PDBsum entry 1wdr

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protein ligands links
Hydrolase PDB id
Protein chain
493 a.a. *
SO4 ×6
Waters ×906
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: The role of an inner loop in the catalytic mechanism of soybean beta-amylase
Structure: Beta-amylase. Chain: a. 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.
1.35Å     R-factor:   0.131     R-free:   0.168
Authors: Y.N.Kang,M.Adachi,S.Utsumi,B.Mikami
Key ref:
Y.N.Kang et al. (2005). Structural analysis of threonine 342 mutants of soybean beta-amylase: role of a conformational change of the inner loop in the catalytic mechanism. Biochemistry, 44, 5106-5116. PubMed id: 15794648 DOI: 10.1021/bi0476580
17-May-04     Release date:   05-Apr-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P10538  (AMYB_SOYBN) -  Beta-amylase
496 a.a.
493 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 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  


DOI no: 10.1021/bi0476580 Biochemistry 44:5106-5116 (2005)
PubMed id: 15794648  
Structural analysis of threonine 342 mutants of soybean beta-amylase: role of a conformational change of the inner loop in the catalytic mechanism.
Y.N.Kang, A.Tanabe, M.Adachi, S.Utsumi, B.Mikami.
Two different conformations of the inner loop (residues 340-346) have been found in the soybean beta-amylase structures. In the "product form", the Thr 342 residue creates hydrogen bonds with Glu 186 (catalytic acid) and with the glucose residues at subsites -1 and +1, whereas most of those interactions are lost in the "apo form". To elucidate the relationship between the structural states of the inner loop and the catalytic mechanism, Thr 342 was mutated to Val, Ser, and Ala, respectively, and their crystal structures complexed with maltose were determined together with that of the apo enzyme at 1.27-1.64 A resolutions. The k(cat) values of the T342V, T342S, and T342A mutants decreased by 13-, 360-, and 1700-fold, respectively, compared to that of the wild-type enzyme. Whereas the inner loops in the wild-type/maltose and T342V/maltose complexes adopted the product form, those of the T342S/maltose and T342A/maltose complexes showed the apo form. Structural analyses suggested that the side chain of Thr 342 in product form plays an important role in distorting the sugar ring at subsite -1, stabilizing the deprotonated form of Glu 186, and grasping the glucose residue of the remaining substrate at subsite +1. The third hypothesis was proved by the fact that T342V hydrolyzes maltoheptaose following only multichain attack in contrast to multiple attack of the wild-type enzyme.