1D9E

STRUCTURE OF E. COLI KDO8P SYNTHASE

Summary for 1D9E

• Entry DOI: 10.2210/pdb1d9e/pdb
• Descriptor: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE, SULFATE ION (3 entities in total)
• Functional Keywords: kdo, kdo8p, tim barrel, dah7p, pep, a5p, lyase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A715
• Total number of polymer chains: 4
• Total formula weight: 124443.33

Authors

Radaev, S.,Dastidar, P.,Patel, M.,Woodard, R.W.,Gatti, D.L. (deposition date: 1999-10-27, release date: 2000-05-10, Last modification date: 2024-02-07)

Primary citation

Radaev, S.,Dastidar, P.,Patel, M.,Woodard, R.W.,Gatti, D.L.
Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
J.Biol.Chem., 275:9476-9484, 2000

PubMed Abstract: 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation of phosphoenolpyruvate (PEP) with arabinose 5-phosphate (A5P) to form KDO8P and inorganic phosphate. KDO8P is the phosphorylated precursor of 3-deoxy-D-manno-octulosonate, an essential sugar of the lipopolysaccharide of Gram-negative bacteria. The crystal structure of the Escherichia coli KDO8P synthase has been determined by multiple wavelength anomalous diffraction and the model has been refined to 2.4 A (R-factor, 19.9%; R-free, 23.9%). KDO8P synthase is a homotetramer in which each monomer has the fold of a (beta/alpha)(8) barrel. On the basis of the features of the active site, PEP and A5P are predicted to bind with their phosphate moieties 13 A apart such that KDO8P synthesis would proceed via a linear intermediate. A reaction similar to KDO8P synthesis, the condensation of phosphoenolpyruvate, and erythrose 4-phosphate to form 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P), is catalyzed by DAH7P synthase. In the active site of DAH7P synthase the two substrates PEP and erythrose 4-phosphate appear to bind in a configuration similar to that proposed for PEP and A5P in the active site of KDO8P synthase. This observation suggests that KDO8P synthase and DAH7P synthase evolved from a common ancestor and that they adopt the same catalytic strategy.

PubMed: 10734095
DOI: 10.1074/jbc.275.13.9476

Experimental method

X-RAY DIFFRACTION (2.4 Å)