2Q5Q

X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and 5-phenyl-2-oxo-valeric acid

Summary for 2Q5Q

• Entry DOI: 10.2210/pdb2q5q/pdb
• Related: 2Q5J 2Q5L 2Q5O 2nxw
• Descriptor: Phenylpyruvate decarboxylase, MAGNESIUM ION, 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE, ... (7 entities in total)
• Functional Keywords: thiamine diphosphate, symmetrical dimer of dimers, closed active site loops, substrate complex, lyase
• Biological source: Azospirillum brasilense
• Total number of polymer chains: 2
• Total formula weight: 122652.07

Authors

Versees, W.,Spaepen, S.,Wood, M.D.,Leeper, F.J.,Vanderleyden, J.,Steyaert, J. (deposition date: 2007-06-01, release date: 2007-10-23, Last modification date: 2023-08-30)

Primary citation

Versees, W.,Spaepen, S.,Wood, M.D.,Leeper, F.J.,Vanderleyden, J.,Steyaert, J.
Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase.
J.Biol.Chem., 282:35269-35278, 2007

PubMed Abstract: Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.

PubMed: 17905741
DOI: 10.1074/jbc.M706048200

Experimental method

X-RAY DIFFRACTION (1.9 Å)