1PHW

Crystal structure of KDO8P synthase in its binary complex with substrate analog 1-deoxy-A5P

Summary for 1PHW

• Entry DOI: 10.2210/pdb1phw/pdb
• Related: 1D9E 1G7U 1PHQ 1PL9 1Q3N
• Descriptor: 2-dehydro-3-deoxyphosphooctonate aldolase, ANY 5'-MONOPHOSPHATE NUCLEOTIDE (3 entities in total)
• Functional Keywords: beta-alpha-barrels, lyase, lipopolysaccharide, a5p analog, transferase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A715
• Total number of polymer chains: 1
• Total formula weight: 31084.79

Authors

Vainer, R.,Belakhov, V.,Rabkin, E.,Baasov, T.,Adir, N. (deposition date: 2003-05-29, release date: 2004-07-13, Last modification date: 2023-08-16)

Primary citation

Vainer, R.,Belakhov, V.,Rabkin, E.,Baasov, T.,Adir, N.
Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility.
J.Mol.Biol., 351:641-652, 2005

PubMed Abstract: The enzyme 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS) catalyses the condensation of arabinose 5-phosphate (A5P) and phosphoenol pyruvate (PEP) to obtain 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P). We have elucidated initial modes of ligand binding in KDO8PS binary complexes by X-ray crystallography. Structures of the apo-enzyme and of binary complexes with the substrate PEP, the product KDO8P and the catalytically inactive 1-deoxy analog of arabinose 5-phosphate (1dA5P) were obtained. The KDO8PS active site resembles an irregular funnel with positive electrostatic potential situated at the bottom of the PEP-binding sub-site, which is the primary attractive force towards negatively charged phosphate moieties of all ligands. The structures of the ligand-free apo-KDO8PS and the binary complex with the product KDO8P visualize for the first time the role of His202 as an active-site gate. Examination of the crystal structures of KDO8PS with the KDO8P or 1dA5P shows these ligands bound to the enzyme in the PEP-binding sub-site, and not as expected to the A5P sub-site. Taken together, the structures presented here strengthen earlier evidence that this enzyme functions predominantly through positional catalysis, map out the roles of active-site residues and provide evidence that explains the total lack of catalytic reversibility.

PubMed: 16023668
DOI: 10.1016/j.jmb.2005.06.021

Experimental method

X-RAY DIFFRACTION (2.36 Å)