PDBsum entry 2q1c

Lyase

PDB id: 2q1c

Contents

Protein chain

291 a.a. *

Ligands

2KT

Metals

_CA

Waters ×88

* Residue conservation analysis

PDB id:

2q1c

Name:

Lyase

Title:

2-keto-3-deoxy-d-arabinonate dehydratase complexed with calcium and 2- oxobutyrate

Structure:

2-keto-3-deoxy-d-arabinonate dehydratase. Chain: x. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Gene: kdad. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.241 R-free: 0.266

Authors:

T.Barends,S.Brouns,P.Worm,J.Akerboom,A.Turnbull,L.Salmon

Key ref:

S.J.Brouns et al. (2008). Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily. J Mol Biol, 379, 357-371. PubMed id: 18448118 DOI: 10.1016/j.jmb.2008.03.064

Date:

24-May-07 Release date: 08-Apr-08

Protein chain

Q97UA0  (KDAD_SULSO) -  2-dehydro-3-deoxy-D-arabinonate dehydratase from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 298 a.a.

Struc: 291 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.141 - 2-dehydro-3-deoxy-D-arabinonate dehydratase.
• Reaction: 2-dehydro-3-deoxy-D-arabinonate = 2,5-dioxopentanoate + H2O

2-dehydro-3-deoxy-D-arabinonate = 2,5-dioxopentanoate (Bound ligand (Het Group name = 2KT) matches with 77.78% similarity) + H2O

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

Added reference

DOI no: 10.1016/j.jmb.2008.03.064

J Mol Biol 379:357-371 (2008)

PubMed id: 18448118

Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily.

S.J.Brouns, T.R.Barends, P.Worm, J.Akerboom, A.P.Turnbull, L.Salmon, J.van der Oost.

ABSTRACT

The archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.

Selected figure(s)

Figure 2.
Fig. 2. (a) Topology diagram showing the connectivity of secondary structure elements and domain organization of the S. solfataricus KdaD monomer. The N terminus of the polypeptide chain (N, in blue) follows a color gradient towards the C terminus (C, in red). (b and c) Ribbon diagrams at two viewing angles of the KdaD monomer with Mg^2+ and 2-oxobutyrate bound.

Figure 4.
Fig. 4. Stereo diagrams are shown of the KdaD active site with Mg^2+ (green spheres), water molecules (red spheres) and (a) 2,5-dioxopentanoate or (b) 2-oxobutyrate bound. To exclude any model bias, simulated annealing F[o]–DF[c] omit electron density maps for the ligand and the metal ion are displayed at the 3σ contour level. (c) Stereo image of a model of the Michaelis complex of KdaD with its substrate 2-keto-3-deoxy-d-arabinonate (D-KDA) bound. Hydrogen atoms for D-KDA are shown as well as the carbon atom numbers.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 379, 357-371) copyright 2008.

Figures were selected by the author.