2Q1D: 2-Keto-3-Deoxy-D-Arabinonate Dehydratase Complexed With Magnesium And 2,5-Dioxopentanoate

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.
PDB ID: 2Q1DDownload
MMDB ID: 63607
PDB Deposition Date: 2007/5/24
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Similar Structures:
Biological Unit for 2Q1D: tetrameric; determined by author
Molecular Components in 2Q1D
Label Count Molecule
Proteins (4 molecules)
2-keto-3-deoxy-d-arabinonate Dehydratase(Gene symbol: SSO_RS15130)
Molecule annotation
Chemicals (8 molecules)
* Click molecule labels to explore molecular sequence information.

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