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PDBsum entry 2d24

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2d24
Jmol
Contents
Protein chains
427 a.a. *
Ligands
XYS-XYS-XYS-XYS-
XYS
×2
XYS-XYS-XYS-XYS
XYS-XYS ×2
SO4 ×2
GOL ×3
Waters ×672
* Residue conservation analysis
PDB id:
2d24
Name: Hydrolase
Title: Crystal structure of es complex of catalytic-site mutant xyl streptomyces olivaceoviridis e-86
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.
Resolution:
1.85Å     R-factor:   0.177     R-free:   0.199
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
Date:
02-Sep-05     Release date:   10-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     3 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.
 
  ABSTRACT  
 
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.