PDBsum entry 5d2f

Lyase

PDB id: 5d2f

Contents

Protein chain

263 a.a.

Ligands

EDO ×12

ACT

Metals

_CL ×2

Waters ×398

PDB id:

5d2f

Name:

Lyase

Title:

4-oxalocrotonate decarboxylase from pseudomonas putida g7 - apo form

Structure:

4-oxalocrotonate decarboxylase nahk. Chain: a. Engineered: yes. Mutation: yes

Source:

Pseudomonas putida. Organism_taxid: 303. Gene: nahk. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.74Å R-factor: 0.170 R-free: 0.211

Authors:

S.L.Guimaraes,R.A.P.Nagem

Key ref:

S.L.Guimarães et al. (2016). Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid. Biochemistry, 55, 2632-2645. PubMed id: 27082660 DOI: 10.1021/acs.biochem.6b00050

Date:

05-Aug-15 Release date: 04-May-16

Protein chain

Q1XGK3  (Q1XGK3_PSEPU) -  4-oxalocrotonate decarboxylase NahK from Pseudomonas putida

Seq: 264 a.a.

Struc: 263 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.1.1.77 - 2-oxo-3-hexenedioate decarboxylase.
• Reaction: (3E)-2-oxohex-3-enedioate + H⁺ = 2-oxopent-4-enoate + CO2

(3E)-2-oxohex-3-enedioate + H(+) = 2-oxopent-4-enoate (Bound ligand (Het Group name = EDO) matches with 50.00% similarity) + CO2 (Bound ligand (Het Group name = ACT) matches with 75.00% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/acs.biochem.6b00050

Biochemistry 55:2632-2645 (2016)

PubMed id: 27082660

Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid.

S.L.Guimarães, J.B.Coitinho, D.M.Costa, S.S.Araújo, C.P.Whitman, R.A.Nagem.

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.