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3pcb
From Proteopedia
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STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-HYDROXYBENZOATE
Overview
Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring, cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis, cis-muconate. Crystal structures of Pseudomonas putida3,4-PCD [quaternary, structure of (alphabetaFe3+)12] complexed with seven competitive, inhibitors [3-hydroxyphenylacetate (MHP), 4-hydroxyphenylacetate (PHP), 3-hydroxybenzoate (MHB), 4-hydroxybenzoate (PHB), 3-fluoro-4-hydroxybenzoate (FHB), 3-chloro-4-hydroxybenzoate (CHB), and, 3-iodo-4-hydroxybenzoate (IHB)] are reported at 2.0-2.2 A resolution with, R-factors of 0. 0.159-0.179. The inhibitors bind in a narrow active site, crevasse lined with residues that provide a microenvironment that closely, matches the chemical characteristics of the inhibitors. This results in as, little as 20% solvent-exposed surface area for the higher-affinity, inhibitors (PHB, CHB, and FHB). In uncomplexed 3,4-PCD, the active site, Fe3+ is bound at the bottom of the active site crevasse by four endogenous, ligands and a solvent molecule (Wat827). The orientations of the, endogenous ligands are relatively unperturbed in each inhibitor complex, but the inhibitors themselves bind to or near the iron in a range of, positions, all of which perturb the position of Wat827. The three, lowest-affinity inhibitors (MHP, PHP, and IHB) yield distorted trigonal, bipyramidal iron coordination geometry in which the inhibitor C4-phenolate, group displaces the solvent ligand. MHB binds within the active site, but, neither its C3-OH group nor the solvent molecule binds to the iron. The, C4-phenolate group of the three highest-affinity inhibitors (PHB, CHB, and, FHB) coordinates the Fe3+ adjacent to Wat827, resulting in a shift in its, position to yield a six-coordinate distorted octahedral geometry. The, range of inhibitor orientations may mimic the mechanistically significant, stages of substrate binding to 3, 4-PCD. The structure of the final, substrate complex is reported in the following paper [Orville, A. M., Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10052-10066].
About this Structure
3PCB is a Protein complex structure of sequences from Pseudomonas putida with FE, BME and 3HB as ligands. Active as Protocatechuate 3,4-dioxygenase, with EC number 1.13.11.3 Structure known Active Sites: ACA, ACB, ACC, ACD, ACE, ACF, VEA, VEB, VEC, VED, VEE and VEF. Full crystallographic information is available from OCA.
Reference
Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site., Orville AM, Elango N, Lipscomb JD, Ohlendorf DH, Biochemistry. 1997 Aug 19;36(33):10039-51. PMID:9254599
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