PDBsum entry 1zal

Lyase

PDB id: 1zal

Contents

Protein chains

363 a.a. *

Ligands

PO4 ×8

Waters ×2215

* Residue conservation analysis

PDB id:

1zal

Name:

Lyase

Title:

Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with partially disordered tagatose-1,6-bisphosphate, a weak competitive inhibitor

Structure:

Fructose-bisphosphate aldolase a. Chain: a, b, c, d. Synonym: muscle-type aldolase. Engineered: yes

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Gene: aldoa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.89Å R-factor: 0.168 R-free: 0.211

Authors:

M.St-Jean,J.Lafrance-Vanasse,B.Liotard,J.Sygusch

Key ref:

M.St-Jean et al. (2005). High resolution reaction intermediates of rabbit muscle fructose-1,6-bisphosphate aldolase: substrate cleavage and induced fit. J Biol Chem, 280, 27262-27270. PubMed id: 15870069 DOI: 10.1074/jbc.M502413200

Date:

06-Apr-05 Release date: 10-May-05

Protein chains

P00883  (ALDOA_RABIT) -  Fructose-bisphosphate aldolase A from Oryctolagus cuniculus

Seq: 364 a.a.

Struc: 363 a.a.

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 = PO4) matches with 50.00% similarity) + dihydroxyacetone phosphate

• Cofactor: Zn(2+)

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

reference

DOI no: 10.1074/jbc.M502413200

J Biol Chem 280:27262-27270 (2005)

PubMed id: 15870069

High resolution reaction intermediates of rabbit muscle fructose-1,6-bisphosphate aldolase: substrate cleavage and induced fit.

M.St-Jean, J.Lafrance-Vanasse, B.Liotard, J.Sygusch.

ABSTRACT

Crystal structures were determined to 1.8 A resolution of the glycolytic enzyme fructose-1,6-bis(phosphate) aldolase trapped in complex with its substrate and a competitive inhibitor, mannitol-1,6-bis(phosphate). The enzyme substrate complex corresponded to the postulated Schiff base intermediate and has reaction geometry consistent with incipient C3-C4 bond cleavage catalyzed Glu-187, which is adjacent by to the Schiff base forming Lys-229. Atom arrangement about the cleaved bond in the reaction intermediate mimics a pericyclic transition state occurring in nonenzymatic aldol condensations. Lys-146 hydrogen-bonds the substrate C4 hydroxyl and assists substrate cleavage by stabilizing the developing negative charge on the C4 hydroxyl during proton abstraction. Mannitol-1,6-bis(phosphate) forms a noncovalent complex in the active site whose binding geometry mimics the covalent carbinolamine precursor. Glu-187 hydrogen-bonds the C2 hydroxyl of the inhibitor in the enzyme complex, substantiating a proton transfer role by Glu-187 in catalyzing the conversion of the carbinolamine intermediate to Schiff base. Modeling of the acyclic substrate configuration into the active site shows Glu-187, in acid form, hydrogen-bonding both substrate C2 carbonyl and C4 hydroxyl, thereby aligning the substrate ketose for nucleophilic attack by Lys-229. The multifunctional role of Glu-187 epitomizes a canonical mechanistic feature conserved in Schiff base-forming aldolases catalyzing carbohydrate metabolism. Trapping of tagatose-1,6-bis(phosphate), a diastereoisomer of fructose 1,6-bis(phosphate), displayed stereospecific discrimination and reduced ketohexose binding specificity. Each ligand induces homologous conformational changes in two adjacent alpha-helical regions that promote phosphate binding in the active site.

Selected figure(s)

Figure 2.
FIG. 2. Electron density showing the Schiff base intermediate trapped in the active site of rabbit muscle aldolase. Difference electron density was calculated from a 1.8-Å annealed F[o] - F[c] omit map encompassing Lys-229 and FBP and contoured at 3 . The green dashes illustrate hydrogen bonds. A, FBP is covalently bound to the Schiff base-forming Lys-229 in all subunits, and the FBP O[4] is hydrogen-bonded to Glu-187 and Lys-146. Orientation is similar to Fig. 1. B, orientation showing the interaction of active site residues contacting the Schiff base intermediate. FBP phosphates interact extensively; the P[1] phosphate makes hydrogen bonding contacts with Ser-271, Gly-272, Arg-303, and Gly-302, whereas the P[6] phosphate interacts with Ser-35, Ser-38, and Lys-107. Orientation differs from Fig. 1 and consists of 100° rotation about the -barrel axis and then viewing approximately perpendicular to the rotation axis. Some hydrogen bonds were omitted for visual clarity.

Figure 4.
FIG. 4. Acyclic form of FBP docked in the active site and superposition with MBP bound structure. The ketohexose-P[2] was docked manually by superposition onto the determined MBP structure, shown in Fig. 3A. The modeled structure was then subjected to 2000 steps of conjugated gradient minimization with CNS using topology and parameters from PRODRG. Hydrogen bonding patterns (green dashes) were conserved when compared with those in FBP and MBP enzyme adducts. The only significant difference with respect to the observed enzyme adducts is an additional hydrogen bond made by Glu-187 with FBP O[2]. The orange dash illustrates the putative nucleophilic face si attack made on FBP C[2] carbonyl by Lys-229. Orientation is similar to Fig. 1.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 27262-27270) copyright 2005.

Figures were selected by an automated process.