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PDBsum entry 1uko

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1uko
Jmol
Contents
Protein chains
490 a.a. *
Ligands
SO4 ×24
Waters ×1461
* Residue conservation analysis
PDB id:
1uko
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.
Resolution:
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
Date:
30-Aug-03     Release date:   10-Feb-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10538  (AMYB_SOYBN) -  Beta-amylase
Seq:
Struc:
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.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     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.
 
  ABSTRACT  
 
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
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.