2ISW

Structure of Giardia fructose-1,6-biphosphate aldolase in complex with phosphoglycolohydroxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia.

Galkin, A.Kulakova, L.Melamud, E.Li, L.Wu, C.Mariano, P.Dunaway-Mariano, D.Nash, T.E.Herzberg, O.

(2007) J.Biol.Chem. 282: 4859-4867

  • DOI: 10.1074/jbc.M609534200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Class I and class II fructose-1,6-bisphosphate aldolases (FBPA), glycolytic pathway enzymes, exhibit no amino acid sequence homology and utilize two different catalytic mechanisms. The mammalian class I FBPA employs a Schiff base mechanism, whereas t ...

    Class I and class II fructose-1,6-bisphosphate aldolases (FBPA), glycolytic pathway enzymes, exhibit no amino acid sequence homology and utilize two different catalytic mechanisms. The mammalian class I FBPA employs a Schiff base mechanism, whereas the human parasitic protozoan Giardia lamblia class II FBPA is a zinc-dependent enzyme. In this study, we have explored the potential exploitation of the Giardia FBPA as a drug target. First, synthesis of FBPA was demonstrated in Giardia trophozoites by using an antibody-based fluorescence assay. Second, inhibition of FBPA gene transcription in Giardia trophozoites suggested that the enzyme is necessary for the survival of the organism under optimal laboratory growth conditions. Third, two crystal structures of FBPA in complex with the transition state analog phosphoglycolohydroxamate (PGH) show that the enzyme is homodimeric and that its active site contains a zinc ion. In one crystal form, each subunit contains PGH, which is coordinated to the zinc ion through the hydroxamic acid hydroxyl and carbonyl oxygen atoms. The second crystal form contains PGH only in one subunit and the active site of the second subunit is unoccupied. Inspection of the two states of the enzyme revealed that it undergoes a conformational transition upon ligand binding. The enzyme cleaves d-fructose-1,6-bisphosphate but not d-tagatose-1,6-bisphosphate, which is a tight binding competitive inhibitor. The essential role of the active site residue Asp-83 in catalysis was demonstrated by amino acid replacement. Determinants of catalysis and substrate recognition, derived from comparison of the G. lamblia FBPA structure with Escherichia coli FBPA and with a closely related enzyme, E. coli tagatose-1,6-bisphosphate aldolase (TBPA), are described.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative fructose-1,6-bisphosphate aldolase
A, B
323Giardia intestinalisMutation(s): 0 
Gene Names: ald
EC: 4.1.2.13
Find proteins for O97447 (Giardia intestinalis)
Go to UniProtKB:  O97447
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGH
Query on PGH

Download SDF File 
Download CCD File 
A
PHOSPHOGLYCOLOHYDROXAMIC ACID
C2 H6 N O6 P
BAXHHWZKQZIJID-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PGHKi: 37 nM BINDINGMOAD
PGHKi: 37 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.020α = 90.00
b = 90.050β = 90.00
c = 166.090γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance