1JCY

Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium

Summary for 1JCY

• Entry DOI: 10.2210/pdb1jcy/pdb
• Related: 1FWW 1JCX
• Descriptor: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE, RIBOSE-5-PHOSPHATE, CADMIUM ION, ... (6 entities in total)
• Functional Keywords: kdo8ps, kdo8p, kdo, r5p, pep, beta/alpha barrel, lyase
• Biological source: Aquifex aeolicus
• Cellular location: Cytoplasm : O66496
• Total number of polymer chains: 2
• Total formula weight: 60434.80

Authors

Wang, J.,Duewel, H.S.,Woodard, R.W.,Gatti, D.L. (deposition date: 2001-06-11, release date: 2002-01-16, Last modification date: 2024-02-07)

Primary citation

Wang, J.,Duewel, H.S.,Woodard, R.W.,Gatti, D.L.
Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis.
Biochemistry, 40:15676-15683, 2001

PubMed Abstract: We have determined the crystal structures of the metalloenzyme 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase from Aquifex aeolicus in complex with phosphoenolpyruvate (PEP) and ribose 5-phosphate (R5P), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. R5P, which is not a substrate for KDO8P synthase, binds in a manner similar to that of arabinose 5-phosphate (A5P), which is the natural substrate. The lack of reactivity of R5P appears to be primarily a consequence of the loss of a water molecule coordinated to Cd(2+) and located on the si side of PEP. This water molecule is no longer present because it cannot form a hydrogen bond with C2-OH(R5P), which is oriented in a different direction from C2-OH(A5P). The bisubstrate inhibitor binds with its phosphate and phosphonate moieties occupying the positions of the phosphate groups of A5P and PEP, respectively. One of the inhibitor hydroxyls replaces water as a ligand of Cd(2+). The current work supports a mechanism for the synthesis of KDO8P, in which a hydroxide ion on the si side of PEP attacks C2(PEP), forming a tetrahedral-like intermediate with a buildup of negative charge at C3(PEP). The ensuing condensation of C3(PEP) with C1(A5P) would be favored by a proton transfer from the phosphate moiety of PEP to the aldehyde carbonyl of A5P to generate the hydroxyl. Overall, the process can be described as a syn addition of water and A5P to the si side of PEP.

PubMed: 11747443
DOI: 10.1021/bi015568e

Experimental method

X-RAY DIFFRACTION (1.9 Å)