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Catalytic Site Atlas

CSA LITERATURE entry for 1b57

E.C. namefructose-bisphosphate aldolase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 4.1.2.13
CSA Homologues of 1b57There are 17 Homologs
CSA Entries With UniProtID P0AB71
CSA Entries With EC Number 4.1.2.13
PDBe Entry 1b57
PDBSum Entry 1b57
MACiE Entry M0052

Literature Report

IntroductionFructose-1,6-bisphosphate aldolase (FBP-aldolase, EC 4.1.2.13) participates in two major metabolic pathways. In gluconeogenesis, they catalyse the aldol condensation of a ketose, dihydroxyacetone phosphate (DHAP) and an aldose, glyceraldehyde 3-phosphate (G3P) to form the acylic form of fructose 1,6-bisphosphate (FBP). In glycolysis, they catalyse the reverse cleavage reaction. In each pathway, the enzyme-catalysed reaction represents a distinctive stage, a switch between six and three carbon units. The aldol condensation is a key reaction in synthetic chemistry that aldolases catalyse with exquisite control of the stereochemistry.
Aldolases have been divided into two groups, class I and class II, depending primarily on the reaction mechanism. This annotation refers to class II aldolases, which are alpha/beta(8) barrel structures. The class II enzymes are not found in mammals, and have an absolute requirement for a divalent cation, usually Zn2+, and are activated by monovalent cations.
MechansimThe aldol condensation carried out by FBP aldolases involves three major covalency changes [3]. (1) Abstraction of the 1-proS proton, DHAP C1-H to produce the ene-diolate. (2) Carbon-carbon bond formation to covalently link DHAP C1 with G3P C1 and so form the FBP C3-C4 bond. (3) A second proton transfer converts C4=O to C4-O-H to complete the synthesis of FBP.
A mechanism could be proposed for the class II FBP-aldolase in the condensation direction as follows [3]:
Step I: DHAP binds either with or following monovalent cation binding and chelates to Zn2+ replacing the two water molecule ligands. Asp-109 is protonated by one of these solvents following zinc stimulated activation of water. Direct coordination of DHAP to the metal assists the precise alignment of catalysis allowing zinc to function as a Lewis acid and to polarise the carbonyl bond of the ketose substrate ready for the condensation. The carbonyl group is polarised, increasing the acidity of the hydroxymethylene hydrogen atoms and promoting abstraction of the proton.
Step II: The deprotonation of DHAP leads to carbanion formation and provides the unsaturated linkage where addition occurs. A base is required to abstract the acidic 1-proS alpha-H. The loop carrying Glu-182 undergoes a conformational change to position the residue closer to the catalytic metal, and carries out the proton abstraction.
Step III: The aldehyde (G3P) binds to Arg-331 and is brought into position to interact with the nucleophilic ene-diolate. The two planes of the ene-diolate nucleophile and the carbonyl acceptor must be near parallel in the initial alignment that precedes C-C bond formation. Asp-109 polarises the carbonyl group of G3P C1.
Step IV: The C-C bond is formed and proton transfer occurs. Asp-109 transfers a proton to convert C4=O to a hydroxyl group either in concert with or very quickly after C-C bond formation.
Step V: Product release is regulated by the relative concentrations of DHAP, G3P and FBP.
Reaction

Catalytic Sites for 1b57

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA109110macie:sideChainIt polarises the carbonyl group of G3P C1 to enhance the aldol reaction. It acts as an acid to donate a proton to convert C4=O to a hydroxyl group to yield the product.
AsnA286287macie:sideChainIt is positioned just below ene-diolate intermediate to stabilise the charged transition state.
GluA182183macie:sideChainIt acts as a base to remove the C1-phoS alpha-H of DHAP.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspB109110macie:sideChainIt polarises the carbonyl group of G3P C1 to enhance the aldol reaction. It acts as an acid to donate a proton to convert C4=O to a hydroxyl group to yield the product.
AsnB286287macie:sideChainIt is positioned just below ene-diolate intermediate to stabilise the charged transition state.
GluB182183macie:sideChainIt acts as a base to remove the C1-phoS alpha-H of DHAP.

Literature References

Notes:Comparisons of the three crystal structures available for the E. coli class II FBP-aldolase indicate significant rearrangements of three loops when the transition analogue phosphoglycolohydroxamate (PGH) and Na+ bind. These loops are from the beta5-loop-alpha7, beta6-loop-alpha8, beta7-loop-alpha9 segments. Similar observations have been made with the archetypal (alpha/beta)8 enzyme, TIM in response to binding PGH. As the loops move in response to PGH binding, the active sites without ligands of type II aldolase from 1dos and 1zen could not be hit.
Blom NS
Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase.
Nat Struct Biol 1996 3 856-862
PubMed: 8836102
Cooper SJ
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.
Structure 1996 4 1303-1315
PubMed: 8939754
Plater AR
Conserved residues in the mechanism of the E. coli Class II FBP-aldolase.
J Mol Biol 1999 285 843-855
PubMed: 9878448
Hall DR
The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity.
J Mol Biol 1999 287 383-394
PubMed: 10080900
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