5UD0

Class II fructose-1,6-bisphosphate aldolase E149A variant of Helicobacter pylori with cleavage products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.

Jacques, B.Coincon, M.Sygusch, J.

(2018) J Biol Chem 293: 7737-7753

  • DOI: 10.1074/jbc.RA117.001098
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Crystal structures of two bacterial metal (Zn 2+ )-dependent d-fructose-1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 Å resolution. The ligand complexes cry ...

    Crystal structures of two bacterial metal (Zn 2+ )-dependent d-fructose-1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 Å resolution. The ligand complexes cryotrapped in native or mutant Helicobacter pylori aldolase crystals enabled a novel mechanistic description of FBP C3-C4 bond cleavage. The reaction mechanism uses active site remodeling during the catalytic cycle, implicating relocation of the Zn 2+ cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes triggered upon P1 phosphate binding, which liberates the Zn 2+ -chelating His-180, allowing it to act as a general base for the proton abstraction at the FBP C4 hydroxyl group. A second zinc-chelating His-83 hydrogen bonds the substrate C4 hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface-exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu-142 is essential for protonation of the enediolate form prior to product release. A d-tagatose 1,6-bisphosphate enzymatic complex reveals how His-180-mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and d-glyceraldehyde 3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp-82 and Asp-255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops β5-α7 and β6-α8 (containing catalytic residues Glu-142 and His-180, respectively) drive active site remodeling, enabling the relocation of the metal cofactor.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada Jurgen.Sygusch@umontreal.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fructose-bisphosphate aldolase
A, B
307Helicobacter pylori 26695Mutation(s): 1 
Gene Names: fbaHP_0176
EC: 4.1.2.13
Find proteins for P56109 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56109
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13P
Query on 13P

Download CCD File 
B
1,3-DIHYDROXYACETONEPHOSPHATE
C3 H7 O6 P
GNGACRATGGDKBX-UHFFFAOYSA-N
 Ligand Interaction
G3H
Query on G3H

Download CCD File 
B
GLYCERALDEHYDE-3-PHOSPHATE
C3 H7 O6 P
LXJXRIRHZLFYRP-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.258α = 90
b = 85.386β = 100.2
c = 91.082γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence