PDBsum entry: 2ot1

Lyase

PDB id: 2ot1

Contents

Protein chains

349 a.a. *

Ligands

N3P ×4

Waters ×1863

* Residue conservation analysis

PDB id:

2ot1

Name:

Lyase

Title:

Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with naphthol as-e phosphate, a 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.

Resolution:

2.05Å R-factor: 0.149 R-free: 0.197

Authors:

M.St-Jean,T.Izard,J.Sygusch

Key ref:

M.St-Jean et al. (2007). A hydrophobic pocket in the active site of glycolytic aldolase mediates interactions with Wiskott-Aldrich syndrome protein. J Biol Chem, 282, 14309-14315. PubMed id: 17329259 DOI: 10.1074/jbc.M611505200

Date:

07-Feb-07 Release date: 27-Feb-07

Protein chains

P00883  (ALDOA_RABIT) -  Fructose-bisphosphate aldolase A

Seq: 364 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: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
• Cofactor: Zinc

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (3 terms)

reference

DOI no: 10.1074/jbc.M611505200

J Biol Chem 282:14309-14315 (2007)

PubMed id: 17329259

A hydrophobic pocket in the active site of glycolytic aldolase mediates interactions with Wiskott-Aldrich syndrome protein.

M.St-Jean, T.Izard, J.Sygusch.

ABSTRACT

Aldolase plays essential catalytic roles in glycolysis and gluconeogenesis. However, aldolase is a highly abundant protein that is remarkably promiscuous in its interactions with other cellular proteins. In particular, aldolase binds to highly acidic amino acid sequences, including the C terminus of the Wiskott-Aldrich syndrome protein, an actin nucleation-promoting factor. Here we report the crystal structure of tetrameric rabbit muscle aldolase in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein. Aldolase recognizes a short, four-residue DEWD motif (residues 498-501), which adopts a loose hairpin turn that folds around the central aromatic residue, enabling its tryptophan side chain to fit into a hydrophobic pocket in the active site of aldolase. The flanking acidic residues in this binding motif provide further interactions with conserved aldolase active site residues Arg-42 and Arg-303, aligning their side chains and forming the sides of the hydrophobic pocket. The binding of Wiskott-Aldrich syndrome protein to aldolase precludes intramolecular interactions of its C terminus with its active site and is competitive with substrate as well as with binding by actin and cortactin. Finally, based on this structure, a novel naphthol phosphate-based inhibitor of aldolase was identified, and its structure in complex with aldolase demonstrated mimicry of the Wiskott-Aldrich syndrome protein-aldolase interaction. The data support a model whereby aldolase exists in distinct forms that regulate glycolysis or actin dynamics.

Selected figure(s)

Figure 3.
FIGURE 3. WASP and the naphthol AS-E phosphate aldolase inhibitor utilize a unique hydrophobic binding site. Comparison of both structures shows that the two ligands compete in muscle aldolase for the same binding pocket made up by the conserved residues Arg-42 and Arg-303. The overlapping binding loci are occupied in both cases by an aromatic moiety, the Trp-500 side chain in the case of WASP (A) and the naphthalene ring in the NASEP inhibitor (B). Surface representations of the aldolase active site were generated using the program PyMOL.

Figure 5.
FIGURE 5. The WASP binding mode is compatible with the interaction of WASP homologues with aldolase. Residues 498-501 corresponding to the sequence DEWD of the WASP peptide were used as a template to model the bound conformation of homologous peptides known to interact with homologous aldolases and also implicating a tryptophan residue. Shown in gray and yellow are aldolase and WASP residues 498-501, respectively. Side chains of WASP residues were substituted using PyMOL software with side chains of the amino acids of homologous sequences DMWM (cyan) and NEWN (magenta), corresponding respectively to the cytoplasmic C-terminal tail of the MIC2 protein from T. gondi and that of the TRAP protein from P. falciparum. Each substitution was made using side chain conformations available in the PyMOL rotamer library and was devoid of steric clashes. The green dashes illustrate hydrogen bonds.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 14309-14315) copyright 2007.

Figures were selected by an automated process.