PDBsum entry: 1dxf

Class ii aldolase

PDB id: 1dxf

Contents

Protein chains

253 a.a. *

Ligands

PYR ×2

Metals

_MG ×2

Waters ×244

* Residue conservation analysis

PDB id:

1dxf

Name:

Class ii aldolase

Title:

2-dehydro-3-deoxy-galactarate aldolase from escherichia coli in complex with pyruvate

Structure:

2-dehydro-3-deoxy-galactarate aldolase. Chain: a, b. Ec: 4.1.2.20

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.6Å R-factor: 0.173 R-free: 0.233

Authors:

T.Izard,N.C.Blackwell

Key ref:

T.Izard and N.C.Blackwell (2000). Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism. EMBO J, 19, 3849-3856. PubMed id: 10921867 DOI: 10.1093/emboj/19.15.3849

Date:

05-Jan-00 Release date: 25-Aug-00

Protein chains

P23522  (GARL_ECOLI) -  5-keto-4-deoxy-D-glucarate aldolase

Seq: 256 a.a.

Struc: 253 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.2.20 - 2-dehydro-3-deoxyglucarate aldolase.
• Reaction: 2-dehydro-3-deoxy-D-glucarate = pyruvate + tartronate semialdehyde

2-dehydro-3-deoxy-D-glucarate = pyruvate (Bound ligand (Het Group name = PYR) corresponds exactly) + tartronate semialdehyde

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: cellular aromatic compound metabolic process (4 terms)
• Biochemical function: catalytic activity (5 terms)

reference

DOI no: 10.1093/emboj/19.15.3849

EMBO J 19:3849-3856 (2000)

PubMed id: 10921867

Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism.

T.Izard, N.C.Blackwell.

ABSTRACT

Carbon-carbon bond formation is an essential reaction in organic chemistry and the use of aldolase enzymes for the stereochemical control of such reactions is an attractive alternative to conventional chemical methods. Here we describe the crystal structures of a novel class II enzyme, 2-dehydro-3-deoxy-galactarate (DDG) aldolase from Escherichia coli, in the presence and absence of substrate. The crystal structure was determined by locating only four Se sites to obtain phases for 506 protein residues. The protomer displays a modified (alpha/beta)(8) barrel fold, in which the eighth alpha-helix points away from the beta-barrel instead of packing against it. Analysis of the DDG aldolase crystal structures suggests a novel aldolase mechanism in which a phosphate anion accepts the proton from the methyl group of pyruvate.

Selected figure(s)

Figure 3.
Figure 3 (A) Space filling representation of the hexameric DDG aldolase looking down the non-crystallographic dyad. Each of the six subunits is colored differently. (B) Cartoon drawing of DDG aldolase oligomer shown in the same orientation as in (A) illustrating the active site pocket location between two 3-fold-related protomers. For clarity, only four of the six protomers within the hexamer are shown. The two phosphates located in the active site pocket and the catalytic magnesium are shown in space filling representation. The active site pocket is mainly lined by residues belonging to one protomer. The 3-fold-related subunit makes contacts with the 'second' phosphate.

Figure 4.
Figure 4 Stereo views of ligands binding to DDG aldolase. The bonds of the ligands are shown in pink while the bonds of the enzyme are shown in white. For clarity, water molecules (drawn as red spheres) are not labeled. The magnesium site is shown and possible ligands coordinating the Mg^2+ are indicated. (A)–(D) are in the same orientation. (A) Residues in contact with the two phosphate anions bound to the active site pocket as seen in the substrate-free DDG aldolase structure. Final [A]-weighted F[o] – F[c] omit electron density map for ligands bound to the enzyme. The contour level of the electron density map is 3 and the resolution is 1.8 Å. Four solvent molecules and the catalytic magnesium interact with the 'first' phosphate and five water molecules are hydrogen bonded to the 'second' phosphate. Ser124' and Val125' belong to a 3-fold-related protomer. (B) Residues in contact with pyruvate. Final [A]-weighted F[o] – F[c] omit electron density map for pyruvate bound to the enzyme. The contour level of the electron density map is 3 and the resolution is 2.6 Å. The ligand's carbonyl and carboxyl reside 2.5 and 2.4 Å, respectively, away from the magnesium. All contacts are made by one subunit within the hexamer. (C) Superposition of the substrate-free structure (white) onto the aldolase–pyruvate complexed structure (gray) to illustrate the possible role of the 'second' phosphate in the reaction mechanism (gray dotted line). The anion's oxygen is 3.4 Å away from the methyl carbon atom. The current distance of 3.9 Å between Arg75 and the 'second' phosphate is easily decreased to hydrogen bonding distance by a slight side chain movement without steric hindrance and/or by moving the 'second' phosphate deeper into the active site. (D) Modeling of the condensed substrate, DDG, into the active site based upon the aldolase–pyruvate structure. The carboxylate at C6 of DDG fills the cavity occupied by the 'second' phosphate. A possible role during catalysis for the solvent molecule bridging the ligand's O4 and His50 is indicated (gray dotted line).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 3849-3856) copyright 2000.

Figures were selected by the author.