5EJA

EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2 min and soaked with isochorismate for 7 min

Summary for 5EJA

• Entry DOI: 10.2210/pdb5eja/pdb
• Related: 5EJ4 5EJ5 5EJ6 5EJ7 5EJ8 5EJ9 5EJM
• Descriptor: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid, MANGANESE (II) ION, ... (5 entities in total)
• Functional Keywords: post-decarboxylation intermediate, transferase
• Biological source: Escherichia coli K12
• Total number of polymer chains: 8
• Total formula weight: 496865.73

Authors

Song, H.G.,Dong, C.,Chen, Y.Z.,Sun, Y.R.,Guo, Z.H. (deposition date: 2015-11-01, release date: 2016-06-01, Last modification date: 2024-03-20)

Primary citation

Song, H.G.,Dong, C.,Qin, M.M.,Chen, Y.Z.,Sun, Y.R.,Liu, J.J.,Chan, W.,Guo, Z.H.
A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
J.Am.Chem.Soc., 138:7244-7247, 2016

PubMed Abstract: Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. However, this intermediate is not found in the thiamine-dependent catalysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and was structurally determined at 1.34 Å resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring nitrogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 Å. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry.

PubMed: 27213829
DOI: 10.1021/jacs.6b03437

Experimental method

X-RAY DIFFRACTION (1.6 Å)