PDBsum entry 1uko

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Hydrolase PDB id
Protein chains
490 a.a. *
SO4 ×24
Waters ×1461
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of soybean beta-amylase mutant substituted at surface region
Structure: Beta-amylase. Chain: a, b, c, d. Synonym: 1,4-alpha-d-glucan maltohydrolase. Engineered: yes. Mutation: yes
Source: Glycine max. Soybean. Organism_taxid: 3847. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.10Å     R-factor:   0.183     R-free:   0.241
Authors: Y.N.Kang,M.Adachi,B.Mikami,S.Utsumi
Key ref: Y.N.Kang et al. (2003). Change in the crystal packing of soybean beta-amylase mutants substituted at a few surface amino acid residues. Protein Eng, 16, 809-817. PubMed id: 14631070
30-Aug-03     Release date:   10-Feb-04    
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Protein chains
Pfam   ArchSchema ?
P10538  (AMYB_SOYBN) -  Beta-amylase
496 a.a.
490 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - 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     3 terms  


Protein Eng 16:809-817 (2003)
PubMed id: 14631070  
Change in the crystal packing of soybean beta-amylase mutants substituted at a few surface amino acid residues.
Y.N.Kang, M.Adachi, B.Mikami, S.Utsumi.
In spite of the high similarity of amino acid sequence and three-dimensional structure between soybean beta-amylase (SBA) and sweet potato beta-amylase (SPB), their quaternary structure is quite different, being a monomer in SBA and a tetramer in SPB. Because most of the differences in amino acid sequences are found in the surface region, we tested the tetramerization of SBA by examining mutations of residues located at the surface. We designed the SBA tetramer using the SPB tetramer structure as a model and calculating the change of accessible surface area (DeltaASA) for each residue in order to select sites for the mutation. Two different mutant genes encoding SB3 (D374Y/L481R/P487D) and SB4 (K462S added to SB3), were constructed for expression in Escherichia coli and the recombinant proteins were purified. They existed as a monomer in solution, but gave completely different crystals from the native SBA. The asymmetric unit of the mutants contains four molecules, while that of native SBA contains one. The interactions of the created interfaces revealed that there were more intermolecular interactions in the SB3 than in the SB4 tetramer. The substituted charged residues on the surface are involved in interactions with adjacent molecules in a different way, forming a new crystal packing pattern.

Literature references that cite this PDB file's key reference

  PubMed id Reference
15223314 Z.Yang, L.Shipman, M.Zhang, B.P.Anton, R.J.Roberts, and X.Cheng (2004).
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.
  J Mol Biol, 340, 695-706.
PDB code: 1t43
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