1C7T

BETA-N-ACETYLHEXOSAMINIDASE MUTANT E540D COMPLEXED WITH DI-N ACETYL-D-GLUCOSAMINE (CHITOBIASE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of chitobiase mutants complexed with the substrate Di-N-acetyl-d-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540.

Prag, G.Papanikolau, Y.Tavlas, G.Vorgias, C.E.Petratos, K.Oppenheim, A.B.

(2000) J.Mol.Biol. 300: 611-617

  • DOI: 10.1006/jmbi.2000.3906
  • Primary Citation of Related Structures:  1C7S

  • PubMed Abstract: 
  • The catalytic domain of chitobiase (beta-N-1-4 acetylhexosaminidase) from Serratia marcescens, is an alpha/beta TIM-barrel. This enzyme belongs to family 20 of glycosyl hydrolases in which a conserved amino acid pair, aspartate-glutamate, is present ...

    The catalytic domain of chitobiase (beta-N-1-4 acetylhexosaminidase) from Serratia marcescens, is an alpha/beta TIM-barrel. This enzyme belongs to family 20 of glycosyl hydrolases in which a conserved amino acid pair, aspartate-glutamate, is present (Asp539-Glu540). It was proposed that catalysis by this enzyme family is carried out by glutamate 540 acting as a proton donor and by the acetamido group of the substrate as a nucleophile. We investigated the role of Asp539 and Glu540 by site-directed mutagenesis, biochemical characterization and by structural analyses of chitobiase -substrate co-crystals. We found that both residues are essential for chitobiase activity. The mutations, however, led to subtle changes in the catalytic site. Our results support the model that Glu540 acts as the proton donor and that Asp539 acts in several different ways. Asp539 restrains the acetamido group of the substrate in a specific orientation by forming a hydrogen bond with N2 of the non-reduced (-1) sugar. In addition, this residue participates in substrate binding. It is also required for the correct positioning of Glu540 and may provide additional negative charge at the active site. Thus, these biochemical and structural studies provide a molecular explanation for the functional importance and conservation of these residues.


    Related Citations: 
    • 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
    • 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.Mol.Biol. 3: 638


    Organizational Affiliation

    The Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-N-ACETYLHEXOSAMINIDASE
A
858Serratia marcescensGene Names: chb
EC: 3.2.1.52
Find proteins for Q54468 (Serratia marcescens)
Go to UniProtKB:  Q54468
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CBS
Query on CBS

Download SDF File 
Download CCD File 
A
DI(N-ACETYL-D-GLUCOSAMINE)
C16 H28 N2 O11
CDOJPCSDOXYJJF-KSKNGZLJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.174α = 90.00
b = 99.416β = 90.00
c = 86.556γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
ARPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance