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Dancs Á, May NV, Selmeczi K, Darula Z, Szorcsik A, Matyuska F, Páli T, Gajda T. Tuning the coordination properties of multi-histidine peptides by using a tripodal scaffold: solution chemical study and catechol oxidase mimicking. NEW J CHEM 2017. [DOI: 10.1039/c6nj03126a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Histidine-rich tripodal peptides form unique oligonuclear complexes with copper(ii), which exhibit efficient catecholase-like activity.
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Affiliation(s)
- Ágnes Dancs
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged
- Hungary
- Université de Lorraine – CNRS
| | - Nóra V. May
- Research Centre for Natural Sciences HAS
- H-1117 Budapest
- Hungary
| | - Katalin Selmeczi
- Université de Lorraine – CNRS
- UMR 7565 SRSMC
- 54506 Vandœuvre-lès-Nancy
- France
| | - Zsuzsanna Darula
- Institute of Biochemistry
- Biological Research Centre
- Hungarian Academy of Sciences
- H-6724 Szeged
- Hungary
| | - Attila Szorcsik
- MTA-SZTE Bioinorganic Chemistry Research Group
- H-6720 Szeged
- Hungary
| | - Ferenc Matyuska
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged
- Hungary
| | - Tibor Páli
- Institute of Biophysics
- Biological Research Centre
- Hungarian Academy of Sciences
- H-6724 Szeged
- Hungary
| | - Tamás Gajda
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged
- Hungary
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2
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Matyuska F, May NV, Bényei A, Gajda T. Control of structure, stability and catechol oxidase activity of copper(ii) complexes by the denticity of tripodal platforms. NEW J CHEM 2017. [DOI: 10.1039/c7nj02013a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The speciation and catecholase-like activity of trinuclear complexes can be fine tuned by the denticity of tripodal platforms.
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Affiliation(s)
- Ferenc Matyuska
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged
- Hungary
| | - Nóra V. May
- Research Centre for Natural Sciences HAS
- H-1117 Budapest
- Hungary
| | - Attila Bényei
- Department of Pharmaceutical Chemistry
- University of Debrecen
- Debrecen H-4032
- Hungary
| | - Tamás Gajda
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged
- Hungary
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3
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Safaei E, Heidari S, Wojtczak A, Cotič P, Kozakiewicz A. 4-Nitrocatecholato iron(III) complexes of 2-aminomethyl pyridine-based bis(phenol) amine as structural models for catechol-bound 3,4-PCD. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Szorcsik A, Matyuska F, Bényei A, Nagy NV, Szilágyi RK, Gajda T. A novel 1,3,5-triaminocyclohexane-based tripodal ligand forms a unique tetra(pyrazolate)-bridged tricopper(ii) core: solution equilibrium, structure and catecholase activity. Dalton Trans 2016; 45:14998-5012. [DOI: 10.1039/c6dt01228k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A polydentate tripodal ligand forms a series of tricopper(ii) complexes, that feature unique pyrazolate-bridged linear core. The Cu3H−3L2 complex is an efficient catecholase mimic with a surprisingly low pH optimum at pH = 5.6.
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Affiliation(s)
- Attila Szorcsik
- MTA-SZTE Bioinorganic Chemistry Research Group
- H-6720 Szeged
- Hungary
| | - Ferenc Matyuska
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged
- Hungary
| | - Attila Bényei
- Department of Physical Chemistry
- University of Debrecen
- Debrecen H-4032
- Hungary
| | - Nóra V. Nagy
- Institute of Organic Chemistry
- Research Centre for Natural Sciences HAS
- H-1117 Budapest
- Hungary
| | - Róbert K. Szilágyi
- Department of Chemistry and Biochemistry
- Montana State University
- Bozeman
- USA
- Department of Analytical Chemistry
| | - Tamás Gajda
- MTA-SZTE Bioinorganic Chemistry Research Group
- H-6720 Szeged
- Hungary
- Department of Inorganic and Analytical Chemistry
- University of Szeged
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5
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Lakk-Bogáth D, Csonka R, Lorencz N, Giorgi M, Speier G, Kaizer J. Oxidant dependent oxidation of copper bound catecholate: Catecholase versus catechol dioxygenase activity. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.09.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Gavazov KB, Delchev VB, Toncheva GK, Georgieva ZG. Extraction-spectrophotometric and theoretical (Hartree-Fock) investigations of a ternary complex of iron(II) with 4-nitrocatechol and 2,3,5-triphenyl-2H-tetrazolium. RUSS J GEN CHEM+ 2015. [DOI: 10.1134/s1070363215080241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Fielding AJ, Lipscomb JD, Que L. Characterization of an O2 adduct of an active cobalt-substituted extradiol-cleaving catechol dioxygenase. J Am Chem Soc 2011; 134:796-9. [PMID: 22175783 DOI: 10.1021/ja2095365] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first example of an O(2) adduct of an active Co-substituted oxygenase has been observed in the extradiol ring cleavage of the electron-poor substrate 4-nitrocatechol (4NC) by Co(II)-homoprotocatechuate 2,3-dioxygenase (Co-HPCD). Upon O(2) binding to the high-spin Co(II) (S = (3)/(2)) enzyme-substrate complex, an S = (1)/(2) EPR signal exhibiting (59)Co hyperfine splitting (A = 24 G) typical of a low-spin Co(III)-superoxide complex was observed. Both the formation and decay of the new intermediate are very slow in comparison to the analogous steps for turnover of 4NC by native high-spin Fe(II)-HPCD, which is likely to remain high-spin upon O(2) binding. A similar but effectively stable S = (1)/(2) intermediate was formed by the inactive [H200N-Co-HPCD(4NC)] variant. The observations presented shed light on the key roles played by the substrate, the second-sphere His200 residue, and the spin state of the metal center in facilitating O(2) binding and activation.
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Affiliation(s)
- Andrew J Fielding
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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8
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Wójcik A, Borowski T, Broclawik E. The mechanism of the reaction of intradiol dioxygenase with hydroperoxy probe. Catal Today 2011. [DOI: 10.1016/j.cattod.2010.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Abstract
Ring-cleaving dioxygenases catalyze the oxygenolytic fission of catecholic compounds, a critical step in the aerobic degradation of aromatic compounds by bacteria. Two classes of these enzymes have been identified, based on the mode of ring cleavage: intradiol dioxygenases utilize non-heme Fe(III) to cleave the aromatic nucleus ortho to the hydroxyl substituents; and extradiol dioxygenases utilize non-heme Fe(II) or other divalent metal ions to cleave the aromatic nucleus meta to the hydroxyl substituents. Recent genomic, structural, spectroscopic, and kinetic studies have increased our understanding of the distribution, evolution, and mechanisms of these enzymes. Overall, extradiol dioxygenases appear to be more versatile than their intradiol counterparts. Thus, the former cleave a wider variety of substrates, have evolved on a larger number of structural scaffolds, and occur in a wider variety of pathways, including biosynthetic pathways and pathways that degrade non-aromatic compounds. The catalytic mechanisms of the two enzymes proceed via similar iron-alkylperoxo intermediates. The ability of extradiol enzymes to act on a variety of non-catecholic compounds is consistent with proposed differences in the breakdown of this iron-alkylperoxo intermediate in the two enzymes, involving alkenyl migration in extradiol enzymes and acyl migration in intradiol enzymes. Nevertheless, despite recent advances in our understanding of these fascinating enzymes, the major determinant of the mode of ring cleavage remains unknown.
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Affiliation(s)
- Frédéric H Vaillancourt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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10
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Kaizer J, Zsigmond Z, Ganszky I, Speier G, Giorgi M, Réglier M. New functional model complexes of intradiol-cleaving catechol dioxygenases: properties and reactivity of CuII(L)(O2Ncat). Inorg Chem 2007; 46:4660-6. [PMID: 17458955 DOI: 10.1021/ic062309a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Complexes Cu(O2Ncat)(tbeda) (1) and Cu(O2Ncat)(tmeda) (2) (tbeda = N,N,N',N'-tetrabenzylethylenediamine, tmeda=N,N,N',N'-tetramethylethylenenediamine, O2NcatH2=4-nitrocatechol) have been prepared by the reaction of copper(II) perchlorate with 4-nitrocatechol in the presence of triethylamine and the appropriate bidentate ligand. These compounds represent structural and functional model systems for the copper-containing catechol 1,2-dioxygenase. Both complexes have been structurally characterized by X-ray crystallography and by UV-vis, IR, and EPR spectroscopies. Upon protonation of 1 and 2 with perchloric acid, the bidentate coordination of O2Ncat could be reversible converted to the monodentate coordination of O2NcatH. The equilibrium constants were found to be 4200 and 3500, respectively, by measuring the UV-vis spectra in DMF. Back-titration with morpholine proved the reversibility of both reactions. Kinetic data on the oxygenation of 1 and 2 revealed overall second-order rate equations with kinetic parameters: ktbeda=(4.63+/-0.23)x10(-2) mol-1 dm3 s-1, DeltaH=51+/-6 kJ mol-1, DeltaS=-137+/-16 J mol-1 K-1; ktmeda=(0.89+/-0.23) mol-1 dm3 s-1, DeltaH=85+/-7 kJ mol-1, DeltaS=-57+/-19 J mol-1 K-1 at 365.16 K. Oxygenation of 1, 2, and [Cu(O2NcatH)(L)]ClO4 (L=tbeda, tmeda) in DMF solution at ambient conditions gives the corresponding intradiol ring-cleaved (2-nitro-muconato)copper(II) complexes. These data support the assumption that the reaction of the differently coordinated catecholate ligand with dioxygen shows only 1,2-dioxygenase activity.
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Affiliation(s)
- József Kaizer
- Department of Organic Chemistry, University of Pannonia, 8201 Veszprém, Hungary
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11
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Borowski T, Siegbahn PEM. Mechanism for Catechol Ring Cleavage by Non-Heme Iron Intradiol Dioxygenases: A Hybrid DFT Study. J Am Chem Soc 2006; 128:12941-53. [PMID: 17002391 DOI: 10.1021/ja0641251] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the catalytic reaction of protocatechuate 3,4-dioxygenase (3,4-PCD), a representative intradiol dioxygenase, was studied with the hybrid density functional method B3LYP. First, a smaller model involving only the iron first-shell ligands (His460, His462, and Tyr408) and the substrates (catechol and dioxygen) was used to probe various a priori plausible reaction mechanisms. Then, an extended model involving also the most important second-shell groups (Arg457, Gln477, and Tyr479) was used for the refinement of the preselected mechanisms. The computational results suggest that the chemical reactions constituting the catalytic cycle of intradiol dioxygenases involve: (1) binding of the substrate as a dianion, in agreement with experimental suggestions, (2) binding of dioxygen to the metal aided by an electron transfer from the substrate to O(2), (3) formation of a bridging peroxo intermediate and its conformational change, which opens the coordination site trans to His462, (4) binding of a neutral XOH ligand (H(2)O or Tyr447) at the open site, (5) proton transfer from XOH to the neighboring peroxo ligand yielding the hydroperoxo intermediate, (6) a Criegee rearrangement leading to the anhydride intermediate, and (7) hydrolysis of the anhydride to the final acyclic product. One of the most important results obtained is that the Criegee mechanism requires an in-plane orientation of the four atoms (two oxygen and two carbon atoms) mainly involved in the reaction. This orientation yields a good overlap between the two sigma orbitals involved, C-C sigma and O-O sigma, allowing an efficient electron flow between them. Another interesting result is that under some conditions, a homolytic O-O bond cleavage might compete with the Criegee rearrangement. The role of the second-shell residues and the substituent effects are also discussed.
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Affiliation(s)
- Tomasz Borowski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland.
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12
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Ishida T, Senda T, Tanaka H, Yamamoto A, Horiike K. Single-turnover kinetics of 2,3-dihydroxybiphenyl 1,2-dioxygenase reacting with 3-formylcatechol. Biochem Biophys Res Commun 2005; 338:223-9. [PMID: 16169514 DOI: 10.1016/j.bbrc.2005.08.218] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 08/30/2005] [Indexed: 11/23/2022]
Abstract
2,3-Dihydroxybiphenyl 1,2-dioxygenase (EC 1.13.11.39) from Pseudomonas sp. strain KKS102 (BphC) catalyzes the proximal extradiol cleavage of the catechol ring of 2,3-dihydroxybiphenyl (DHB), a key step in the biodegradation of polychlorinated biphenyl. Because the active site Fe(II) ion of the extradiol dioxygenase is colorless, it has been difficult to monitor the reaction cycle kinetics. Here, we have found that BphC binds strongly the chromophoric substrate 3-formylcatechol (3FC) as a monoanion (Kd=0.8 microM) and cleaves it two orders of magnitude slower compared to DHB under air-saturation conditions. By utilizing 3FC as a probe, the reaction cycle kinetics of BphC was monitored for the first time. The binding of 3FC occurred in a three-step process involving rapid deprotonation of 3FC. The bound monoanionic 3FC reacted slowly with O2 in three steps, occurring in sequence, the ring opening step being the slowest one.
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Affiliation(s)
- Tetsuo Ishida
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Seta, Ohtsu, Shiga 520-2192, Japan.
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13
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Emerson JP, Wagner ML, Reynolds MF, Que L, Sadowsky MJ, Wackett LP. The role of histidine 200 in MndD, the Mn(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis CM-2, a site-directed mutagenesis study. J Biol Inorg Chem 2005; 10:751-60. [PMID: 16217642 DOI: 10.1007/s00775-005-0017-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Accepted: 08/01/2005] [Indexed: 11/28/2022]
Abstract
The manganese-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase (MndD) from Arthrobacter globiformis CM-2 is an extradiol-cleaving catechol dioxygenase that catalyzes aromatic ring cleavage of 3,4-dihydroxyphenylacetate (DHPA). Based on the recent crystal structure of the MndD-DHPA complex, a series of site-directed mutations were made at a conserved second-sphere residue, histidine 200, to gain insight into and clarify the role this residue plays in the Mn(II)-dependent catalytic mechanism. In this study, we report the activities and spectroscopic data of these H200 variants and their DHPA and 4-nitrocatechol (4-NC) complexes. The data collected from wild-type and mutant MndDs are consistent with a role for H200 interacting with a manganese-bound dioxygen moiety and are inconsistent with other previously proposed roles involving proton transfer. Spectroscopic observations, including unique low-field EPR signals found when DHPA and 4-NC are bound to the Mn(II) center of MndD, are discussed and their relationship to dioxygen activation catalyzed in MndD is explored.
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Affiliation(s)
- Joseph P Emerson
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA
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14
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Brown CK, Vetting MW, Earhart CA, Ohlendorf DH. Biophysical analyses of designed and selected mutants of protocatechuate 3,4-dioxygenase1. Annu Rev Microbiol 2004; 58:555-85. [PMID: 15487948 DOI: 10.1146/annurev.micro.57.030502.090927] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The catechol dioxygenases allow a wide variety of bacteria to use aromatic compounds as carbon sources by catalyzing the key ring-opening step. These enzymes use specifically either catechol or protocatechuate (2,3-dihydroxybenozate) as their substrates; they use a bare metal ion as the sole cofactor. To learn how this family of metalloenzymes functions, a structural analysis of designed and selected mutants of these enzymes has been undertaken. Here we review the results of this analysis on the nonheme ferric iron intradiol dioxygenase protocatechuate 3,4-dioxygenase.
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Affiliation(s)
- C Kent Brown
- Center for Metals in Biocatalysis and Department of Biochemistry, Molecular Biology, and Biophysics , Minneapolis, Minnesota 55455, USA.
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15
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Vetting MW, Wackett LP, Que L, Lipscomb JD, Ohlendorf DH. Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. J Bacteriol 2004; 186:1945-58. [PMID: 15028678 PMCID: PMC374394 DOI: 10.1128/jb.186.7.1945-1958.2004] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2003] [Accepted: 12/04/2003] [Indexed: 11/20/2022] Open
Abstract
The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Molecular Biology and Biophysics, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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16
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Costas M, Mehn MP, Jensen MP, Que L. Dioxygen Activation at Mononuclear Nonheme Iron Active Sites: Enzymes, Models, and Intermediates. Chem Rev 2004; 104:939-86. [PMID: 14871146 DOI: 10.1021/cr020628n] [Citation(s) in RCA: 2014] [Impact Index Per Article: 100.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miquel Costas
- Departament de Quimica, Universitat de Girona, 17071, Girona, Spain
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17
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Vaillancourt FH, Barbosa CJ, Spiro TG, Bolin JT, Blades MW, Turner RFB, Eltis LD. Definitive evidence for monoanionic binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl 1,2-dioxygenase from UV resonance Raman spectroscopy, UV/Vis absorption spectroscopy, and crystallography. J Am Chem Soc 2002; 124:2485-96. [PMID: 11890797 DOI: 10.1021/ja0174682] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet resonance Raman spectroscopy (UVRRS), electronic absorption spectroscopy, and X-ray crystallography were used to probe the nature of the binding of 2,3-dihydroxybiphenyl (DHB) to the extradiol ring-cleavage enzyme, 2,3-dihydroxybiphenyl 1,2-dioxygenase (DHBD; EC 1.13.11.39). The lowest lying transitions in the electronic absorption spectrum of DHBD-bound DHB occurred at 299 nm, compared to 305 nm for the monoanionic DHB species in buffer. In contrast, the corresponding transitions in neutral and dianionic DHB occurred at 283 and 348 nm, respectively, indicating that DHBD-bound DHB is monoanionic. These binding-induced spectral changes, and the use of custom-designed optical fiber probes, facilitated UVRR experiments. The strongest feature of the UVRR spectrum of DHB was a Y8a-like mode around 1600 cm(-1), whose position depended strongly on the protonation state of the DHB. In the spectrum of the DHBD-bound species, this feature occurred at 1603 cm(-1), as observed in the spectrum of monoanionic DHB. Raman band shifts were observed in deuterated solvent, ruling out dianionic binding of the substrate. Thus, the electronic absorption and UVRRS data demonstrate that DHBD binds its catecholic substrate as a monoanion, definitively establishing this feature of the proposed mechanism of extradiol dioxygenases. This conclusion is supported by a crystal structure of the DHBD:DHB complex at 2.0 A resolution, which suggests that the substrate's 2-hydroxyl substituent, and not the 3-hydroxyl group, deprotonates upon binding. The structural data also show that the aromatic rings of the enzyme-bound DHB are essentially orthogonal to each other. Thus, the 6 nm blue shift of the transition for bound DHB relative to the monoanion in solution could indicate a conformational change upon binding. Catalytic roles of active site residues are proposed based on the structural data and previously proposed mechanistic schemes.
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Affiliation(s)
- Frédéric H Vaillancourt
- Department of Biochemistry, The University of British Columbia, 300-6174 University Boulevard, Vancouver, B.C., V6T 1Z3, Canada
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18
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Contzen M, Bürger S, Stolz A. Cloning of the genes for a 4-sulphocatechol-oxidizing protocatechuate 3,4-dioxygenase from Hydrogenophaga intermedia S1 and identification of the amino acid residues responsible for the ability to convert 4-sulphocatechol. Mol Microbiol 2001; 41:199-205. [PMID: 11454212 DOI: 10.1046/j.1365-2958.2001.02505.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genes for a protocatechuate 3,4-dioxygenase (P34O-II) with the ability to oxidize 4-sulphocatechol were cloned from the 4-aminobenzenesulphonate(sulphanilate)-degrading bacterium Hydrogenophaga intermedia strain S1 (DSMZ 5680). Sequence comparisons of the deduced amino acid sequences of both subunits of the P34O-II from H. intermedia S1 (PcaH-II and PcaG-II) with those of another P34O-II, previously obtained from Agrobacterium radiobacter S2, and the corresponding sequences from the protocatechuate 3,4-dioxygenases from other bacterial genera demonstrated that seven amino acid residues, which were conserved in all previously known P34Os (P34O-Is), were different in both P34O-IIs. According to previously published structural data for the P34O of Pseudomonas putida only two of these amino acid residues were located near the catalytical centre. The respective amino acid residues were mutated in the P34O-I from A. radiobacter S2 by site-specific mutagenesis, and it was found that a single amino acid exchange enabled the protocatechuate converting P34O also to oxidize 4-sulphocatechol.
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Affiliation(s)
- M Contzen
- Institut für Mikrobiologie, Universität Stuttgart, 70569 Stuttgart, Germany
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19
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Vetting MW, D'Argenio DA, Ornston LN, Ohlendorf DH. Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase. Biochemistry 2000; 39:7943-55. [PMID: 10891075 DOI: 10.1021/bi000151e] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria Acinetobacterstrain ADP1 (Ac 3,4-PCD) have been determined in space group I23 at pH 8.5 and 5.75. In addition, the structures of Ac 3,4-PCD complexed with its substrate 3, 4-dihydroxybenzoic acid (PCA), the inhibitor 4-nitrocatechol (4-NC), or cyanide (CN(-)) have been solved using native phases. The overall tertiary and quaternary structures of Ac 3,4-PCD are similar to those of the same enzyme from Pseudomonas putida[Ohlendorf et al. (1994) J. Mol. Biol. 244, 586-608]. At pH 8.5, the catalytic non-heme Fe(3+) is coordinated by two axial ligands, Tyr447(OH) (147beta) and His460(N)(epsilon)(2) (160beta), and three equatorial ligands, Tyr408(OH) (108beta), His462(N)(epsilon)(2) (162beta), and a hydroxide ion (d(Fe-OH) = 1.91 A) in a distorted bipyramidal geometry. At pH 5.75, difference maps suggest a sulfate binds to the Fe(3+) in an equatorial position and the hydroxide is shifted [d(Fe-OH) = 2.3 A] yielding octahedral geometry for the active site Fe(3+). This change in ligation geometry is concomitant with a shift in the optical absorbance spectrum of the enzyme from lambda(max) = 450 nm to lambda(max) = 520 nm. Binding of substrate or 4-NC to the Fe(3+) is bidentate with the axial ligand Tyr447(OH) (147beta) dissociating. The structure of the 4-NC complex supports the view that resonance delocalization of the positive character of the nitrogen prevents substrate activation. The cyanide complex confirms previous work that protocatechuate 3,4-dioxygenases have three coordination sites available for binding by exogenous substrates. A significant conformational change extending away from the active site is seen in all structures when compared to the native enzyme at pH 8.5. This conformational change is discussed in its relevance to enhancing catalysis in protocatechuate 3,4-dioxygenases.
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Affiliation(s)
- M W Vetting
- Center of Metals in Biocatalysis and Department of Biochemistry, Molecular Biology and Biophysics, 6-155 Jackson Hall, 321 Church St. S.E., University of Minnesota Medical School, Minneapolis, Minnesota 55455-0347, USA
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Öhrström L, Michaud-Soret I. Fe−Catecholate and Fe−Oxalate Vibrations and Isotopic Substitution Shifts from DFT Quantum Chemistry. J Phys Chem A 1999. [DOI: 10.1021/jp981508f] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lars Öhrström
- Institutionen för Oorganisk kemi, Chalmers Tekniska Högskola, SE-412 96 Göteborg, Sweden, and CEA/Département de Recherche Fondamentale sur la Matière Condensée, Service de Chimie Inorganique et Biologique, Laboratoire de Chimie de Coordination (Unité de Recherche Associée au CNRS No 1194), CEA-Grenoble, F-38054 Grenoble cedex 9, France
| | - Isabelle Michaud-Soret
- Institutionen för Oorganisk kemi, Chalmers Tekniska Högskola, SE-412 96 Göteborg, Sweden, and CEA/Département de Recherche Fondamentale sur la Matière Condensée, Service de Chimie Inorganique et Biologique, Laboratoire de Chimie de Coordination (Unité de Recherche Associée au CNRS No 1194), CEA-Grenoble, F-38054 Grenoble cedex 9, France
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Orville AM, Lipscomb JD, Ohlendorf DH. Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding. Biochemistry 1997; 36:10052-66. [PMID: 9254600 DOI: 10.1021/bi970469f] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protocatechuate 3,4-dioxygenase (3,4-PCD) utilizes a ferric ion to catalyze the aromatic ring cleavage of 3,4-dihydroxybenzoate (PCA) by incorporation of both atoms of dioxygen to yield beta-carboxy-cis, cis-muconate. The crystal structures of the anaerobic 3,4-PCD.PCA complex, aerobic complexes with two heterocyclic PCA analogs, 2-hydroxyisonicotinic acid N-oxide (INO) and 6-hydroxynicotinic acid N-oxide (NNO), and ternary complexes of 3,4-PCD.INO.CN and 3,4-PCD. NNO.CN have been determined at 2.1-2.2 A resolution and refined to R-factors between 0.165 and 0.184. PCA, INO, and NNO form very similar, asymmetrically chelated complexes with the active site Fe3+ that result in dissociation of the endogenous axial tyrosinate Fe3+ ligand, Tyr447 (147beta). After its release from the iron, Tyr447 is stabilized by hydrogen bonding to Tyr16 (16alpha) and Asp413 (113beta) and forms the top of a small cavity adjacent to the C3-C4 bond of PCA. The equatorial Fe3+ coordination site within this cavity is unoccupied in the anaerobic 3,4-PCD.PCA complex but coordinates a solvent molecule in the 3,4-PCD.INO and 3,4-PCD.NNO complexes and CN- in the 3,4-PCD.INO.CN and 3,4-PCD.NNO.CN complexes. This shows that an O2 analog can occupy the cavity and suggests that electrophilic O2 attack on PCA is initiated from this site. Both the dissociation of the endogenous Tyr447 and the expansion of the iron coordination sphere are novel features of the 3,4-PCD. substrate complex which appear to play essential roles in the activation of substrate for O2 attack. Together, the structures presented here and in the preceding paper [Orville, A. M., Elango, N. , Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10039-10051] provide atomic models for several steps in the reaction cycle of 3,4-PCD and related Fe3+-containing dioxygenases.
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Affiliation(s)
- A M Orville
- Department of Biochemistry, Medical School, and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455-0347, USA
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Öhrström L, Michaud-Soret I. Quantum Chemical Approach to the Assignment of Iron−Catecholate Vibrations and Isotopic Substitution Shifts. J Am Chem Soc 1996. [DOI: 10.1021/ja953409a] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lars Öhrström
- CEA/Département de Recherche Fondamentale sur la Matière Condensée CNRS/Laboratoire de Chimie de Coordination (URA 1194) SCIB, Centre d'Etudes Nucléaires de Grenoble F-38054 Grenoble cedex 9, France
| | - Isabelle Michaud-Soret
- CEA/Département de Recherche Fondamentale sur la Matière Condensée CNRS/Laboratoire de Chimie de Coordination (URA 1194) SCIB, Centre d'Etudes Nucléaires de Grenoble F-38054 Grenoble cedex 9, France
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Contzen M, Wittich RM, Knackmuss HJ, Stolz A. Degradation of benzene 1,3-disulfonate by a mixed bacterial culture. FEMS Microbiol Lett 1996. [DOI: 10.1111/j.1574-6968.1996.tb08023.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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24
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Simultaneous binding of nitric oxide and isotopically labeled substrates or inhibitors by reduced protocatechuate 3,4-dioxygenase. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)52917-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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Byrnes RW, Fiel RJ, Datta-Gupta N. DNA strand scission by iron complexes of meso-tetra(N-methylpyridyl)porphines. Chem Biol Interact 1988; 67:225-41. [PMID: 3191535 DOI: 10.1016/0009-2797(88)90060-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The DNA strand scission activities of three positional isomers of Fe(III) meso-tetra(N-methylpyridyl)porphine (Fe(III)TnMPyP, where n = 2, 3 or 4) have been investigated using PM2 DNA as a substrate. A significant degree of strand scission activity was noted in the presence of oxygen without the addition of a reducing agent. This activity was probably due to the presence of reducing agents in the agarose gels used to separate the DNA forms, as higher levels were recorded with reducing agents added to the strand scission mixture. The relative order of strand scission activity in the absence of added reducing agents was found to be Fe(III)T2MPyP greater than Fe(III)T4MPyP greater than Fe(III)T3MPyP. Comparative studies were also made with Fe(II)bleomycin. High concentrations of some reducing agents inhibited strand scission. Oxygen was required to produce optimal strand scission activity for all three porphyrins. It was also noted from spectroscopic measurements that the reduced porphyrins were degraded in the presence of oxygen. Studies with a series of potential strand scission inhibitors suggest that hydrogen peroxide and possibly peroxy radicals are intermediates in the reaction mechanism, while diffusible hydroxyl radicals appear to be excluded. However, superoxide radicals cannot be ruled out.
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Affiliation(s)
- R W Byrnes
- Department of Biophysics, Roswell Park Memorial Institute, Buffalo, NY
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Transition state analogs for protocatechuate 3,4-dioxygenase. Spectroscopic and kinetic studies of the binding reactions of ketonized substrate analogs. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43072-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Lands WE. Biological consequences of fatty acid oxygenase reaction mechanisms. PROSTAGLANDINS, LEUKOTRIENES, AND MEDICINE 1984; 13:35-46. [PMID: 6424135 DOI: 10.1016/0262-1746(84)90100-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Fatty acid oxygenases catalyze the insertion of molecular oxygen into polyunsaturated fatty acids. The enzymic reactions that have been studied in detail exhibit a continuous requirement for a hydroperoxide activator and appear to proceed by a free radical chain reaction. The self-limiting nature of fatty acid oxygenase-catalyzed reactions appears to be due to enzyme self-inactivation during the reaction rather than to product inhibition. Thus "suicide" substrates are potential regulators of overall enzyme activity, although linoleate is a much weaker inactivator than the highly unsaturated fatty acids. Inhibition by added glutathione peroxidase has demonstrated the need for hydroperoxide activator in the cyclooxygenase reaction catalyzed by prostaglandin H synthase and the lipoxygenase reactions catalyzed by lung, leukocyte, and soybean enzyme preparations. The regulation of cellular hydroperoxide levels may influence the formation of prostaglandins and other autacoids by fatty acid oxygenases.
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Halogenated protocatechuates as substrates for protocatechuate dioxygenase from Pseudomonas cepacia. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)43877-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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29
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Que L, Epstein RM. Resonance Raman studies on protocatechuate 3,4-dioxygenase-inhibitor complexes. Biochemistry 1981; 20:2545-9. [PMID: 6786338 DOI: 10.1021/bi00512a028] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Resonance Raman spectra of a number of protocatechuate 3,4-dioxygenase-inhibitor complexes were studied by use of the available lines of an argon and a krypton laser. Three types of inhibitors were investigated-hydroxybenzoates, dicarboxylates, and 4-nitrocatechol. The hydroxybenzoate study shows that the hydroxy group in 3-hydroxybenzoate does not coordinate to the active site iron, in agreement with earlier suggestions, and confirms the coordination of the hydroxy group in the isomeric 4-hydroxybenzoate. The dicarboxylate study demonstrates that both glutarate and terephthalate perturb the active-site environment, shifting the charge-transfer interaction to lower energy. The pH dependence of terephthalate binding as well as the spectral similarities of the dicarboxylate complexes to the ESO2 intermediate provides further evidence for the suggestion that this intermediate is a tightly bound enzyme-product complex. The 4-nitrocatechol study indicates that, unlike the substrate catechols, 4-nitrocatechol does not bind to the iron; a binding configuration wherein the acidic phenolate group interacts with the carboxylate binding site has been suggested by others. Finally the spectra of the 4-hydroxybenzoate and terephthalate complexes demonstrate the presence of two tyrosines coordinated to the active-site iron as suggested by others; these tyrosines have different vCO's and excitation profiles.
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Spaapen LJ, Verhagen J, Veldink GA, Vliegenthart JF. Properties of a complex of Fe(III)-soybean lipoxygenase-1 and 4-nitrocatechol. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 617:132-40. [PMID: 6766321 DOI: 10.1016/0005-2760(80)90230-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fe(III)-soybean lipoxygenase-1 yields with 4-nitrocatechol a green coloured 1 : 1 complex, which shows at pH 7.0 absorption maxima at 385 nm and 650 nm. The formation of this complex is reversible. The circular dichroism spectrum of the complex of Fe(III)-lipoxygenase-1 and 4-nitrocatechol has a positive band at around 380 nm and a negative band at around 450 nm and is significantly different from that of the Fe(III)-enzyme as such. 4-Nitrocatechol can be displaced from the green complex by 13-L-hydroperoxy-cis-9, trans-11-octadecadienoic acid, resulting in the formation of the blue complex between the Fe(III)-enzyme and 13-L-hydroperoxy-cis-9,trans-11-octadecadienoic acid both under aerobic and anaerobic conditions. Also linoleic acid competes with 4-nitrocatechol for the binding site on the Fe(III)-enzyme, as can be demonstrated under anaerobic conditions, ultimately leading to reduction of the Fe(III)-enzyme. The oxygenation of linoleic acid by Fe(III)-lipoxygenase-1 is inhibited by 4-nitrocatechol. From steady-state kinetics a non-competitive inhibition pattern is obtained. Probably it has to be considered as pseudo non-competitive because of the slow establishment of the complex equilibrium. An inhibition constant (K4NC) of 16.3 microM is found. On prolonged incubation of Fe(III)-lipoxygenase-1 and 4-nitrocatechol the green complex converts into a brown species. This conversion is found to be coupled with a change in the nature of the inhibition from reversible to irreversible. A complex between native lipoxygenase-1 and 4-nitrocatechol is found to be unlikely.
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May SW, Phillips RS. Protocatechuate 3,4-dioxygenase: implications of ionization effects on binding and dissociation of halohydroxybenzoates and on catalytic turnover. Biochemistry 1979; 18:5933-9. [PMID: 42436 DOI: 10.1021/bi00593a027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Veldink GA, Vliegenthart JF, Boldingh J. Plant lipoxygenases. PROGRESS IN THE CHEMISTRY OF FATS AND OTHER LIPIDS 1977; 15:131-66. [PMID: 195311 DOI: 10.1016/0079-6832(77)90014-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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