1E48

L-Fuculose 1-Phosphate Aldolase from Escherichia coli Mutant E73Q/Y113F/Y209F

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 

Literature

Structures of L-Fuculose-1-Phosphate Aldolase Mutants Outlining Motions During Catalysis

Joerger, A.C., Mueller-Dieckmann, C., Schulz, G.E.

(2000) J.Mol.Biol. 303: 531

  • DOI: 10.1006/jmbi.2000.4153
  • Primary Citation of Related Structures:  
  • Also Cited By: 1OJR, 1GT7

  • PubMed Abstract: 

    • The crystal structures of l-fuculose-1-phosphate aldolase (FucA) with and without a ligated analogue of dihydroxyacetone phosphate (DHAP) and of a number of active center mutants have resulted in a model of the catalytic mechanism. This model has now ...

    The crystal structures of l-fuculose-1-phosphate aldolase (FucA) with and without a ligated analogue of dihydroxyacetone phosphate (DHAP) and of a number of active center mutants have resulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of further mutations at the zinc coordination sphere and at the phosphate site. In addition, these mutants have revealed new aspects of the catalysis: the hydroxyl group of Tyr113' (from a neighboring subunit), which sits just outside the zinc coordination sphere, steers DHAP towards a productive binding mode at the zinc ion; Glu73 contacts zinc in between the two ligand positions intended for the DHAP oxygen atoms and thus avoids blocking of these positions by a tetrahedrally coordinated hydroxy ion; the FucA polypeptide does not assume its minimum energy state but oscillates between two states of elevated energy as demonstrated by a mutant in a minimum energy state. The back and forth motion involves a mobile loop connecting the phosphate site with intersubunit motions and thus with the Brownian motion of the solvent. The phosphate group is bound strongly at a given distance to the zinc ion, which prevents the formation of too tight a DHAP:zinc complex. This observation explains our failure to find mutants that accept phosphate-free substitutes for DHAP. The FucA zinc coordination sphere is compared with that of carbonic anhydrase.

    Related Citations: 
    • Catalytic Mechanism of the Metal-Dependent Fuculose Aldolase from Escherichia Coli as Derived from the Structure
      Dreyer, M.K.,Schulz, G.E.
      (1996) J.Mol.Biol. 259: 458
    • The Spatial Structure of the Class II L-Fuculose-1-Phosphate Aldolase from Escherichia Coli
      Dreyer, M.K.,Schulz, G.E.
      (1993) J.Mol.Biol. 231: 549
    • Catalytic Action of Fuculose 1-Phosphate Aldolase (Class II) as Derived by Structure-Directed Mutagenesis
      Joerger, A.C.,Gosse, C.,Fessner, W.-D.,Schulz, G.E.
      (2000) Biochemistry 39: 6033

    Organizational Affiliation: 

    Institut für Organische Chemie und Biochemie, Freiburg im Breisgau, Germany-79104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-FUCULOSE 1-PHOSPHATE ALDOLASE
P
215Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: fucA (fucC, prd)
EC: 4.1.2.17
Find proteins for P0AB87 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AB87
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
P
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
13P
Query on 13P
Download SDF File 
Download CCD File 
P
1,3-DIHYDROXYACETONEPHOSPHATE
C3 H7 O6 P
GNGACRATGGDKBX-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME
Download SDF File 
Download CCD File 
P
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.171 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.700α = 90.00
b = 93.700β = 90.00
c = 43.200γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Data collection
  • Version 1.4: 2017-07-12
    Type: Advisory, Derived calculations
  • Version 1.5: 2019-01-30
    Type: Data collection, Experimental preparation