5D2K

4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with magnesium and 2-oxoadipate

Summary for 5D2K

• Entry DOI: 10.2210/pdb5d2k/pdb
• Related: 5D2F 5D2G 5D2H 5D2I 5D2J
• Descriptor: 4-oxalocrotonate decarboxylase NahK, MAGNESIUM ION, 2-OXOADIPIC ACID, ... (6 entities in total)
• Functional Keywords: naphthalene degradation, lyase
• Biological source: Pseudomonas putida
• Total number of polymer chains: 2
• Total formula weight: 59103.03

Authors

Guimaraes, S.L.,Nagem, R.A.P. (deposition date: 2015-08-05, release date: 2016-05-04, Last modification date: 2023-09-27)

Primary citation

Guimaraes, S.L.,Coitinho, J.B.,Costa, D.M.,Araujo, S.S.,Whitman, C.P.,Nagem, R.A.
Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous beta-Keto Acid.
Biochemistry, 55:2632-2645, 2016

PubMed Abstract: The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.

PubMed: 27082660
DOI: 10.1021/acs.biochem.6b00050

Experimental method

X-RAY DIFFRACTION (1.571 Å)