1FWT

AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP, E4P AND CADMIUM

Summary for 1FWT

• Entry DOI: 10.2210/pdb1fwt/pdb
• Related: 1FWN 1FWS 1FWW 1FX6 1FXP 1FXQ 1FY6
• Descriptor: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE, CADMIUM ION, PHOSPHOENOLPYRUVATE, ... (6 entities in total)
• Functional Keywords: kdo8ps, kdo8p, kdo, pep, a5p, beta/alpha barrel, lyase
• Biological source: Aquifex aeolicus
• Cellular location: Cytoplasm : O66496
• Total number of polymer chains: 2
• Total formula weight: 60404.77

Authors

Duewel, H.S.,Radaev, S.,Wang, J.,Woodard, R.W.,Gatti, D.L. (deposition date: 2000-09-24, release date: 2001-04-21, Last modification date: 2024-02-07)

Primary citation

Duewel, H.S.,Radaev, S.,Wang, J.,Woodard, R.W.,Gatti, D.L.
Substrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism.
J.Biol.Chem., 276:8393-8402, 2001

PubMed Abstract: 3-Deoxy-D-manno-octulosonate-8-phosphate synthase (KDO8PS) from the hyperthermophilic bacterium Aquifex aeolicus differs from its Escherichia coli counterpart in the requirement of a divalent metal for activity (Duewel, H. S., and Woodard, R. W. (2000) J. Biol. Chem. 275, 22824-22831). Here we report the crystal structure of the A. aeolicus enzyme, which was determined by molecular replacement using E. coli KDO8PS as a model. The structures of the metal-free and Cd(2+) forms of the enzyme were determined in the uncomplexed state and in complex with various combinations of phosphoenolpyruvate (PEP), arabinose 5-phosphate (A5P), and erythrose 4-phosphate (E4P). Like the E. coli enzyme, A. aeolicus KDO8PS is a homotetramer containing four distinct active sites at the interface between subunits. The active site cavity is open in the substrate-free enzyme or when either A5P alone or PEP alone binds, and becomes isolated from the aqueous phase when both PEP and A5P (or E4P) bind together. In the presence of metal, the enzyme is asymmetric and appears to alternate catalysis between the active sites located on one face of the tetramer and those located on the other face. In the absence of metal, the asymmetry is lost. Details of the active site that may be important for catalysis are visible at the high resolution achieved in these structures. Most notably, the shape of the PEP-binding pocket forces PEP to assume a distorted geometry at C-2, which might anticipate the conversion from sp(2) to sp(3) hybridization occurring during intermediate formation and which may modulate PEP reactivity toward A5P. Two water molecules are located in van der Waals contact with the si and re sides of C-2(PEP), respectively. Abstraction of a proton from either of these water molecules by a protein group is expected to elicit a nucleophilic attack of the resulting hydroxide ion on the nearby C-2(PEP), thus triggering the beginning of the catalytic cycle.

PubMed: 11115499
DOI: 10.1074/jbc.M007884200

Experimental method

X-RAY DIFFRACTION (1.9 Å)