5d2h | pdb_00005d2h

4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with magnesium and alpha-ketoglutarate

spinqualitylabelsall models 5d2h, resolution 1.94Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5d2h is a 1 chain structure with sequence from "bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ACT, AKG, CL, EDO, MG, SO4 Related: 5d2f, 5d2g, 5d2i, 5d2j, 5d2k Gene: nahK ("Bacillus fluorescens putidus" Flugge 1886) Activity: 2-oxo-3-hexenedioate decarboxylase, with EC number 4.1.1.77 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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 Mg2+ 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 beta-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous beta-keto acid decarboxylase and the first crystal structure of a 4-OD. Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous beta-Keto Acid.,Guimaraes SL, Coitinho JB, Costa DM, Araujo SS, Whitman CP, Nagem RA Biochemistry. 2016 Apr 27. PMID:27082660 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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