PDBsum entry 2d22

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Hydrolase PDB id
Protein chains
427 a.a. *
SO4 ×5
GOL ×8
Waters ×863
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of covalent glycosyl-enzyme intermediate o catalytic-site mutant xylanase from streptomyces olivaceovi
Structure: Endo-1,4-beta-d-xylanase. Chain: a, b. Synonym: glycoside hydrolase family 10 xylanase. Engineered: yes. Mutation: yes
Source: Streptomyces olivaceoviridis. Organism_taxid: 1921. Strain: e-86. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.70Å     R-factor:   0.186     R-free:   0.207
Authors: R.Suzuki,A.Kuno,Z.Fujimoto,S.Ito,S.I.Kawahara,S.Kaneko,T.Has K.Taira
Key ref: R.Suzuki et al. (2009). Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86. J Biochem, 146, 61-70. PubMed id: 19279191
02-Sep-05     Release date:   10-Oct-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q7SI98  (Q7SI98_STROI) -  Beta-xylanase
436 a.a.
427 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Endo-1,4-beta-xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     4 terms  


J Biochem 146:61-70 (2009)
PubMed id: 19279191  
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, A.Kuno.
Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates. Furthermore, during structural analyses of glycosyl hydrolases with hydrolytic reaction products by the conventional soaking method, mutarotation of an anomeric carbon in the reaction products promptly and certainly occurs. This undesirable structural alteration hinders visualization of the second step in the reaction. Here, we investigated X-ray crystallographic visualization as a possible method for visualizing the conformational itinerary of a retaining xylanase from Streptomyces olivaceoviridis E-86. To clearly define the stereochemistry at the anomeric carbon during the deglycosylation step, extraneous nucleophiles, such as azide, were adopted to substitute for the missing base catalyst in an appropriate mutant. The X-ray crystallographic visualization provided snapshots of the components of the entire reaction, including the E*S complex, the covalent intermediate, breakdown of the intermediate and the enzyme-product (E*P)complex.