6P3J
Crystal structure of LigU
Summary for 6P3J
| Entry DOI | 10.2210/pdb6p3j/pdb |
| Descriptor | (4E)-oxalomesaconate Delta-isomerase, CHLORIDE ION, CALCIUM ION, ... (5 entities in total) |
| Functional Keywords | lignin degradation, protocatechuate 4, 5-cleavage pathway, prpf superfamily, (4e)-oxalomesaconate isomerase mechanism, isomerase |
| Biological source | Novosphingobium sp. (strain KA1) |
| Total number of polymer chains | 2 |
| Total formula weight | 76342.85 |
| Authors | Cory, S.A.,Hogancamp, T.N.,Raushel, F.M.,Barondeau, D.P. (deposition date: 2019-05-23, release date: 2019-07-31, Last modification date: 2023-10-11) |
| Primary citation | Hogancamp, T.N.,Cory, S.A.,Barondeau, D.P.,Raushel, F.M. Structure and Chemical Reaction Mechanism of LigU, an Enzyme That Catalyzes an Allylic Isomerization in the Bacterial Degradation of Lignin. Biochemistry, 58:3494-3503, 2019 Cited by PubMed Abstract: LigU from sp. strain KA1 catalyzes the isomerization of (4)-oxalomesaconate (OMA) to (3)-2-keto-4-carboxy-3-hexenedioate (KCH) as part of the protocatechuate (PCA) 4,5-cleavage pathway during the degradation of lignin. The three-dimensional structure of the apo form of the wild-type enzyme was determined by X-ray crystallography, and the structure of the K66M mutant enzyme was determined in the presence of the substrate OMA. LigU is a homodimer requiring no cofactors or metal ions with a diaminopimelate epimerase structural fold, consisting of two domains with similar topologies. Each domain has a central α-helix surrounded by a β-barrel composed of antiparallel β-strands. The active site is at the cleft of the two domains. H nuclear magnetic resonance spectroscopy demonstrated that the enzyme catalyzes the exchange of the pro- hydrogen at C5 of KCH with DO during the isomerization reaction. Solvent-deuterium exchange experiments demonstrated that mutation of Lys-66 eliminated the isotope exchange at C5 and that mutation of C100 abolished exchange at C3. The positioning of these two residues in the active site of LigU is consistent with a reaction mechanism that is initiated by the abstraction of the pro- hydrogen at C3 of OMA by the thiolate anion of Cys-100 and the donation of a proton at C5 of the proposed enolate anion intermediate by the side chain of Lys-66 to form the product KCH. The 1,3-proton transfer is suprafacial. PubMed: 31339729DOI: 10.1021/acs.biochem.9b00549 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.02 Å) |
Structure validation
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