1G7U

CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE

Summary for 1G7U

• Entry DOI: 10.2210/pdb1g7u/pdb
• Related: 1G7V
• Descriptor: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE, PHOSPHOENOLPYRUVATE (3 entities in total)
• Functional Keywords: beta-alpha-barrels, lyase, lipopolysaccharide
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A715
• Total number of polymer chains: 1
• Total formula weight: 31080.80

Authors

Asojo, O.A.,Friedman, J.M.,Belakhov, V.,Shoham, Y.,Adir, N.,Baasov, T. (deposition date: 2000-11-14, release date: 2001-05-16, Last modification date: 2024-02-07)

Primary citation

Asojo, O.,Friedman, J.,Adir, N.,Belakhov, V.,Shoham, Y.,Baasov, T.
Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor.
Biochemistry, 40:6326-6334, 2001

PubMed Abstract: The crystal structures of 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDOPS) from Escherichia coli complexed with the substrate phosphoenolpyruvate (PEP) and with a mechanism-based inhibitor (K(d) = 0.4 microM) were determined by molecular replacement using X-ray diffraction data to 2.8 and 2.3 A resolution, respectively. Both the KDOPS.PEP and KDOPS.inhibitor complexes crystallize in the cubic space group I23 with cell constants a = b = c = 117.9 and 117.6 A, respectively, and one subunit per asymmetric unit. The two structures are nearly identical, and superposition of their Calpha atoms indicates an rms difference of 0.41 A. The PEP in the KDOPS.PEP complex is anchored to the enzyme in a conformation that blocks its si face and leaves its re face largely devoid of contacts. This results from KDOPS's selective choice of a PEP conformer in which the phosphate group of PEP is extended toward the si face. Furthermore, the structure reveals that the bridging (P-O-C) oxygen atom and the carboxylate group of PEP are not strongly hydrogen-bonded to the enzyme. The resulting high degree of negative charge on the carboxylate group of PEP would then suggest that the condensation step between PEP and D-arabinose-5-phosphate (A5P) should proceed in a stepwise fashion through the intermediacy of a transient oxocarbenium ion at C2 of PEP. The molecular structural results are discussed in light of the chemically similar but mechanistically distinct reaction that is catalyzed by the enzyme 3-deoxy-D-arabino-2-heptulosonate-7-phosphate synthase and in light of the preferred enzyme-bound states of the substrate A5P.

PubMed: 11371194
DOI: 10.1021/bi010339d

Experimental method

X-RAY DIFFRACTION (2.8 Å)