1QBB

BACTERIAL CHITOBIASE COMPLEXED WITH CHITOBIOSE (DINAG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease.

Tews, I.Perrakis, A.Oppenheim, A.Dauter, Z.Wilson, K.S.Vorgias, C.E.

(1996) Nat Struct Biol 3: 638-648

  • DOI: 10.1038/nsb0796-638
  • Primary Citation of Related Structures:  
    1QBA, 1QBB

  • PubMed Abstract: 
  • Chitin, the second most abundant polysaccharide on earth, is degraded by chitinases and chitobiases. The structure of Serratia marcescens chitobiase has been refined at 1.9 A resolution. The mature protein is folded into four domains and its active site is situated at the C-terminal end of the central (beta alpha)8-barrel ...

    Chitin, the second most abundant polysaccharide on earth, is degraded by chitinases and chitobiases. The structure of Serratia marcescens chitobiase has been refined at 1.9 A resolution. The mature protein is folded into four domains and its active site is situated at the C-terminal end of the central (beta alpha)8-barrel. Based on the structure of the complex with the substrate disaccharide chitobiose, we propose an acid-base reaction mechanism, in which only one protein carboxylate acts as catalytic acid, while the nucleophile is the polar acetamido group of the sugar in a substrate-assisted reaction. The structural data lead to the hypothesis that the reaction proceeds with retention of anomeric configuration. The structure allows us to model the catalytic domain of the homologous hexosaminidases to give a structural rationale to pathogenic mutations that underlie Tay-Sachs and Sandhoff disease.


    Related Citations: 
    • N-Acetylglucosaminidase (Chitobiase) from Serratia Marcescens: Gene Sequence, and Protein Production and Purification in Escherichia Coli
      Tews, I., Vincentelli, R., Vorgias, C.E.
      (1996) Gene 170: 63
    • Cloning of the Gene Coding for Chitobiase of Serratia Marcescens
      Kless, H., Sitrit, Y., Chet, I., Oppenheim, A.B.
      (1989) Mol Gen Genet 217: 471
    • The Crystal Structure of a B-(1,4) Linked Disaccharide A-N,N'Diacetylchitobiose Monohydrate
      Mo, F., Jensen, L.H.
      (1978) Acta Crystallogr B 34: 1562

    Organizational Affiliation

    European Molecular Biology Laboratory, Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHITOBIASEA858Serratia marcescensMutation(s): 0 
Gene Names: chb
EC: 3.2.1.52
Find proteins for Q54468 (Serratia marcescens)
Explore Q54468 
Go to UniProtKB:  Q54468
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2 N/A Oligosaccharides Interaction
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.7α = 90
b = 99.9β = 90
c = 87.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary