6p3j | pdb_00006p3j

Crystal structure of LigU

spinqualitylabelsall models 6p3j, resolution 2.02Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6p3j is a 2 chain structure with sequence from Novk1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, CL, NA Gene: ligU, ORF100 (NOVK1) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [LIGU_NOVK1] Contributes to the degradation of lignin at the level of the protocatechuate 4,5-cleavage pathway. Catalyzes the isomerization of the double bond between C4 and C5 in (4E)-oxalomesaconate (OMA) to (3Z)-2-keto-4-carboxy-3-hexenedioate (KCH), where the double bond has migrated between C3 and C4 via a 1,3-allylic isomerization. Publication Abstract from PubMed LigU from Novosphingobium sp. strain KA1 catalyzes the isomerization of (4E)-oxalomesaconate (OMA) to (3Z)-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 of similar topology to one another. Each domain has a central alpha-helix surrounded by a beta-barrel composed of antiparallel beta-strands. The active site is at the cleft of the two domains. 1H NMR spectroscopy demonstrated that the enzyme catalyzes the exchange of the proS hydrogen at C5 of KCH with D2O 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 proS 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. Structure and Chemical Reaction Mechanism of LigU, an Enzyme that Catalyzes an Allylic Isomerization in the Bacterial Degradation of Lignin.,Hogancamp TN, Cory SA, Barondeau DP, Raushel FM Biochemistry. 2019 Jul 24. doi: 10.1021/acs.biochem.9b00549. PMID:31339729 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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