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PDBsum entry 5d2h
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References listed in PDB file
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Key reference
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Title
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Crystal structures of apo and liganded 4-Oxalocrotonate decarboxylase uncover a structural basis for the metal-Assisted decarboxylation of a vinylogous β-Keto acid.
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Authors
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S.L.Guimarães,
J.B.Coitinho,
D.M.Costa,
S.S.Araújo,
C.P.Whitman,
R.A.Nagem.
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Ref.
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Biochemistry, 2016,
55,
2632-2645.
[DOI no: ]
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PubMed id
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Abstract
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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.
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