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PDBsum entry 1b1y

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protein ligands links
Hydrolase PDB id
1b1y
Jmol
Contents
Protein chain
500 a.a. *
Ligands
GLC-BGC
BGC
Waters ×140
* Residue conservation analysis
PDB id:
1b1y
Name: Hydrolase
Title: Sevenfold mutant of barley beta-amylase
Structure: Protein (beta-amylase). Chain: a. Engineered: yes. Mutation: yes
Source: Hordeum vulgare. Organism_taxid: 4513. Variant: cv. Haruna. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: jm 109.
Resolution:
2.50Å     R-factor:   0.187     R-free:   0.256
Authors: B.Mikami,H.J.Yoon,N.Yoshigi
Key ref:
B.Mikami et al. (1999). The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution. J Mol Biol, 285, 1235-1243. PubMed id: 9918723 DOI: 10.1006/jmbi.1998.2379
Date:
25-Nov-98     Release date:   02-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16098  (AMYB_HORVU) -  Beta-amylase
Seq:
Struc:
 
Seq:
Struc:
535 a.a.
500 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.2  - Beta-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1006/jmbi.1998.2379 J Mol Biol 285:1235-1243 (1999)
PubMed id: 9918723  
 
 
The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution.
B.Mikami, H.J.Yoon, N.Yoshigi.
 
  ABSTRACT  
 
The three-dimensional structure of the sevenfold mutant of barley beta-amylase (BBA-7s) with increased thermostability was determined by X-ray crystallography. The enzyme was purified as a single component and crystallized by a hanging drop method in the presence of 14 % PEG 6000. The crystals belong to space group P43212 with cell dimensions a=b=72.11 A, c=250.51 A. The diffraction data up to 2.5 A were collected after soaking the crystal in 100 mM maltose with Rsym of 8.6 %. The structure was determined by a molecular replacement method using soybean beta-amylase (SBA) as a search model and refined to an R-factor of 18.7 %. The final model included 500 amino acid residues, 141 water molecules and three glucose residues, which were located at subsites 1-2 and 4 in the active site. The r.m.s. distance of 485 Calpha atoms between BBA-7s and SBA was 0.62 A. Out of the seven mutated amino acids, four (Ser295Ala, Ile297Val, Ser351Pro and Ala376Ser) were substitutions from the common residues with SBA to the thermostable forms. A comparison of the structures of BBA-7s and SBA indicated that the side-chain of Ser376 makes new hydrogen bonds to the main-chain of an adjacent beta-strand, and that the side-chains of Val297 reduce an unfavorable interaction between the side-chains of Ala314. The mutation of Ser295Ala breaks the hydrogen bond between Ser295 OG and Tyr195 OH, which seems to be the reason for the unoccupied glucose residue at subsite 3. The tandem mutations at 350-352 including substitutions to two Pro residues suggested the reduction of main-chain entropy in the unfolded structure of this solvent-exposed protruded loop.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Superposition of the mutated sites of Ser295 and Val297 and the bound maltose from BBA-7s on the corresponding sites from SBA (stereo view). BBA-7s and SBA protein models are colored purple and green, respectively. Maltose models in BBA-7s and SBA are colored red and cyan, respectively. Two molecular models are superimposed by a fitting program implemented in Turbo-Frodo.
Figure 6.
Figure 6. Superposition of the mutated site of Pro350- Asp352 from BBA-7s onto the corresponding site from SBA (stereo view). BBA-7s and SBA models are colored purple and green, respectively. Two molecular models are superimposed by a fitting program implemented in Turbo-Frodo.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 1235-1243) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21085740 M.Rejzek, C.E.Stevenson, A.M.Southard, D.Stanley, K.Denyer, A.M.Smith, M.J.Naldrett, D.M.Lawson, and R.A.Field (2011).
Chemical genetics and cereal starch metabolism: structural basis of the non-covalent and covalent inhibition of barley β-amylase.
  Mol Biosyst, 7, 718-730.
PDB codes: 2xff 2xfr 2xfy 2xg9 2xgb 2xgi
20192737 S.C.Zeeman, J.Kossmann, and A.M.Smith (2010).
Starch: its metabolism, evolution, and biotechnological modification in plants.
  Annu Rev Plant Biol, 61, 209-234.  
14638688 A.Hirata, M.Adachi, A.Sekine, Y.N.Kang, S.Utsumi, and B.Mikami (2004).
Structural and enzymatic analysis of soybean beta-amylase mutants with increased pH optimum.
  J Biol Chem, 279, 7287-7295.
PDB codes: 1q6c 1q6d 1q6e 1q6f 1q6g
11063571 Y.F.Ma, J.K.Eglinton, D.E.Evans, S.J.Logue, and P.Langridge (2000).
Removal of the four C-terminal glycine-rich repeats enhances the thermostability and substrate binding affinity of barley beta-amylase.
  Biochemistry, 39, 13350-13355.  
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.