PDBsum entry 1hvx

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protein metals links
Hydrolase PDB id
Protein chain
483 a.a. *
_CA ×3
Waters ×320
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Bacillus stearothermophilus alpha-amylase
Structure: Alpha-amylase. Chain: a. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: amyt631. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
2.00Å     R-factor:   0.154     R-free:   0.197
Authors: D.Suvd,Z.Fujimoto,K.Takase,M.Matsumura,H.Mizuno
Key ref: D.Suvd et al. (2001). Crystal structure of Bacillus stearothermophilus alpha-amylase: possible factors determining the thermostability. J Biochem, 129, 461-468. PubMed id: 11226887
08-Jan-01     Release date:   31-Jan-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06279  (AMY_GEOSE) -  Alpha-amylase
549 a.a.
483 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!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     8 terms  


J Biochem 129:461-468 (2001)
PubMed id: 11226887  
Crystal structure of Bacillus stearothermophilus alpha-amylase: possible factors determining the thermostability.
D.Suvd, Z.Fujimoto, K.Takase, M.Matsumura, H.Mizuno.
The crystal structure of a thermostable alpha-amylase from Bacillus stearothermophilus (BSTA) has been determined at 2.0 A resolution. The main-chain fold is almost identical to that of the known crystal structure of Bacillus licheniformis alpha-amylase (BLA). BLA is known to be more stable than BSTA. A structural comparison between the crystal structures of BSTA and BLA showed significant differences that may account for the difference in their thermostabilities, as follows. (i) The two-residue insertion in BSTA, Ile181-Gly182, pushes away the spatially contacting region including Asp207, which corresponds to Ca(2+)-coordinating Asp204 in BLA. As a result, Asp207 cannot coordinate the Ca(2+). (ii) BSTA contains nine fewer hydrogen bonds than BLA, which costs about 12 kcal/mol. This tendency is prominent in the (beta/alpha)(8)-barrel, where 10 fewer hydrogen bonds were observed in BSTA. BLA forms a denser hydrogen bond network in the inter-helical region, which may stabilize alpha-helices in the barrel. (iii) A few small voids observed in the alpha-helical region of the (beta/alpha)(8)-barrel in BSTA decrease inter-helical compactness and hydrophobic interactions. (iv) The solvent-accessible surface area of charged residues in BLA is about two times larger than that in BSTA.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153672 D.Chakravorty, S.Parameswaran, V.K.Dubey, and S.Patra (2011).
In silico characterization of thermostable lipases.
  Extremophiles, 15, 89.  
19756583 F.M.Reyes-Sosa, F.P.Molina-Heredia, and M.A.De la Rosa (2010).
A novel alpha-amylase from the cyanobacterium Nostoc sp. PCC 7119.
  Appl Microbiol Biotechnol, 86, 131-141.  
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.  
17598074 R.Priyadharshini, and P.Gunasekaran (2007).
Site-directed mutagenesis of the calcium-binding site of alpha-amylase of Bacillus licheniformis.
  Biotechnol Lett, 29, 1493-1499.  
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
15848038 W.F.Li, X.X.Zhou, and P.Lu (2005).
Structural features of thermozymes.
  Biotechnol Adv, 23, 271-281.  
15466542 S.J.Yang, H.S.Lee, C.S.Park, Y.R.Kim, T.W.Moon, and K.H.Park (2004).
Enzymatic analysis of an amylolytic enzyme from the hyperthermophilic archaeon Pyrococcus furiosus reveals its novel catalytic properties as both an alpha-amylase and a cyclodextrin-hydrolyzing enzyme.
  Appl Environ Microbiol, 70, 5988-5995.  
15384039 Y.Guiavarc'h, A.Van Loey, F.Zuber, and M.Hendrickx (2004).
Development characterization and use of a high-performance enzymatic time-temperature integrator for the control of sterilization process' impacts.
  Biotechnol Bioeng, 88, 15-25.  
  16233519 A.Tanaka, and E.Hoshino (2003).
Secondary calcium-binding parameter of Bacillus amyloliquefaciens alpha-amylase obtained from inhibition kinetics.
  J Biosci Bioeng, 96, 262-267.  
12676725 R.J.Shiau, H.C.Hung, and C.L.Jeang (2003).
Improving the thermostability of raw-starch-digesting amylase from a Cytophaga sp. by site-directed mutagenesis.
  Appl Environ Microbiol, 69, 2383-2385.  
12581203 S.Janecek, B.Svensson, and E.A.MacGregor (2003).
Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.
  Eur J Biochem, 270, 635-645.  
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