56-14-4Relevant articles and documents
Atomic-Resolution 1.3 ? Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE
Kochert, Matthew,Nocek, Boguslaw P.,Habeeb Mohammad, Thahani S.,Gild, Elliot,Lovato, Kaitlyn,Heath, Tahirah K.,Holz, Richard C.,Olsen, Kenneth W.,Becker, Daniel P.
, p. 908 - 917 (2021/04/07)
We report the atomic-resolution (1.3 ?) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in the active site that mimic the binding of the terminal carboxylates of the N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) substrate. We demonstrated inhibition of DapE by sulfate (IC50 = 13.8 ± 2.8 mM). Comparison with other DapE structures in the PDB demonstrates the flexibility of the interdomain connections of this protein. This high-resolution structure was then utilized as the starting point for targeted molecular dynamics experiments revealing the conformational change from the open form to the closed form that occurs when DapE binds l,l-SDAP and cleaves the amide bond. These simulations demonstrated closure from the open to the closed conformation, the change in RMS throughout the closure, and the independence in the movement of the two DapE subunits. This conformational change occurred in two phases with the catalytic domains moving toward the dimerization domains first, followed by a rotation of catalytic domains relative to the dimerization domains. Although there were no targeting forces, the substrate moved closer to the active site and bound more tightly during the closure event.
Reduction of maleate and fumarate by the CO2.- anion radical
Schutz, Osnat,Meyerstein, Dan
, p. 1093 - 1096 (2007/10/03)
The radical anion CO2.- reacts with fumarate and maleate at pH 5.3 mainly via electron transfer. The final products are a mixture of (-O2CCH2-)2, trans-( -O2CCH)2 and products with higher molecular weight. At higher pHs, the yield of fumarate and succinate decreases. The results suggest that though the radical anions formed by the reduction of fumarate and maleate have different structures, the final products are probably the same.
