1EUN

STRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE FROM ESCHERICHIA COLI

Summary for 1EUN

• Entry DOI: 10.2210/pdb1eun/pdb
• Related: 1EUA
• Descriptor: KDPG ALDOLASE, SULFATE ION (3 entities in total)
• Functional Keywords: 2-keto-3-deoxy-6-phosphogluconate aldolase, sulfate, trimer, beta-barrel, lyase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A955
• Total number of polymer chains: 3
• Total formula weight: 67491.23

Authors

Allard, J.,Grochulski, P.,Sygusch, J. (deposition date: 2000-04-17, release date: 2001-02-07, Last modification date: 2024-02-07)

Primary citation

Allard, J.,Grochulski, P.,Sygusch, J.
Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution.
Proc.Natl.Acad.Sci.USA, 98:3679-3684, 2001

PubMed Abstract: 2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. The enzyme is a class I aldolase whose reaction mechanism involves formation of Schiff base intermediates between Lys-133 and a keto substrate. A covalent adduct was trapped by flash freezing KDPG aldolase crystals soaked with 10 mM pyruvate in acidic conditions at pH 4.6. Structure determination to 1.95-A resolution showed that pyruvate had undergone nucleophilic attack with Lys-133, forming a protonated carbinolamine intermediate, a functional Schiff base precursor, which was stabilized by hydrogen bonding with active site residues. Carbinolamine interaction with Glu-45 indicates general base catalysis of several rate steps. Stereospecific addition is ensured by aromatic interaction of Phe-135 with the pyruvate methyl group. In the native structure, Lys-133 donates all of its hydrogen bonds, indicating the presence of an epsilon-ammonium salt group. Nucleophilic activation is postulated to occur by proton transfer in the monoprotonated zwitterionic pair (Glu-45/Lys-133). Formation of the zwitterionic pair requires prior side chain rearrangement by protonated Lys-133 to displace a water molecule, hydrogen bonded to the zwitterionic residues.

PubMed: 11274385
DOI: 10.1073/pnas.071380898

Experimental method

X-RAY DIFFRACTION (2 Å)