The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold.
BACKGROUND
[corrected] Aldolases catalyze a variety of condensation and cleavage reactions, with exquisite control on the stereochemistry. These enzymes, therefore, are attractive catalysts for synthetic chemistry. There are two classes of aldolase: class I aldolases utilize Schiff base formation with an active-site lysine whilst class II enzymes require a divalent metal ion, in particular zinc. Fructose-1,6-bisphosphate aldolase (FBP-aldolase) is used in gluconeogenesis and glycolysis; the enzyme controls the condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to yield fructose-1,6-bisphosphate. Structures are available for class I FBP-aldolases but there is a paucity of detail on the class II enzymes. Characterization is sought to enable a dissection of structure/activity relationships which may assist the construction of designed aldolases for use as biocatalysts in synthetic chemistry.


RESULTS
The structure of the dimeric class II FBP-aldolase from Escherichia coli has been determined using data to 2.5 A resolution. The asymmetric unit is one subunit which presents a familiar fold, the (alpha/beta)8 barrel. The active centre, at the C-terminal end of the barrel, contains a novel bimetallic-binding site with two metal ions 6.2 A apart. One ion, the identity of which is not certain, is buried and may play a structural or activating role. The other metal ion is zinc and is positioned at the surface of the barrel to participate in catalysis.


CONCLUSIONS
Comparison of the structure with a class II fuculose aldolase suggests that these enzymes may share a common mechanism. Nevertheless, the class II enzymes should be subdivided into two categories on consideration of subunit size and fold, quaternary structure and metal-ion binding sites.
Cooper
S J
SJ
Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. wnhunter@bad.dundee.ac.uk
Leonard
G A
GA
McSweeney
S M
SM
Thompson
A W
AW
Naismith
J H
JH
Qamar
S
S
Plater
A
A
Berry
A
A
Hunter
W N
WN
D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D001665:Binding Sites; D002412:Cations / Q000737:chemistry; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019281:Dimerization; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins; D005634:Fructose-Bisphosphate Aldolase / Q000737:chemistry* / Q000145:classification; D008667:Metalloproteins / Q000737:chemistry* / Q000145:classification; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011188:Potassium / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D015032:Zinc / Q000737:chemistry*
D001426:Bacterial Proteins; D002412:Cations; D029968:Escherichia coli Proteins; D008667:Metalloproteins; C103622:FucA protein, bacteria; C491231:fucA protein, E coli; D005634:Fructose-Bisphosphate Aldolase; D015032:Zinc; D011188:Potassium