., Borchert, T. V., Dauter, Z., Wilson, K. S. & Davies, G. J. (2000). Biochemistry, 39, 9099-9107.]).
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 190-193) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19396237 A.Novinscak, N.J.DeCoste, C.Surette, and M.Filion (2009).
Characterization of bacterial and fungal communities in composted biosolids over a 2 year period using denaturing gradient gel electrophoresis.
  Can J Microbiol, 55, 375-387.  
17154418 T.Shirai, K.Igarashi, T.Ozawa, H.Hagihara, T.Kobayashi, K.Ozaki, and S.Ito (2007).
Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins.
  Proteins, 66, 600-610.
PDB code: 2die
  16946462 L.Lyhne-Iversen, T.J.Hobley, S.G.Kaasgaard, and P.Harris (2006).
Structure of Bacillus halmapalus alpha-amylase crystallized with and without the substrate analogue acarbose and maltose.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 849-854.
PDB codes: 2gjp 2gjr
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
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
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 code is shown on the right.