PDBsum entry 3a3v

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Hydrolase PDB id
Protein chain
376 a.a. *
GOL ×4
Waters ×516
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of reducing-end-xylose releasing exo-oligo y198f mutant
Structure: Xylanase y. Chain: a. Synonym: reducing-end-xylose releasing exo-oligoxylanase. Engineered: yes. Mutation: yes
Source: Bacillus halodurans. Organism_taxid: 86665. Strain: c-125. Gene: bh2105. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
1.39Å     R-factor:   0.178     R-free:   0.198
Authors: M.Hidaka,S.Fushinobu,Y.Honda,M.Kitaoka
Key ref: M.Hidaka et al. (2010). Structural explanation for the acquisition of glycosynthase activity. J Biochem, 147, 237-244. PubMed id: 19819900
22-Jun-09     Release date:   03-Nov-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9KB30  (REOX_BACHD) -  Reducing end xylose-releasing exo-oligoxylanase
388 a.a.
376 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.  - Oligosaccharide reducing-end xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     5 terms  


J Biochem 147:237-244 (2010)
PubMed id: 19819900  
Structural explanation for the acquisition of glycosynthase activity.
M.Hidaka, S.Fushinobu, Y.Honda, T.Wakagi, H.Shoun, M.Kitaoka.
Glycosynthases are engineered glycoside hydrolases (GHs) that catalyse the synthesis of glycoside from glycosyl-fluoride donors and suitable acceptors. We have determined five crystal structures of the glycosynthase mutants reducing-end xylose-releasing exo-oligoxylanase, an inverting GH, that exhibit various levels of glycosynthetic activities. At the active site of the Y198F mutant, the most efficient glycosynthase, a water molecule is observed at the same position as nucleophilic water (NW) in the parent enzyme, and the loss of the fixation of the direction of the lone pair of water molecules in the mutant drastically decreases hydrolytic activity. Water molecules were also observed at each active site of the general base mutant, but they were shifted 1.0-3.0 A from the NW in the wild type. Their positions exhibited a strong correlation with the strength of glycosynthase activity. Here, we propose that a structural prerequisite for the sufficient glycosynthase reaction is the presence of a water molecule at the NW position, and mutation at the NW holder provides a general strategy for inverting GHs. The idea on the position of a water molecule may also be applicable to the design of efficient glycosynthases from retaining GHs.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21150123 S.Fushinobu (2010).
Unique sugar metabolic pathways of bifidobacteria.
  Biosci Biotechnol Biochem, 74, 2374-2384.  
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