An EXAFS study of the interaction of substrate with the ferric active site of protocatechuate 3,4-dioxygenase

• Published in: Biochemistry (Easton) Vol. 29; no. 48; pp. 10847 - 10854
• Main Authors: True, Anne E, Orville, Allen M, Pearce, Linda L, Lipscomb, John D, Que, Lawrence
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 04.12.1990
• Subjects: 3,4-Dihydroxyphenylacetic Acid - metabolism; 550602 - Medicine- External Radiation in Diagnostics- (1980-); ABSORPTION SPECTROSCOPY; active sites; AMINO ACIDS; Analytical, structural and metabolic biochemistry; BACTERIA; Binding Sites; Biological and medical sciences; Brevibacterium - enzymology; CARBOXYLIC ACIDS; Chemical Phenomena; Chemistry, Physical; COHERENT SCATTERING; CRYSTALLOGRAPHY; DIFFRACTION; ELECTRON SPIN RESONANCE; ENZYMES; Enzymes and enzyme inhibitors; Fourier Analysis; Fundamental and applied biological sciences. Psychology; Histidine - chemistry; HYDROGEN COMPOUNDS; HYDROXIDES; HYDROXY ACIDS; iron; Iron - chemistry; MAGNETIC RESONANCE; MICROORGANISMS; MOLECULAR STRUCTURE; Nitrogen - chemistry; ORGANIC ACIDS; ORGANIC COMPOUNDS; OXIDOREDUCTASES; Oxygen - chemistry; OXYGEN COMPOUNDS; OXYGENASES; Phthalic Acids - metabolism; protocatechuate 3,4-dioxygenase; Protocatechuate-3,4-Dioxygenase - chemistry; Protocatechuate-3,4-Dioxygenase - metabolism; PSEUDOMONAS; Pseudomonas aeruginosa; RADIOLOGY AND NUCLEAR MEDICINE; RESONANCE; SCATTERING; SPECTROSCOPY; TYROSINE; X-ray crystallography; X-RAY DIFFRACTION; X-RAY SPECTROSCOPY; Substrate; Protocatechuate 3,4-dioxygenase; Enzyme; Active site; Brevibacterium; Brevibacteriaceae; Bacteria; Molecular interaction; Actinomycetes; Iron; Crystallography; EXAFS spectrometry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00500a019

X-ray crystallographic studies of the intradiol cleaving protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa have shown that the enzyme has a trigonal bipyramidal ferric active site with two histidines, two tyrosines, and a solvent molecule as ligands [Ohlendorf, D.H., Lipscomb, J.D., & Weber, P.C. (1988) Nature 336, 403-405]. Fe K-edge EXAFS studies of the spectroscopically similar protocatechuate 3,4-dioxygenase from Brevibacterium fuscum are consistent with a pentacoordinate geometry of the iron active site with 3 O/N ligands at 1.90 A and 2 O/N ligands at 2.08 A. The 2.08-A bonds are assigned to the two histidines, while the 1.90-A bonds are associated with the two tyrosines and the coordinated solvent. The short Fe-O distance for the solvent suggests that it coordinates as hydroxide rather than water. When the inhibitor terephthalate is bound to the enzyme, the XANES data indicate that the ferric site becomes 6-coordinate and the EXAFS data show a beat pattern which can only be simulated with an additional Fe-O/N interaction at 2.46 A. Together, the data suggest that the oxygens of the carboxylate group in terephthalate displace the hydroxide and chelate to the ferric site but in an asymmetric fashion. In contrast, protocatechuate 3,4-dioxygenase remains 5-coordinate upon the addition of the slow substrate homoprotocatechuic acid (HPCA). Previous EPR data have indicated that HPCA forms an iron chelate via the two hydroxyl functions.