5TK3

Crystal structure of FBP aldolase from Toxoplasma gondii, burst-phase ternary complex

Summary for 5TK3

• Entry DOI: 10.2210/pdb5tk3/pdb
• Related: 5TJS 5TKC 5TKL 5TKN 5TKP
• Descriptor: Fructose-bisphosphate aldolase, 1,3-DIHYDROXYACETONEPHOSPHATE, GLYCERALDEHYDE-3-PHOSPHATE, ... (5 entities in total)
• Functional Keywords: tim barrel, aldolase, glycolysis, lyase, substrate, intermediate, enamine, covalent
• Biological source: Toxoplasma gondii
• Total number of polymer chains: 1
• Total formula weight: 39579.03

Authors

Heron, P.W.,Sygusch, J. (deposition date: 2016-10-06, release date: 2017-10-04, Last modification date: 2024-10-09)

Primary citation

Heron, P.W.,Sygusch, J.
Isomer activation controls stereospecificity of class I fructose-1,6-bisphosphate aldolases.
J. Biol. Chem., 292:19849-19860, 2017

PubMed Abstract: Fructose-1,6-bisphosphate (FBP) aldolase, a glycolytic enzyme, catalyzes the reversible and stereospecific aldol addition of dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (d-G3P) by an unresolved mechanism. To afford insight into the molecular determinants of FBP aldolase stereospecificity during aldol addition, a key ternary complex formed by DHAP and d-G3P, comprising 2% of the equilibrium population at physiological pH, was cryotrapped in the active site of aldolase crystals to high resolution. The growth of aldolase crystals in acidic conditions enabled trapping of the ternary complex as a dominant population. The obligate 3()-4() stereochemistry at the nascent C3-C4 bond of FBP requires a -face attack by the covalent DHAP nucleophile on the d-G3P aldehyde -face in the active site. The -isomer of the d-G3P aldehyde, representing the dominant population trapped in the ternary complex, would lead to -face attack on the aldehyde and yield tagatose 1,6-bisphosphate, a competitive inhibitor of the enzyme. We propose that unhindered rotational isomerization by the d-G3P aldehyde moiety in the ternary complex generates the active -isomer competent for carbonyl bond activation by active-site residues, thereby enabling -face attack by the DHAP enamine. C-C bond formation by the -isomer is suppressed by hydrogen bonding of the -aldehyde carbonyl with the DHAP enamine phosphate dianion through a tetrahedrally coordinated water molecule. The active site geometry further suppresses C-C bond formation with the l-G3P enantiomer of d-G3P. Understanding C-C formation is of fundamental importance in biological reactions and has considerable relevance to biosynthetic reactions in organic chemistry.

PubMed: 28972169
DOI: 10.1074/jbc.M117.811034

Experimental method

X-RAY DIFFRACTION (1.83 Å)