1QBA | pdb_00001qba

BACTERIAL CHITOBIASE, GLYCOSYL HYDROLASE FAMILY 20

• PDB DOI: https://doi.org/10.2210/pdb1QBA/pdb

• Classification: GLYCOSYL HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-06-06 Released: 1997-01-11 
• Deposition Author(s): Tews, I., Perrakis, A., Oppenheim, A., Dauter, Z., Wilson, K.S., Vorgias, C.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.196 (Depositor) 
• R-Value Work: 
  0.139 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

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

• PubMed: 8673609 
• DOI: https://doi.org/10.1038/nsb0796-638
• Primary Citation 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. 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.

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.31 kDa 
• Atom Count: 7,596 
• Modeled Residue Count: 858 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITOBIASE	A	858	Serratia marcescens	Mutation(s): 0  EC: 3.2.1.52
UniProt
Find proteins for Q54468 (Serratia marcescens) Explore Q54468  Go to UniProtKB:  Q54468

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.196 (Depositor) 
• R-Value Work:  0.139 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.7	α = 90
b = 99.9	β = 90
c = 87.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-01-11 
Deposition Author(s): Tews, I., Perrakis, A., Oppenheim, A., Dauter, Z., Wilson, K.S., Vorgias, C.E.

Revision History  

• Version 1.0: 1997-01-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary