PDBsum entry 5tk3

Lyase

PDB id: 5tk3

Contents

Protein chain

349 a.a.

Ligands

13P

G3H-GOL

Waters ×291

PDB id:

5tk3

Name:

Lyase

Title:

Crystal structure of fbp aldolase from toxoplasma gondii, burst-phase ternary complex

Structure:

Fructose-bisphosphate aldolase. Chain: a. Engineered: yes

Source:

Toxoplasma gondii. Organism_taxid: 5811. Gene: ald-1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.83Å R-factor: 0.163 R-free: 0.191

Authors:

P.W.Heron,J.Sygusch

Key ref:

P.W.Heron and J.Sygusch (2017). Isomer activation controls stereospecificity of class I fructose-1,6-bisphosphate aldolases. J Biol Chem, 292, 19849-19860. PubMed id: 28972169

Date:

06-Oct-16 Release date: 04-Oct-17

Protein chain

Q8I8I2  (ALF1_TOXGO) -  Fructose-bisphosphate aldolase 1 from Toxoplasma gondii

Seq: 363 a.a.

Struc: 349 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.1.2.13 - fructose-bisphosphate aldolase.
• Reaction: beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate

beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate (Bound ligand (Het Group name = G3H) corresponds exactly) + dihydroxyacetone phosphate

• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

J Biol Chem 292:19849-19860 (2017)

PubMed id: 28972169

Isomer activation controls stereospecificity of class I fructose-1,6-bisphosphate aldolases.

P.W.Heron, J.Sygusch.

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 ofToxoplasma gondiialdolase crystals to high resolution. The growth ofT. gondiialdolase crystals in acidic conditions enabled trapping of the ternary complex as a dominant population. The obligate 3(S)-4(R) stereochemistry at the nascent C3-C4 bond of FBP requires asi-face attack by the covalent DHAP nucleophile on the d-G3P aldehydesi-face in the active site. Thecis-isomer of the d-G3P aldehyde, representing the dominant population trapped in the ternary complex, would lead tore-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 activetrans-isomer competent for carbonyl bond activation by active-site residues, thereby enablingsi-face attack by the DHAP enamine. C-C bond formation by thecis-isomer is suppressed by hydrogen bonding of thecis-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.