251
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Morphological transitions governed by density dependence and lipoxygenase activity in Aspergillus flavus. Appl Environ Microbiol 2008; 74:5674-85. [PMID: 18658287 DOI: 10.1128/aem.00565-08] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspergillus flavus differentiates to produce asexual dispersing spores (conidia) or overwintering survival structures called sclerotia. Results described here show that these two processes are oppositely regulated by density-dependent mechanisms and that increasing the cell density (from 10(1) to 10(7) cells/plate) results in the lowest numbers of sclerotial and the highest numbers of conidial. Extract from spent medium of low-cell-density cultures induced a high-sclerotium-number phenotype, whereas high-cell-density extract increased conidiation. Density-dependent development is also modified by changes in lipid availability. Exogenous linoleic acid increased sclerotial production at intermediate cell densities (10(4) and 10(5) cells/plate), whereas oleic and linolenic acids inhibited sclerotium formation. Deletion of Aflox encoding a lipoxygenase (LOX) greatly diminished density-dependent development of both sclerotia and conidia, resulting in an overall increase in the number of sclerotia and a decrease in the number of conidia at high cell densities (>10(5) cells/plate). Aflox mutants showed decreased linoleic acid LOX activity. Taken together, these results suggest that there is a quorum-sensing mechanism in which a factor(s) produced in dense cultures, perhaps a LOX-derived metabolite, activates conidium formation, while a factor(s) produced in low-density cultures stimulates sclerotium formation.
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252
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Mayilmurugan R, Stoeckli-Evans H, Palaniandavar M. Novel Iron(III) Complexes of Sterically Hindered 4N Ligands: Regioselectivity in Biomimetic Extradiol Cleavage of Catechols. Inorg Chem 2008; 47:6645-58. [DOI: 10.1021/ic702410d] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ramasamy Mayilmurugan
- School of Chemistry, Bharathidasan University, Tiruchirapalli 620 024, India, and Department of Chemistry, University of Neuchatel, Neuchatel, Switzerland
| | - Helen Stoeckli-Evans
- School of Chemistry, Bharathidasan University, Tiruchirapalli 620 024, India, and Department of Chemistry, University of Neuchatel, Neuchatel, Switzerland
| | - Mallayan Palaniandavar
- School of Chemistry, Bharathidasan University, Tiruchirapalli 620 024, India, and Department of Chemistry, University of Neuchatel, Neuchatel, Switzerland
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253
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Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state. Proc Natl Acad Sci U S A 2008; 105:7347-52. [PMID: 18492808 DOI: 10.1073/pnas.0711179105] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biological O(2) activation often occurs after binding to a reduced metal [e.g., M(II)] in an enzyme active site. Subsequent M(II)-to-O(2) electron transfer results in a reactive M(III)-superoxo species. For the extradiol aromatic ring-cleaving dioxygenases, we have proposed a different model where an electron is transferred from substrate to O(2) via the M(II) center to which they are both bound, thereby obviating the need for an integral change in metal redox state. This model is tested by using homoprotocatechuate 2,3-dioxygenases from Brevibacterium fuscum (Fe-HPCD) and Arthrobacter globiformis (Mn-MndD) that share high sequence identity and very similar structures. Despite these similarities, Fe-HPCD binds Fe(II) whereas Mn-MndD incorporates Mn(II). Methods are described to incorporate the nonphysiological metal into each enzyme (Mn-HPCD and Fe-MndD). The x-ray crystal structure of Mn-HPCD at 1.7 A is found to be indistinguishable from that of Fe-HPCD, while EPR studies show that the Mn(II) sites of Mn-MndD and Mn-HPCD, and the Fe(II) sites of the NO complexes of Fe-HPCD and Fe-MndD, are very similar. The uniform metal site structures of these enzymes suggest that extradiol dioxygenases cannot differentially compensate for the 0.7-V gap in the redox potentials of free iron and manganese. Nonetheless, all four enzymes exhibit nearly the same K(M) and V(max) values. These enzymes constitute an unusual pair of metallo-oxygenases that remain fully active after a metal swap, implicating a different way by which metals are used to promote oxygen activation without an integral change in metal redox state.
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254
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Weigert A, Brüne B. Nitric oxide, apoptosis and macrophage polarization during tumor progression. Nitric Oxide 2008; 19:95-102. [PMID: 18486631 DOI: 10.1016/j.niox.2008.04.021] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 04/18/2008] [Indexed: 12/31/2022]
Abstract
Decreased oxygen availability evokes adaptive responses, which are primarily under the gene regulatory control of hypoxia inducible factor-1 (HIF-1). Hypoxic cores of a growing tumor cell mass use this signaling circuit to gain access to further blood and nutrient supply that guarantees their continuing growth. Interestingly, NO shares with hypoxia the ability to block prolyl-hydroxylase (PHD) activity, and thus the ability to stabilize hypoxia inducible factor 1 alpha (HIF-1 alpha). Under these conditions NO mimics hypoxia, which might contribute to tumor development. Stimulating/triggering innate immune responses associated with macrophage activation often correlated with iNOS induction and massive NO release, which is known to kill NO-sensitive tumors. However, this safeguard mechanism will only be effective if all tumor cells are eliminated because apoptotic death of tumor cells implies mechanisms to stop macrophages from attacking the survivors. Apoptotic cells release factors, among others sphingosine-1-phosphate (S1P), which reprogram macrophages. Macrophage reprogramming shifts responses from a M1 and thus pro-inflammatory and killing phenotype, to a M2 phenotype, which is anti-inflammatory and pro-angiogenic. These polarized tumor associated macrophages (TAM) are actively contributing to tumor development. Apparently NO uses distinct signaling pathways that could serve as an explanation to understand how NO affects tumor development. Some of these pathways, especially the ability of NO to mimic hypoxia at the level of HIF-1 alpha, as well as the role of macrophage polarization by apoptotic cells with accompanying changes in the iNOS versus arginase ratio and activities, will be discussed to better understand how NO affects tumor growth.
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Affiliation(s)
- Andreas Weigert
- Institute of Biochemistry I/ZAFES, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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255
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Catechol oxidase and phenoxazinone synthase activity of a manganese(II) isoindoline complex. J Inorg Biochem 2008; 102:773-80. [DOI: 10.1016/j.jinorgbio.2007.11.014] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 10/11/2007] [Accepted: 11/08/2007] [Indexed: 11/20/2022]
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256
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Guo S, Boyd J, Sammynaiken R, Loewen MC. Identification and characterization of a unique cysteine residue proximal to the catalytic site of Arabidopsis thaliana carotenoid cleavage enzyme 1. Biochem Cell Biol 2008; 86:262-70. [DOI: 10.1139/o08-031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
AtCCD1 and AtNCED3 are related carotenoid cleavage enzymes from Arabidopsis thaliana that catalyze the oxidative cleavage of, respectively, the 9,10 (9′,10′) double bonds of carotenoid substrates such as β-carotene, and the 11,12 double bond of 9-cis epoxycarotenoids. Although the cellular and cleavage functionalities of these enzymes have been reported, their mechanisms and related structural environments mediating these disparate specificities in homologous enzymes have not been well characterized. By relating the differences observed in UV and visible light absorption and Cu(II) electron paramagnetic signals to variations in sequence alignments and 3-D homology models of the two A. thaliana enzymes, we identified a putatively proximal cysteine residue (Cys352) in AtCCD1 that is not conserved in AtNCED3. Spectral analysis of the Cys to Ala mutant confirmed its uniqueness and proximity to the metal binding site, but precluded any role for the residue in the mediation of the observed metal binding affinity or associated steric constraint differences. Further analysis of kinetic substrate cleavage properties indicated a decrease in Vmax and a subtle increase in Km for the C352A mutant compared with those observed for the wild-type, thus confirming catalytic site proximity and suggesting possible roles for the unique cysteine in the modulation of substrate affinity and (or) the reaction rate of AtCCD1.
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Affiliation(s)
- Shukui Guo
- Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- SK Structural Science Centre, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Jason Boyd
- Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- SK Structural Science Centre, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Ramaswami Sammynaiken
- Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- SK Structural Science Centre, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Michèle C. Loewen
- Plant Biotechnology Institute, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- SK Structural Science Centre, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
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257
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Kovaleva EG, Lipscomb JD. Versatility of biological non-heme Fe(II) centers in oxygen activation reactions. Nat Chem Biol 2008; 4:186-93. [PMID: 18277980 PMCID: PMC2720164 DOI: 10.1038/nchembio.71] [Citation(s) in RCA: 492] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oxidase and oxygenase enzymes allow the use of relatively unreactive O2 in biochemical reactions. Many of the mechanistic strategies used in nature for this key reaction are represented within the 2-histidine-1-carboxylate facial triad family of non-heme Fe(II)-containing enzymes. The open face of the metal coordination sphere opposite the three endogenous ligands participates directly in the reaction chemistry. Here, data from several studies are presented showing that reductive O2 activation within this family is initiated by substrate (and in some cases cosubstrate or cofactor) binding, which then allows coordination of O2 to the metal. From this starting point, the O2 activation process and the reactions with substrates diverge broadly. The reactive species formed in these reactions have been proposed to encompass four oxidation states of iron and all forms of reduced O2 as well as several of the reactive oxygen species that derive from O-O bond cleavage.
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Affiliation(s)
- Elena G Kovaleva
- Elena G. Kovaleva and John D. Lipscomb are in the Department of Biochemistry, Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, 6-155 Jackson Hall, Minneapolis, Minnesota, 55455 USA
| | - John D Lipscomb
- Elena G. Kovaleva and John D. Lipscomb are in the Department of Biochemistry, Molecular Biology and Biophysics and the Center for Metals in Biocatalysis, University of Minnesota, 6-155 Jackson Hall, Minneapolis, Minnesota, 55455 USA
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258
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Gibbons HS, Reynolds CM, Guan Z, Raetz CRH. An inner membrane dioxygenase that generates the 2-hydroxymyristate moiety of Salmonella lipid A. Biochemistry 2008; 47:2814-25. [PMID: 18254598 DOI: 10.1021/bi702457c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The lipid A residues of certain Gram-negative bacteria, including most strains of Salmonella and Pseudomonas, are esterified with one or two secondary S-2-hydroxyacyl chains. The S-2 hydroxylation process is O 2-dependent in vivo, but the relevant enzymatic pathways have not been fully characterized because in vitro assays have not been developed. We previously reported that expression of the Salmonella lpxO gene confers upon Escherichia coli K-12 the ability to synthesize 2-hydroxymyristate modified lipid A ( J. Biol. Chem. (2000) 275, 32940-32949). We now demonstrate that inactivation of lpxO, which encodes a putative Fe (2+)/O 2/alpha-ketoglutarate-dependent dioxygenase, abolishes S-2-hydroxymyristate formation in S. typhimurium. Membranes of E. coli strains expressing lpxO are able to hydroxylate Kdo 2-[4'- (32)P]-lipid A in vitro in the presence of Fe (2+), O 2, alpha-ketoglutarate, ascorbate, and Triton X-100. The Fe (2+) chelator 2,2'-bipyridyl inhibits the reaction. The product generated in vitro is a monohydroxylated Kdo 2-lipid A derivative. The [4'- (32)P]-lipid A released by mild acid hydrolysis from the in vitro product migrates with authentic S-2-hydroxlyated lipid A isolated from (32)P-labeled S. typhimurium cells. Electrospray ionization mass spectrometry and gas chromatography/mass spectrometry of the in vitro product are consistent with the 2-hydroxylation of the 3'-secondary myristoyl chain of Kdo 2-lipid A. LpxO contains two predicted trans-membrane helices (one at each end of the protein), and its active site likely faces the cytoplasm. LpxO is an unusual example of an integral membrane protein that is a member of the Fe (2+)/O 2/alpha-ketoglutarate-dependent dioxygenase family.
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Affiliation(s)
- Henry S Gibbons
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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259
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Burzlaff N. Tripodal N,N,O-ligands for metalloenzyme models and organometallics. ADVANCES IN INORGANIC CHEMISTRY 2008. [DOI: 10.1016/s0898-8838(08)00004-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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260
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Bruijnincx PCA, van Koten G, Klein Gebbink RJM. Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies. Chem Soc Rev 2008; 37:2716-44. [DOI: 10.1039/b707179p] [Citation(s) in RCA: 412] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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261
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Cook KM, Schofield CJ. Therapeutic Strategies that Target the HIF System. Angiogenesis 2008. [DOI: 10.1007/978-0-387-71518-6_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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262
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Substrate activation for O2 reactions by oxidized metal centers in biology. Proc Natl Acad Sci U S A 2007; 104:18355-62. [PMID: 18003930 DOI: 10.1073/pnas.0704191104] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The uncatalyzed reactions of O(2) (S = 1) with organic substrates (S = 0) are thermodynamically favorable but kinetically slow because they are spin-forbidden and the one-electron reduction potential of O(2) is unfavorable. In nature, many of these important O(2) reactions are catalyzed by metalloenzymes. In the case of mononuclear non-heme iron enzymes, either Fe(II) or Fe(III) can play the catalytic role in these spin-forbidden reactions. Whereas the ferrous enzymes activate O(2) directly for reaction, the ferric enzymes activate the substrate for O(2) attack. The enzyme-substrate complex of the ferric intradiol dioxygenases exhibits a low-energy catecholate to Fe(III) charge transfer transition that provides a mechanism by which both the Fe center and the catecholic substrate are activated for the reaction with O(2). In this Perspective, we evaluate how the coupling between this experimentally observed charge transfer and the change in geometry and ligand field of the oxidized metal center along the reaction coordinate can overcome the spin-forbidden nature of the O(2) reaction.
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263
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Neidig ML, Brown CD, Light KM, Fujimori DG, Nolan EM, Price JC, Barr EW, Bollinger JM, Krebs C, Walsh CT, Solomon EI. CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases. J Am Chem Soc 2007; 129:14224-31. [PMID: 17967013 DOI: 10.1021/ja074557r] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alpha-ketoglutarate (alpha-KG)-dependent oxygenases are a large and diverse class of mononuclear non-heme iron enzymes that require FeII, alpha-KG, and dioxygen for catalysis with the alpha-KG cosubstrate supplying the additional reducing equivalents for oxygen activation. While these systems exhibit a diverse array of reactivities (i.e., hydroxylation, desaturation, ring closure, etc.), they all share a common structural motif at the FeII active site, termed the 2-His-1-carboxylate facial triad. Recently, a new subclass of alpha-KG-dependent oxygenases has been identified that exhibits novel reactivity, the oxidative halogenation of unactivated carbon centers. These enzymes are also structurally unique in that they do not contain the standard facial triad, as a Cl- ligand is coordinated in place of the carboxylate. An FeII methodology involving CD, MCD, and VTVH MCD spectroscopies was applied to CytC3 to elucidate the active-site structural effects of this perturbation of the coordination sphere. A significant decrease in the affinity of FeII for apo-CytC3 was observed, supporting the necessity of the facial triad for iron coordination to form the resting site. In addition, interesting differences observed in the FeII/alpha-KG complex relative to the cognate complex in other alpha-KG-dependent oxygenases indicate the presence of a distorted 6C site with a weak water ligand. Combined with parallel studies of taurine dioxygenase and past studies of clavaminate synthase, these results define a role of the carboxylate ligand of the facial triad in stabilizing water coordination via a H-bonding interaction between the noncoordinating oxygen of the carboxylate and the coordinated water. These studies provide initial insight into the active-site features that favor chlorination by CytC3 over the hydroxylation reactions occurring in related enzymes.
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Affiliation(s)
- Michael L Neidig
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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264
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Bursy J, Pierik AJ, Pica N, Bremer E. Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase. J Biol Chem 2007; 282:31147-55. [PMID: 17636255 DOI: 10.1074/jbc.m704023200] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
By using natural abundance (13)C NMR spectroscopy, we investigated the types of compatible solutes synthesized in a variety of Bacilli under high salinity growth conditions. Glutamate, proline, and ectoine were the dominant compatible solutes synthesized by the various Bacillus species. The majority of the inspected Bacilli produced the tetrahydropyrimidine ectoine in response to high salinity stress, and a subset of these also synthesized a hydroxylation derivative of ectoine, 5-hydroxyectoine. In Salibacillus salexigens, a representative of the ectoine- and 5-hydroxyectoine-producing species, ectoine production was linearly correlated with the salinity of the growth medium and dependent on an ectABC biosynthetic operon. The formation of 5-hydroxyectoine was primarily a stationary growth phase phenomenon. The enzyme responsible for ectoine hydroxylation (EctD) was purified from S. salexigens to apparent homogeneity. The EctD protein was shown in vitro to directly hydroxylate ectoine in a reaction dependent on iron(II), molecular oxygen, and 2-oxoglutarate. We identified the structural gene (ectD) for the ectoine hydroxylase in S. salexigens. Northern blot analysis showed that the transcript levels of the ectABC and ectD genes increased as a function of salinity. Many EctD-related proteins can be found in data base searches in various Bacteria. Each of these bacterial species also contains an ectABC ectoine biosynthetic gene cluster, suggesting that 5-hydroxyectoine biosynthesis strictly depends on the prior synthesis of ectoine. Our data base searches and the biochemical characterization of the EctD protein from S. salexigens suggest that the EctD-related ectoine hydroxylases are members of a new subfamily within the non-heme-containing, iron(II)- and 2-oxoglutarate-dependent dioxygenase superfamily (EC 1.14.11).
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Amino Acids, Diamino/biosynthesis
- Amino Acids, Diamino/chemistry
- Amino Acids, Diamino/genetics
- Bacillus/classification
- Bacillus/genetics
- Bacillus/growth & development
- Bacillus/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Carbon Isotopes/metabolism
- Chromatography, High Pressure Liquid
- Conserved Sequence
- Culture Media
- Databases, Protein
- Dose-Response Relationship, Drug
- Escherichia coli/genetics
- Evolution, Molecular
- Genes, Bacterial
- Mixed Function Oxygenases/genetics
- Mixed Function Oxygenases/isolation & purification
- Mixed Function Oxygenases/metabolism
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Osmosis/physiology
- Sequence Homology, Amino Acid
- Sodium Chloride/pharmacology
- Solutions/metabolism
- Transcription, Genetic
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Affiliation(s)
- Jan Bursy
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, D-35032 Marburg, Germany
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265
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Kovaleva EG, Neibergall MB, Chakrabarty S, Lipscomb JD. Finding intermediates in the O2 activation pathways of non-heme iron oxygenases. Acc Chem Res 2007; 40:475-83. [PMID: 17567087 PMCID: PMC2720168 DOI: 10.1021/ar700052v] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intermediates in the reaction cycle of an oxygenase are usually very informative with respect to the chemical mechanism of O 2 activation and insertion. However, detection of these intermediates is often complicated by their short lifetime and the regulatory mechanism of the enzyme designed to ensure specificity. Here, the methods used to detect the intermediates in an extradiol dioxygenase, a Rieske cis-dihydrodiol dioxygenase, and soluble methane monooxygenase are discussed. The methods include the use of alternative, chromophoric substrates, mutagenesis of active site catalytic residues, forced changes in substrate binding order, control of reaction rates using regulatory proteins, and initialization of catalysis in crystallo.
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Affiliation(s)
| | | | | | - J. D. Lipscomb
- Corresponding author. Telephone: (612) 625-6454; Fax: (612) 624-5121; E-mail:
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266
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Rådmark O, Werz O, Steinhilber D, Samuelsson B. 5-Lipoxygenase: regulation of expression and enzyme activity. Trends Biochem Sci 2007; 32:332-41. [PMID: 17576065 DOI: 10.1016/j.tibs.2007.06.002] [Citation(s) in RCA: 342] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 05/01/2007] [Accepted: 06/04/2007] [Indexed: 11/16/2022]
Abstract
5-Lipoxygenase (5-LO) catalyzes the first two steps in the biosynthesis of leukotrienes, a group of pro-inflammatory lipid mediators derived from arachidonic acid. Leukotriene antagonists are used in the treatment of asthma, and the potential role of leukotrienes in atherosclerosis, another chronic inflammatory disease, has recently received considerable attention. In addition, some possible effects of 5-LO metabolites in tumorigenesis have emerged. Thus, knowledge of the biochemistry of this enzyme has potential implications for the treatment of various diseases. Recent advances have expanded our understanding of the regulatory mechanisms underlying the expression and control of 5-LO activity. With regard to the control of enzyme activity, many of these findings focus on the N-terminal domain of 5-LO.
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Affiliation(s)
- Olof Rådmark
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, S-17177 Stockholm, Sweden.
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267
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Straganz GD, Nidetzky B. Variations of the 2-His-1-carboxylate theme in mononuclear non-heme FeII oxygenases. Chembiochem 2007; 7:1536-48. [PMID: 16858718 DOI: 10.1002/cbic.200600152] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A facial triad of two histidine side chains and one aspartate or glutamate side chain forms the canonical metal-coordinating motif in the catalytic centers of various mononuclear non-heme Fe(II) enzymes. Although these active sites are based on totally unrelated protein folds and bring about a wide range of chemical transformations, most of them share the ability to couple dioxygen reduction with the oxygenation of an organic substrate. With the increasing number of protein structures now solved, it has become clear that the 2-His-1-carboxylate signature is less of a paradigm for non-heme Fe(II) active sites than had long been thought and that it can be replaced by alternative metal centers in various oxygenases, the structure-function relationships and proposed catalytic mechanisms of which are reviewed here. Metal coordination through three histidines and one glutamate constitutes the classical motif described for enzyme members of the cupin protein superfamily, such as aci-reductone dioxygenase and quercetin dioxygenase, multiple metal forms of which (including the Fe(II) type) are found in nature. Cysteine dioxygenase and diketone dioxygenase, which are strictly Fe(II)-dependent oxygenases based on the cupin fold, bind the catalytic metal through the homologous triad of histidines, but lack the fourth glutamate ligand. An alpha-ketoglutarate-dependent Fe(II) halogenase shows metal coordination by two histidines as the only protein-derived ligands, whilst carotene oxygenase, from a different protein fold family, features an Fe(II) site consisting of four histidine side chains. These recently discovered metallocenters are discussed with respect to their metal-binding properties and the reaction coordinates of the O(2)-dependent conversions they catalyze.
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Affiliation(s)
- G D Straganz
- Institute of Biotechnology and Biochemical Engineering Graz University of Technology Petersgasse 12/I, 8010 Graz, Austria.
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268
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Brown CD, Neidig ML, Neibergall MB, Lipscomb JD, Solomon EI. VTVH-MCD and DFT studies of thiolate bonding to [FeNO]7/[FeO2]8 complexes of isopenicillin N synthase: substrate determination of oxidase versus oxygenase activity in nonheme Fe enzymes. J Am Chem Soc 2007; 129:7427-38. [PMID: 17506560 PMCID: PMC2536647 DOI: 10.1021/ja071364v] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isopenicillin N synthase (IPNS) is a unique mononuclear nonheme Fe enzyme that catalyzes the four-electron oxidative double ring closure of its substrate ACV. A combination of spectroscopic techniques including EPR, absorbance, circular dichroism (CD), magnetic CD, and variable-temperature, variable-field MCD (VTVH-MCD) were used to evaluate the geometric and electronic structure of the [FeNO]7 complex of IPNS coordinated with the ACV thiolate ligand. Density Function Theory (DFT) calculations correlated to the spectroscopic data were used to generate an experimentally calibrated bonding description of the Fe-IPNS-ACV-NO complex. New spectroscopic features introduced by the binding of the ACV thiolate at 13 100 and 19 800 cm-1 are assigned as the NO pi*(ip) --> Fe dx2-y2 and S pi--> Fe dx2-y2 charge transfer (CT) transitions, respectively. Configuration interaction mixes S CT character into the NO pi*(ip) --> Fe dx2-y2 CT transition, which is observed experimentally from the VTVH-MCD data from this transition. Calculations on the hypothetical {FeO2}8 complex of Fe-IPNS-ACV reveal that the configuration interaction present in the [FeNO]7 complex results in an unoccupied frontier molecular orbital (FMO) with correct orientation and distal O character for H-atom abstraction from the ACV substrate. The energetics of NO/O2 binding to Fe-IPNS-ACV were evaluated and demonstrate that charge donation from the ACV thiolate ligand renders the formation of the FeIII-superoxide complex energetically favorable, driving the reaction at the Fe center. This single center reaction allows IPNS to avoid the O2 bridged binding generally invoked in other nonheme Fe enzymes that leads to oxygen insertion (i.e., oxygenase function) and determines the oxidase activity of IPNS.
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Affiliation(s)
- Christina D Brown
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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269
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Kovaleva EG, Lipscomb JD. Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates. Science 2007; 316:453-7. [PMID: 17446402 PMCID: PMC2720167 DOI: 10.1126/science.1134697] [Citation(s) in RCA: 306] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The x-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been predicted, but not structurally characterized, in an oxygenase. The intermediates define the major chemical steps of the dioxygenase mechanism and point to a general mechanistic strategy for the diverse 2-His-1-carboxylate enzyme family.
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270
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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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271
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Purpero V, Moran GR. The diverse and pervasive chemistries of the alpha-keto acid dependent enzymes. J Biol Inorg Chem 2007; 12:587-601. [PMID: 17431691 DOI: 10.1007/s00775-007-0231-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 03/15/2007] [Indexed: 12/01/2022]
Abstract
The number of identified and confirmed alpha-keto acid dependent oxygenases is increasing rapidly. All of these enzymes have a relatively simple liganding arrangement for a single ferrous ion but collectively conduct a highly diverse set of chemistries. While hydroxylations and a variety of oxidation reactions have been most commonly observed, new reactions involving dealkylations, epimerizations and halogenations have recently been discovered. In this minireview we present what is known of the alpha-keto acid dependent enzymes and offer an argument that the chemistry that is unique to each enzyme occurs only after the production of a pivotal ferryl-oxo intermediate.
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Affiliation(s)
- Vincent Purpero
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211-3029, USA
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272
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Grzyska PK, Müller TA, Campbell MG, Hausinger RP. Metal ligand substitution and evidence for quinone formation in taurine/alpha-ketoglutarate dioxygenase. J Inorg Biochem 2007; 101:797-808. [PMID: 17350690 DOI: 10.1016/j.jinorgbio.2007.01.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 01/05/2007] [Accepted: 01/19/2007] [Indexed: 11/30/2022]
Abstract
The three metal-binding ligands of the archetype Fe(II)/alpha-ketoglutarate (alphaKG)-dependent hydroxylase, taurine/alphaKG dioxygenase (TauD), were systematically mutated to examine the effects of various ligand substitutions on enzyme activity and metallocenter properties. His99, coplanar with alphaKG and Fe(II), is unalterable in terms of maintaining an active enzyme. Asp101 can be substituted only by a longer carboxylate, with the D101E variant exhibiting 22% the k(cat) and threefold the K(m) of wild-type enzyme. His255, located opposite the O(2)-binding site, is less critical for activity and can be substituted by Gln or even the negatively charged Glu (81% and 33% active, respectively). Transient kinetic studies of the three highly active mutant proteins reveal putative Fe(IV)-oxo intermediates as reported in wild-type enzyme, but with distinct kinetics. Supplementation of the buffer with formate enhances activity of the D101A variant, consistent with partial chemical rescue of the missing metal ligand. Upon binding Fe(II), anaerobic samples of wild-type TauD and the three highly active variants generate a weak green chromophore resembling a catecholate-Fe(III) species. Evidence is presented that the quinone oxidation state of dihydroxyphenylalanine, formed by aberrant self-hydroxylation of a protein side chain of TauD during aerobic bacterial growth, reacts with Fe(II) to form this species. The spectra associated with Fe(II)-TauD and Co(II)-TauD in the presence of alphaKG and taurine were examined for all variants to gain additional insights into perturbations affecting the metallocenter. These studies present the first systematic mutational analysis of metallocenter ligands in an Fe(II)/alphaKG-dependent hydroxylase.
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Affiliation(s)
- Piotr K Grzyska
- Department of Microbiology & Molecular Genetics and Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824-4320, USA
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273
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Pau MYM, Davis MI, Orville AM, Lipscomb JD, Solomon EI. Spectroscopic and electronic structure study of the enzyme-substrate complex of intradiol dioxygenases: substrate activation by a high-spin ferric non-heme iron site. J Am Chem Soc 2007; 129:1944-58. [PMID: 17256852 PMCID: PMC2536531 DOI: 10.1021/ja065671x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Various mechanisms have been proposed for the initial O(2) attack in intradiol dioxygenases based on different electronic descriptions of the enzyme-substrate (ES) complex. We have examined the geometric and electronic structure of the high-spin ferric ES complex of protocatechuate 3,4-dioxygenase (3,4-PCD) with UV/visible absorption, circular dichroism (CD), magnetic CD (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. The experimental data were coupled with DFT and INDO/S-CI calculations, and an experimentally calibrated bonding description was obtained. The broad absorption spectrum for the ES complex in the 6000-31000 cm(-1) region was resolved into at least five individual transitions, assigned as ligand-to-metal charge transfer (LMCT) from the protocatechuate (PCA) substrate and Tyr408. From our DFT calculations, all five LMCT transitions originate from the PCA and Tyr piop orbitals to the ferric dpi orbitals. The strong pi covalent donor interactions dominate the bonding in the ES complex. Using hypothetical Ga(3+)-catecholate/semiquinone complexes as references, 3,4-PCD-PCA was found to be best described as a highly covalent Fe(3+)-catecholate complex. The covalency is distributed unevenly among the four PCA valence orbitals, with the strongest interaction between the piop-sym and Fe dxz orbitals. This strong pi interaction, as reflected in the lowest energy PCA-to-Fe(3+) LMCT transition, is responsible for substrate activation for the O(2) reaction of intradiol dioxygenases. This involves a multi-electron-transfer (one beta and two alpha) mechanism, with Fe3+ acting as a buffer for the spin-forbidden two-electron redox process between PCA and O(2) in the formation of the peroxy-bridged ESO2 intermediate. The Fe ligand field overcomes the spin-forbidden nature of the triplet O(2) reaction, which potentially results in an intermediate spin state (S = 3/2) on the Fe(3+) center which is stabilized by a change in coordination along the reaction coordinate.
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Affiliation(s)
- Monita Y M Pau
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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274
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Abstract
Decreased oxygen availability evokes adaptive responses, which are primarily under the gene regulatory control of hypoxia-inducible factor 1 (HIF-1). HIF-1 is a heterodimer composed of the basic helix-loop-helix Per-ARNT-Sim (bHLH-PAS) protein HIF-1alpha (alpha) and the aryl hydrocarbon nuclear translocator (ARNT), also known as HIF-1beta (beta). The HIF-1 transcriptional system senses decreased oxygen availability and transmits this signal into pathophysiological responses, such as angiogenesis, erythropoiesis, vasomotor control, an altered energy metabolism, and/or cell survival decisions. It is now appreciated that nitric oxide (NO) and/or derived reactive nitrogen species (RNS) participate in stability control of HIF-1alpha. Although initial observations showed that NO inhibits hypoxia-induced HIF-1alpha stabilization and HIF-1 transcriptional activation, later studies revealed that the exposure of cells from different species to chemically diverse NO donors, or conditions of endogenous NO formation, induced HIF-1alpha accumulation, HIF-1-DNA binding, and activation of downstream target gene expression under normoxic conditions. The opposing effects of NO under hypoxia versus normoxia are discussed based on direct and indirect reaction properties of NO, taking metal interactions as well as secondary reaction products, generated in the presence of oxygen or superoxide, into account. Considering HIF-1alpha as a target that is controlled by the bioavailability of NO helps in the understanding of how signaling mechanisms are attributed to physiological and pathological transmission of NO actions with broad implications for medicine.
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275
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Brines LM, Kovacs JA. Understanding the Mechanism of Superoxide Reductase Promoted Reduction of Superoxide. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200600461] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lisa M. Brines
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA, Fax: +1‐206‐685‐8665
| | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA, Fax: +1‐206‐685‐8665
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276
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Bassan A, Borowski T, Schofield CJ, Siegbahn PEM. Ethylene Biosynthesis by 1-Aminocyclopropane-1-Carboxylic Acid Oxidase: A DFT Study. Chemistry 2006; 12:8835-46. [PMID: 16933342 DOI: 10.1002/chem.200501459] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO(2), cyanide and two water molecules. A model including the mononuclear iron complex with ACC in the first coordination sphere was used to study the details of O-O bond cleavage and cyclopropane ring opening. Calculations imply that this unusual and complex reaction is triggered by a hydrogen atom abstraction step generating a radical on the amino nitrogen of ACC. Subsequently, cyclopropane ring opening followed by O-O bond heterolysis leads to a very reactive iron(IV)-oxo intermediate, which decomposes to ethylene and cyanoformate with very low energy barriers. The reaction is assisted by bicarbonate located in the second coordination sphere of the metal.
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Affiliation(s)
- Arianna Bassan
- Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 10691 Stockholm, Sweden.
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277
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Pavon JA, Fitzpatrick PF. Insights into the catalytic mechanisms of phenylalanine and tryptophan hydroxylase from kinetic isotope effects on aromatic hydroxylation. Biochemistry 2006; 45:11030-7. [PMID: 16953590 PMCID: PMC1945167 DOI: 10.1021/bi0607554] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenylalanine hydroxylase (PheH) and tryptophan hydroxylase (TrpH) catalyze the aromatic hydroxylation of phenylalanine and tryptophan, forming tyrosine and 5-hydroxytryptophan, respectively. The reactions of PheH and TrpH have been investigated with [4-(2)H]-, [3,5-(2)H(2)]-, and (2)H(5)-phenylalanine as substrates. All (D)k(cat) values are normal with Delta117PheH, the catalytic core of rat phenylalanine hydroxylase, ranging from 1.12-1.41. In contrast, for Delta117PheH V379D, a mutant protein in which the stoichiometry between tetrahydropterin oxidation and amino acid hydroxylation is altered, the (D)k(cat) value with [4-(2)H]-phenylalanine is 0.92 but is normal with [3,5-(2)H(2)]-phenylalanine. The ratio of tetrahydropterin oxidation to amino acid hydroxylation for Delta117PheH V379D shows a similar inverse isotope effect with [4-(2)H]-phenylalanine. Intramolecular isotope effects, determined from the deuterium contents of the tyrosine formed from [4-(2)H]-and [3,5(2)H(2)]-phenylalanine, are identical for Delta117PheH and Delta117PheH V379D, suggesting that steps subsequent to oxygen addition are unaffected in the mutant protein. The inverse effects are consistent with the reaction of an activated ferryl-oxo species at the para position of the side chain of the amino acid to form a cationic intermediate. The normal effects on the (D)k(cat) value for the wild-type enzyme are attributed to an isotope effect of 5.1 on the tautomerization of a dienone intermediate to tyrosine with a rate constant 6- to7-fold that for hydroxylation. In addition, there is a slight ( approximately 34%) preference for the loss of the hydrogen originally at C4 of phenylalanine. With (2)H(5)-indole-tryptophan as a substrate for Delta117PheH, the (D)k(cat) value is 0.89, consistent with hydroxylation being rate-limiting in this case. When deuterated phenylalanines are used as substrates for TrpH, the (D)k(cat) values are within error of those for Delta117PheH V379D. Overall, these results are consistent with the aromatic amino acid hydroxylases all sharing the same chemical mechanism, but with the isotope effect for hydroxylation by PheH being masked by tautomerization of an enedione intermediate to tyrosine.
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Affiliation(s)
- Jorge Alex Pavon
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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278
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Müller TA, Fleischmann T, van der Meer JR, Kohler HPE. Purification and characterization of two enantioselective alpha-ketoglutarate-dependent dioxygenases, RdpA and SdpA, from Sphingomonas herbicidovorans MH. Appl Environ Microbiol 2006; 72:4853-61. [PMID: 16820480 PMCID: PMC1489315 DOI: 10.1128/aem.02758-05] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 05/02/2006] [Indexed: 02/04/2023] Open
Abstract
Alpha-ketoglutarate-dependent (R)-dichlorprop dioxygenase (RdpA) and alpha-ketoglutarate-dependent (S)-dichlorprop dioxygenase (SdpA), which are involved in the degradation of phenoxyalkanoic acid herbicides in Sphingomonas herbicidovorans MH, were expressed and purified as His6-tagged fusion proteins from Escherichia coli BL21(DE3)(pLysS). RdpA and SdpA belong to subgroup II of the alpha-ketoglutarate-dependent dioxygenases and share the specific motif HXDX(24)TX(131)HX(10)R. Amino acids His-111, Asp-113, and His-270 and amino acids His-102, Asp-104, and His 257 comprise the 2-His-1-carboxylate facial triads and were predicted to be involved in iron binding in RdpA and SdpA, respectively. RdpA exclusively transformed the (R) enantiomers of mecoprop [2-(4-chloro-2-methylphenoxy)propanoic acid] and dichlorprop [2-(2,4-dichlorophenoxy)propanoic acid], whereas SdpA was specific for the (S) enantiomers. The apparent Km values were 99 microM for (R)-mecoprop, 164 microM for (R)-dichlorprop, and 3 microM for alpha-ketoglutarate for RdpA and 132 microM for (S)-mecoprop, 495 microM for (S)-dichlorprop, and 20 microM for alpha-ketoglutarate for SdpA. Both enzymes had high apparent Km values for oxygen; these values were 159 microM for SdpA and >230 microM for RdpA, whose activity was linearly dependent on oxygen at the concentration range measured. Both enzymes had narrow cosubstrate specificity; only 2-oxoadipate was able to replace alpha-ketoglutarate, and the rates were substantially diminished. Ferrous iron was necessary for activity of the enzymes, and other divalent cations could not replace it. Although the results of growth experiments suggest that strain MH harbors a specific 2,4-dichlorophenoxyacetic acid-converting enzyme, tfdA-, tfdAalpha-, or cadAB-like genes were not discovered in a screening analysis in which heterologous hybridization and PCR were used.
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Affiliation(s)
- Tina A Müller
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Uberlandstrasse 133, CH-8600 Dübendorf, Switzerland
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279
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Suenaga H, Goto M, Furukawa K. Active-site engineering of biphenyl dioxygenase: effect of substituted amino acids on substrate specificity and regiospecificity. Appl Microbiol Biotechnol 2006; 71:168-76. [PMID: 16217654 DOI: 10.1007/s00253-005-0135-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 07/19/2005] [Accepted: 08/08/2005] [Indexed: 10/25/2022]
Abstract
Biphenyl dioxygenase (Bph Dox) catalyzes the initial dioxygenation step in the metabolism of biphenyl. The large subunit (BphA1) of Bph Dox plays a crucial role in the determination of the substrate specificity of biphenyl-related compounds including polychlorinated biphenyls (PCBs). Previously, the substitution of Asn at Thr-376 near the active-site iron in the BphA1 of Pseudomonas pseudoalcaligenes KF707 expanded the oxidation range and altered the regiospecificity of Bph Dox for PCBs. In this study, we replaced Thr-376 with Gly, Ser, Gln, Tyr, Val, Phe, Asp, and Lys and expressed these enzymes in Escherichia coli. Bph Dox mutants of Thr376Asn, Thr376Val, Thr376Phe, and Thr376Lys showed novel degradation activity for dibenzofuran, which is a poor substrate for KF707 Bph Dox. All active Bph Dox mutants showed altered regiospecificity with 2,2'-dichlorobiphenyl and 2,5,4'-trichlorobiphenyl. The Thr376Gly, Thr376Val, Thr376Phe, and Thr376Asp Bph Dox mutants introduced molecular oxygen at the 2,3 position of 2,2'-dichlorobiphenyl, forming 2-chloro-2',3'-dihydroxybiphenyl with concomitant dechlorination. The Bph Dox mutants of Thr376Gly, Thr376Ser, Thr376Asp, and Thr376Lys attacked 2,5,4'-trichlorobiphenyl via both 2',3'- and 3,4-dioxygenation activities. In particular, the Thr376Phe Bph Dox mutant exhibited enhanced and expanded degradation activities toward all of the compounds tested. Further site-directed mutation was induced to change the oxidizing character of KF707 Bph Dox to that of the Bph Dox of Burkholderia xenovorans LB400 by the substitution of two amino acids, Ile335Phe and Thr376Asn, near the active-site.
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Affiliation(s)
- Hikaru Suenaga
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
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280
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Cloos PAC, Christensen J, Agger K, Maiolica A, Rappsilber J, Antal T, Hansen KH, Helin K. The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 2006; 442:307-11. [PMID: 16732293 DOI: 10.1038/nature04837] [Citation(s) in RCA: 560] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Accepted: 04/27/2006] [Indexed: 12/25/2022]
Abstract
Methylation of lysine and arginine residues on histone tails affects chromatin structure and gene transcription. Tri- and dimethylation of lysine 9 on histone H3 (H3K9me3/me2) is required for the binding of the repressive protein HP1 and is associated with heterochromatin formation and transcriptional repression in a variety of species. H3K9me3 has long been regarded as a 'permanent' epigenetic mark. In a search for proteins and complexes interacting with H3K9me3, we identified the protein GASC1 (gene amplified in squamous cell carcinoma 1), which belongs to the JMJD2 (jumonji domain containing 2) subfamily of the jumonji family, and is also known as JMJD2C. Here we show that three members of this subfamily of proteins demethylate H3K9me3/me2 in vitro through a hydroxylation reaction requiring iron and alpha-ketoglutarate as cofactors. Furthermore, we demonstrate that ectopic expression of GASC1 or other JMJD2 members markedly decreases H3K9me3/me2 levels, increases H3K9me1 levels, delocalizes HP1 and reduces heterochromatin in vivo. Previously, GASC1 was found to be amplified in several cell lines derived from oesophageal squamous carcinomas, and in agreement with a contribution of GASC1 to tumour development, inhibition of GASC1 expression decreases cell proliferation. Thus, in addition to identifying GASC1 as a histone trimethyl demethylase, we suggest a model for how this enzyme might be involved in cancer development, and propose it as a target for anti-cancer therapy.
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Affiliation(s)
- Paul A C Cloos
- Biotech Research & Innovation Centre, Fruebjergvej 3, 2100 Copenhagen, Denmark
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281
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Exploring the cupin-type metal-coordinating signature of acetylacetone dioxygenase Dke1 with site-directed mutagenesis: Catalytic reaction profile and Fe2+ binding stability of Glu-69→Gln mutant. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcatb.2006.01.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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282
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Basis for specificity in methane monooxygenase and related non-heme iron-containing biological oxidation catalysts. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcata.2006.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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283
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Bassan A, Blomberg MRA, Borowski T, Siegbahn PEM. Theoretical studies of enzyme mechanisms involving high-valent iron intermediates. J Inorg Biochem 2006; 100:727-43. [PMID: 16513176 DOI: 10.1016/j.jinorgbio.2006.01.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 01/12/2006] [Accepted: 01/16/2006] [Indexed: 01/21/2023]
Abstract
Recent theoretical contributions to the elucidation of mechanisms for iron containing enzymes are reviewed. The method used in most of these studies is hybrid density functional theory with the B3LYP functional. Three classes of enzymes are considered, the mononuclear non-heme enzymes, enzymes containing iron dimers, and heme-containing enzymes. Mechanisms for both dioxygen and substrate activations are discussed. The reactions usually go through two half-cycles, where a high-valent intermediate Fe(IV)O species is created in the first half-cycle, and the substrate reactions involving this intermediate occur in the second half-cycle. Similarities between the three classes of enzymes dominate, but significant differences also exist.
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Affiliation(s)
- Arianna Bassan
- Department of Physics, Stockholm University, AlbaNova University Center, Stockholm Center for Physics, Astronomy and Biotechnology, SE-106 91, Stockholm, Sweden
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284
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Clifton IJ, McDonough MA, Ehrismann D, Kershaw NJ, Granatino N, Schofield CJ. Structural studies on 2-oxoglutarate oxygenases and related double-stranded β-helix fold proteins. J Inorg Biochem 2006; 100:644-69. [PMID: 16513174 DOI: 10.1016/j.jinorgbio.2006.01.024] [Citation(s) in RCA: 335] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 01/12/2006] [Accepted: 01/12/2006] [Indexed: 01/09/2023]
Abstract
Mononuclear non-heme ferrous iron dependent oxygenases and oxidases constitute an extended enzyme family that catalyze a wide range of oxidation reactions. The largest known sub-group employs 2-oxoglutarate as a cosubstrate and catalysis by these and closely related enzymes is proposed to proceed via a ferryl intermediate coordinated to the active site via a conserved HXD/E...H motif. Crystallographic studies on the 2-oxoglutarate oxygenases and related enzymes have revealed a common double-stranded beta-helix core fold that supports the residues coordinating the iron. This fold is common to proteins of the cupin and the JmjC transcription factor families. The crystallographic studies on 2-oxoglutarate oxygenases and closely related enzymes are reviewed and compared with other metallo-enzymes/related proteins containing a double-stranded beta-helix fold. Proposals regarding the suitability of the active sites and folds of the 2-oxoglutarate oxygenases to catalyze reactions involving reactive oxidizing species are described.
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Affiliation(s)
- Ian J Clifton
- The Oxford Centre for Molecular Sciences and the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, Oxon OX1 3TA, UK
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285
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Decker A, Clay MD, Solomon EI. Spectroscopy and electronic structures of mono- and binuclear high-valent non-heme iron-oxo systems. J Inorg Biochem 2006; 100:697-706. [PMID: 16510189 DOI: 10.1016/j.jinorgbio.2006.01.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 01/04/2006] [Indexed: 10/25/2022]
Abstract
High-valent iron-oxo intermediates are known or believed to be key oxidizing species in the catalytic mechanisms of many mononuclear and binuclear non-heme iron enzymes. So far only limited experimental data on their electronic structures are available. In this study we extend knowledge from the experimentally well characterized mononuclear Fe(IV)=O (S=1) biomimetic model system to computational insight into the spectroscopy and electronic structures of mono-and binuclear high-valent iron-oxo enzyme intermediates. In the mononuclear Fe(IV)=O complexes, we predict the spectroscopy and energies of the electronic transitions to be very different for the S=1 and S=2 spin states, but the iron-oxo bonding for both spin states to be very similar. A comparison of the S=2 mono- and binuclear high-valent iron-sites predicts similar electronic transitions. However, the bent iron-oxo bridge and interactions with the second iron-center in the dimer shift the transitions to higher energies and splits the d(xz/yz) orbital set. These electronic structure and TD-DFT results provide a basis for understanding the spectroscopy and electronic structures of high-valent intermediates in mono- and binuclear non-heme iron enzymes.
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Affiliation(s)
- Andrea Decker
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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286
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Oster LM, Lester DR, Terwisscha van Scheltinga A, Svenda M, van Lun M, Généreux C, Andersson I. Insights into cephamycin biosynthesis: the crystal structure of CmcI from Streptomyces clavuligerus. J Mol Biol 2006; 358:546-58. [PMID: 16527306 DOI: 10.1016/j.jmb.2006.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 01/27/2006] [Accepted: 02/02/2006] [Indexed: 10/25/2022]
Abstract
Cephamycin C-producing microorganisms use two enzymes to convert cephalosporins to their 7alpha-methoxy derivatives. Here we report the X-ray structure of one of these enzymes, CmcI, from Streptomyces clavuligerus. The polypeptide chain of the enzyme folds into a C-terminal Rossmann domain and a smaller N-terminal domain, and the molecule packs as a hexamer in the crystal. The Rossmann domain binds S-adenosyl-L-methionine (SAM) and the demethylated product, S-adenosyl-L-homocysteine, in a fashion similar to the common binding mode of this cofactor in SAM-dependent methyltransferases. There is a magnesium-binding site in the vicinity of the SAM site with a bound magnesium ion ligated by residues Asp160, Glu186 and Asp187. The expected cephalosporin binding site near the magnesium ion is occupied by polyethyleneglycol (PEG) from the crystallisation medium. The geometry of the SAM and the magnesium binding sites is similar to that found in cathechol O-methyltransferase. The results suggest CmcI is a methyltransferase, and its most likely function is to catalyse the transfer of a methyl group from SAM to the 7alpha-hydroxy cephalosporin in the second catalytic reaction of cephamycin formation. Based on the docking of the putative substrate, 7alpha-hydroxy-O-carbamoyldeacetylcephalosporin C, to the structure of the ternary CmcI-Mg2+-SAM complex, we propose a model for substrate binding and catalysis. In this model, the 7-hydroxy group of the beta-lactam ring ligates the Mg2+ with its alpha-side facing the methyl group of SAM at a distance that would allow methylation of the hydroxyl-group.
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Affiliation(s)
- Linda M Oster
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, S-751 24 Uppsala, Sweden
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287
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Rådmark O, Samuelsson B. Regulation of 5-lipoxygenase enzyme activity. Biochem Biophys Res Commun 2005; 338:102-10. [PMID: 16122704 DOI: 10.1016/j.bbrc.2005.08.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 08/04/2005] [Indexed: 11/27/2022]
Abstract
In this article, regulation of human 5-lipoxygenase enzyme activity is reviewed. First, structural properties and enzyme activities are described. This is followed by the activating factors: Ca2+, membranes, ATP, and lipid hydroperoxide. Also, studies on phosphorylation of 5-lipoxygenase and nuclear localization sequences are reviewed.
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Affiliation(s)
- Olof Rådmark
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, S-17177 Stockholm, Sweden.
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288
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Koehntop KD, Marimanikkuppam S, Ryle MJ, Hausinger RP, Que L. Self-hydroxylation of taurine/alpha-ketoglutarate dioxygenase: evidence for more than one oxygen activation mechanism. J Biol Inorg Chem 2005; 11:63-72. [PMID: 16320009 DOI: 10.1007/s00775-005-0059-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Accepted: 10/13/2005] [Indexed: 10/25/2022]
Abstract
2-Aminoethanesulfonic acid (taurine)/alpha-ketoglutarate (alphaKG) dioxygenase (TauD) is a mononuclear non-heme iron enzyme that catalyzes the hydroxylation of taurine to generate sulfite and aminoacetaldehyde in the presence of O2, alphaKG, and Fe(II). Fe(II)TauD complexed with alphaKG or succinate, the decarboxylated product of alphaKG, reacts with O2 in the absence of prime substrate to generate 550- and 720-nm chromophores, respectively, that are interconvertible by the addition or removal of bound bicarbonate and have resonance Raman features characteristic of an Fe(III)-catecholate complex. Mutagenesis studies suggest that both reactions result in the self-hydroxylation of the active-site residue Tyr73, and liquid chromatography nano-spray mass spectrometry/mass spectrometry evidence corroborates this result for the succinate reaction. Furthermore, isotope-labeling resonance Raman studies demonstrate that the oxygen atom incorporated into the tyrosyl residue derives from H2 18O and 18O2 for the alphaKG and succinate reactions, respectively, suggesting distinct mechanistic pathways. Whereas the alphaKG-dependent hydroxylation likely proceeds via an Fe(IV) = O intermediate that is known to be generated during substrate hydroxylation, we propose Fe(III)-OOH (or Fe(V) = O) as the oxygenating species in the succinate-dependent reaction. These results demonstrate the two oxygenating mechanisms available to enzymes with a 2-His-1-carboxylate triad, depending on whether the electron source donates one or two electrons.
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Affiliation(s)
- Kevin D Koehntop
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455, USA
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289
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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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290
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Yan F, Li T, Lipscomb JD, Liu A, Liu HW. Site-directed mutagenesis and spectroscopic studies of the iron-binding site of (S)-2-hydroxypropylphosphonic acid epoxidase. Arch Biochem Biophys 2005; 442:82-91. [PMID: 16150418 DOI: 10.1016/j.abb.2005.07.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 07/28/2005] [Accepted: 07/29/2005] [Indexed: 11/17/2022]
Abstract
(S)-2-Hydroxylpropanylphosphonic acid epoxidase (HppE) is a novel type of mononuclear non-heme iron-dependent enzyme that catalyzes the O2 coupled, oxidative epoxide ring closure of HPP to form fosfomycin, which is a clinically useful antibiotic. Sequence alignment of the only two known HppE sequences led to the speculation that the conserved residues His138, Glu142, and His180 are the metal binding ligands of the Streptomyces wedmorensis enzyme. Substitution of these residues with alanine resulted in significant reduction of metal binding affinity, as indicated by EPR analysis of the enzyme-Fe(II)-substrate-nitrosyl complex and the spectral properties of the Cu(II)-reconstituted mutant proteins. The catalytic activities for both epoxidation and self-hydroxylation were also either eliminated or diminished in proportion to the iron content in these mutants. The complete loss of enzymatic activity for the E142A and H180A mutants in vivo and in vitro is consistent with the postulated roles of the altered residues in metal binding. The H138A mutant is also inactive in vivo, but in vitro it retains 27% of the active site iron and nearly 20% of the wild-type activity. Thus, it cannot be unequivocally stated whether H138 is an iron ligand or simply facilitates iron binding due to proximity. The results reported herein provide initial evidence implicating an unusual histidine/carboxylate iron ligation in HppE. By analogy with other well-characterized enzymes from the 2-His-1-carboxylate family, this type of iron core is consistent with a mechanism in which both oxygen and HPP bind to the iron as a first step in the in the conversion of HPP to fosfomycin.
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Affiliation(s)
- Feng Yan
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
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291
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Howard-Jones AR, Rutledge PJ, Clifton IJ, Adlington RM, Baldwin JE. Unique binding of a non-natural l,l,l-substrate by isopenicillin N synthase. Biochem Biophys Res Commun 2005; 336:702-8. [PMID: 16143309 DOI: 10.1016/j.bbrc.2005.08.155] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 08/08/2005] [Indexed: 11/26/2022]
Abstract
Isopenicillin N synthase (IPNS) is a non-haem iron oxidase that catalyses the formation of isopenicillin N from the tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. In this report, we describe the crystal structure of the enzyme with a non-natural L,L,L-tripeptide substrate, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-L-3,3,3,3',3',3'-hexafluorovaline. This structure reveals a strong binding interaction of the tripeptide within the active site and a unique conformation for the non-natural L,L,L-diastereomer. Taken together, these findings provide a possible rationale for the previously observed inhibitory effects of L,L,L-tripeptide substrates on IPNS activity.
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292
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Ferraro DJ, Gakhar L, Ramaswamy S. Rieske business: structure-function of Rieske non-heme oxygenases. Biochem Biophys Res Commun 2005; 338:175-90. [PMID: 16168954 DOI: 10.1016/j.bbrc.2005.08.222] [Citation(s) in RCA: 249] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2005] [Accepted: 08/30/2005] [Indexed: 11/20/2022]
Abstract
Rieske non-heme iron oxygenases (RO) catalyze stereo- and regiospecific reactions. Recently, an explosion of structural information on this class of enzymes has occurred in the literature. ROs are two/three component systems: a reductase component that obtains electrons from NAD(P)H, often a Rieske ferredoxin component that shuttles the electrons and an oxygenase component that performs catalysis. The oxygenase component structures have all shown to be of the alpha3 or alpha3beta3 types. The transfer of electrons happens from the Rieske center to the mononuclear iron of the neighboring subunit via a conserved aspartate, which is shown to be involved in gating electron transport. Molecular oxygen has been shown to bind side-on in naphthalene dioxygenase and a concerted mechanism of oxygen activation and hydroxylation of the ring has been proposed. The orientation of binding of the substrate to the enzyme is hypothesized to control the substrate selectivity and regio-specificity of product formation.
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Affiliation(s)
- Daniel J Ferraro
- Department of Biochemistry, University of Iowa Roy J. and Lucille A. Carver College of Medicine, 51 Newton Road, 4-403 BSB, Iowa City, IA 52242, USA
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293
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Vaillancourt FH, Yeh E, Vosburg DA, O'Connor SE, Walsh CT. Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis. Nature 2005; 436:1191-4. [PMID: 16121186 DOI: 10.1038/nature03797] [Citation(s) in RCA: 252] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 05/12/2005] [Indexed: 01/16/2023]
Abstract
Enzymatic incorporation of chlorine, bromine or iodine atoms occurs during the biosynthesis of more than 4,000 natural products. Halogenation can have significant consequences for the bioactivity of these products so there is great interest in understanding the biological catalysts that perform these reactions. Enzymes that halogenate unactivated aliphatic groups have not previously been characterized. Here we report the activity of five proteins-CmaA, CmaB, CmaC, CmaD and CmaE-in the construction of coronamic acid (CMA; 1-amino-1-carboxy-2-ethylcyclopropane), a constituent of the phytotoxin coronatine synthesized by the phytopathogenic bacterium Pseudomonas syringae. CMA derives from l-allo-isoleucine, which is covalently attached to CmaD through the actions of CmaA, a non-ribosomal peptide synthetase module, and CmaE, an unusual acyltransferase. We show that CmaB, a member of the non-haem Fe(2+), alpha-ketoglutarate-dependent enzyme superfamily, is the first of its class to show halogenase activity, chlorinating the gamma-position of l-allo-isoleucine. Another previously undescribed enzyme, CmaC, catalyses the formation of the cyclopropyl ring from the gamma-Cl-l-allo-isoleucine product of the CmaB reaction. Together, CmaB and CmaC execute gamma-halogenation followed by intramolecular gamma-elimination, in which biological chlorination is a cryptic strategy for cyclopropyl ring formation.
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Affiliation(s)
- Frédéric H Vaillancourt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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294
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Higgins LJ, Yan F, Liu P, Liu HW, Drennan CL. Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme. Nature 2005; 437:838-44. [PMID: 16015285 DOI: 10.1038/nature03924] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Accepted: 06/15/2005] [Indexed: 11/08/2022]
Abstract
The biosynthetic pathway of the clinically important antibiotic fosfomycin uses enzymes that catalyse reactions without precedent in biology. Among these is hydroxypropylphosphonic acid epoxidase, which represents a new subfamily of non-haem mononuclear iron enzymes. Here we present six X-ray structures of this enzyme: the apoenzyme at 2.0 A resolution; a native Fe(II)-bound form at 2.4 A resolution; a tris(hydroxymethyl)aminomethane-Co(II)-enzyme complex structure at 1.8 A resolution; a substrate-Co(II)-enzyme complex structure at 2.5 A resolution; and two substrate-Fe(II)-enzyme complexes at 2.1 and 2.3 A resolution. These structural data lead us to suggest how this enzyme is able to recognize and respond to its substrate with a conformational change that protects the radical-based intermediates formed during catalysis. Comparisons with other family members suggest why substrate binding is able to prime iron for dioxygen binding in the absence of alpha-ketoglutarate (a co-substrate required by many mononuclear iron enzymes), and how the unique epoxidation reaction of hydroxypropylphosphonic acid epoxidase may occur.
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Affiliation(s)
- Luke J Higgins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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295
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Okamoto H, Hammarberg T, Zhang YY, Persson B, Watanabe T, Samuelsson B, Rådmark O. Mutation analysis of the human 5-lipoxygenase C-terminus: support for a stabilizing C-terminal loop. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:123-31. [PMID: 15848143 DOI: 10.1016/j.bbapap.2005.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Revised: 03/09/2005] [Accepted: 03/09/2005] [Indexed: 10/25/2022]
Abstract
Lipoxygenases contain prosthetic iron, in human 5-lipoxygenase (5LO) the C-terminal isoleucine carboxylate constitutes one of five identified ligands. ATP is one of several factors determining 5LO activity. We compared properties of a series of 5LO C-terminal deletion mutants (one to six amino acid residues deleted). All mutants were enzymatically inactive (expected due to loss of iron), but expression yield (in E. coli) and affinity to ATP-agarose was markedly different. Deletion of up to four C-terminal residues was compatible with good expression and retained affinity to the ATP-column, as for wild-type 5LO. However when also the fifth residue was deleted (Asn-669) expression yield decreased and the affinity to ATP was markedly diminished. This was interpreted as a result of deranged structure and stability, due to loss of a hydrogen bond between Asn-669 and His-399. Mutagenesis of these residues supported this conclusion. In the structure of soybean lipoxygenase-1, a C-terminal loop was pointed out as important for correct orientation of the C-terminus. Accordingly, a hydrogen bond appears to stabilize such a C-terminal loop also in 5LO.
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Affiliation(s)
- Hisayo Okamoto
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry II, Karolinska Institutet, S-171 77 Stockholm, Sweden
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296
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Vaillancourt FH, Yin J, Walsh CT. SyrB2 in syringomycin E biosynthesis is a nonheme FeII alpha-ketoglutarate- and O2-dependent halogenase. Proc Natl Acad Sci U S A 2005; 102:10111-6. [PMID: 16002467 PMCID: PMC1177402 DOI: 10.1073/pnas.0504412102] [Citation(s) in RCA: 254] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The nine-residue lipodepsipeptide syringomycin E, elaborated as a phytotoxin by Pseudomonas syringae pv. syringae B301D contains a 4-Cl-L-Thr-9 moiety where failure to chlorinate results in a 3-fold drop in biological activity. The proteins SyrB1 and SyrB2 encoded by the biosynthetic cluster are shown to act as a substrate and enzyme pair for SyrB2-mediated chlorination of the aminoacyl-S-enzyme L-Thr-S-SyrB1. SyrB2 is a member of the nonheme Fe(II) alpha-ketoglutarate-dependent enzyme superfamily, and requires O2 and alpha-ketoglutarate as well as chloride ion to carry out monochlorination of the -CH3 group of L-Thr-S-SyrB1. Chlorination of L-Thr-S-SyrB1 was validated by thioesterase-mediated release of L-Thr and 4-Cl-L-Thr, N-derivatization as fluorescent isoindoles, and HPLC separation compared with authentic standards. Incubations with L-[14C]Thr and [36Cl-] as well as MS of the released products further validated identification. Enzymatic oxidative halogenation is a previously uncharacterized reaction type for nonheme Fe(II) enzymes and may be the general mode for biosynthetic halogenation of aliphatic carbons of natural products.
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Affiliation(s)
- Frédéric H Vaillancourt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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297
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Chakraborty S, Behrens M, Herman PL, Arendsen AF, Hagen WR, Carlson DL, Wang XZ, Weeks DP. A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: purification and characterization. Arch Biochem Biophys 2005; 437:20-8. [PMID: 15820213 DOI: 10.1016/j.abb.2005.02.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 02/16/2005] [Indexed: 10/25/2022]
Abstract
Dicamba O-demethylase is a multicomponent enzyme that catalyzes the conversion of the herbicide 2-methoxy-3,6-dichlorobenzoic acid (dicamba) to 3,6-dichlorosalicylic acid (DCSA). The three components of the enzyme were purified and characterized. Oxygenase(DIC) is a homotrimer (alpha)3 with a subunit molecular mass of approximately 40 kDa. FerredoxinDIC and reductaseDIC are monomers with molecular weights of approximately 14 and 45 kDa, respectively. EPR spectroscopic analysis suggested the presence of a single [2Fe-2S](2+/1+) cluster in ferredoxinDIC and a single Rieske [2Fe-2S](2+; 1+) cluster within oxygenaseDIC. Consistent with the presence of a Rieske iron-sulfur cluster, oxygenaseDIC displayed a high reduction potential of E(m,7.0) = -21 mV whereas ferredoxinDIC exhibited a reduction potential of approximately E(m,7.0) = -171 mV. Optimal oxygenaseDIC activity in vitro depended on the addition of Fe2+. The identification of formaldehyde and DCSA as reaction products demonstrated that dicamba O-demethylase acts as a monooxygenase. Taken together, these data suggest that oxygenaseDIC is an important new member of the Rieske non-heme iron family of oxygenases.
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Affiliation(s)
- Sarbani Chakraborty
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0664, USA
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298
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Poliakov E, Gentleman S, Cunningham FX, Miller-Ihli NJ, Redmond TM. Key role of conserved histidines in recombinant mouse beta-carotene 15,15'-monooxygenase-1 activity. J Biol Chem 2005; 280:29217-23. [PMID: 15951442 DOI: 10.1074/jbc.m500409200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alignment of sequences of vertebrate beta-carotene 15,15'-monooxygenase-1 (BCMO1) and related oxygenases revealed four perfectly conserved histidines and five acidic residues (His172, His237, His308, His514, Asp52, Glu140, Glu314, Glu405, and Glu457 in mouse BCMO1). Because BCMO1 activity is iron-dependent, we propose that these residues participate in iron coordination and therefore are essential for catalytic activity. To test this hypothesis, we produced mutant forms of mouse BCMO1 by replacing the conserved histidines and acidic residues as well as four histidines and one glutamate non-conserved in the overall family with alanines by site-directed mutagenesis. Our in vitro and in vivo data showed that mutation of any of the four conserved histidines and Glu405 caused total loss of activity. However, mutations of non-conserved histidines or any of the other conserved acidic residues produced impaired although enzymatically active proteins, with a decrease in activity mostly due to changes in V(max). The iron bound to protein was determined by inductively coupled plasma atomic emission spectrometry. Bound iron was much lower in preparations of inactive mutants than in the wild-type protein. Therefore, the conserved histidines and Glu405 are absolutely required for the catalytic mechanism of BCMO1. Because the mutant proteins are impaired in iron binding, these residues are concluded to coordinate iron required for catalytic activity. These data are discussed in the context of the predicted structure for the related eubacterial apocarotenal oxygenase.
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Affiliation(s)
- Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, NEI, National Institutes of Health, Bethesda, MD 20892-0706, USA
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299
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Karlsson A, Parales JV, Parales RE, Gibson DT, Eklund H, Ramaswamy S. NO binding to naphthalene dioxygenase. J Biol Inorg Chem 2005; 10:483-9. [PMID: 15942729 DOI: 10.1007/s00775-005-0657-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Accepted: 04/26/2005] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) is commonly used as an analogue for dioxygen in structural and spectroscopic studies of oxygen binding and oxygen activation. In this study, crystallographic structures of naphthalene dioxygenase (NDO) in complex with nitric oxide are reported. In the presence of the aromatic substrate indole, NO is bound end-on to the active-site mononuclear iron of NDO. The structural observations correlate well with spectroscopic measurements of NO binding to NDO in solution. However, the end-on binding of NO is in contrast to the recently reported structure of oxygen to the active-site iron of NDO that binds side-on. While NO is a good oxygen analogue with many similarities to O(2), the different binding mode of NO to the active-site iron atom leads to different mechanistic implications. Hence, caution needs to be used in extrapolating NO as an analogue to O(2) binding.
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Affiliation(s)
- Andreas Karlsson
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, 75124 Uppsala, Sweden
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Veldhuizen E, Vaillancourt F, Whiting C, Hsiao MY, Gingras G, Xiao Y, Tanguay R, Boukouvalas J, Eltis L. Steady-state kinetics and inhibition of anaerobically purified human homogentisate 1,2-dioxygenase. Biochem J 2005; 386:305-14. [PMID: 15479158 PMCID: PMC1134795 DOI: 10.1042/bj20041370] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 09/22/2004] [Accepted: 10/13/2004] [Indexed: 11/17/2022]
Abstract
HGO (homogentisate 1,2-dioxygenase; EC 1.13.11.5) catalyses the O2-dependent cleavage of HGA (homogentisate) to maleylacetoacetate in the catabolism of tyrosine. Anaerobic purification of heterologously expressed Fe(II)-containing human HGO yielded an enzyme preparation with a specific activity of 28.3+/- 0.6 micromol x min(-1) x mg(-1) (20 mM Mes, 80 mM NaCl, pH 6.2, 25 degrees C), which is almost twice that of the most active preparation described to date. Moreover, the addition of reducing agents or other additives did not increase the specific activity, in contrast with previous reports. The apparent specificity of HGO for HGA was highest at pH 6.2 and the steady-state cleavage of HGA fit a compulsory-order ternary-complex mechanism (K(m) value of 28.6+/-6.2 microM for HGA, K(m) value of 1240+/-160 microM for O2). Free HGO was subject to inactivation in the presence of O2 and during the steady-state cleavage of HGA. Both cases involved the oxidation of the active site Fe(II). 3-Cl HGA, a potential inhibitor of HGO, and its isosteric analogue, 3-Me HGO, were synthesized. At saturating substrate concentrations, HGO cleaved 3-Me and 3-Cl HGA 10 and 100 times slower than HGA respectively. The apparent specificity of HGO for HGA was approx. two orders of magnitude higher than for either 3-Me or 3-Cl HGA. Interestingly, 3-Cl HGA inactivated HGO only twice as rapidly as HGA. This contrasts with what has been observed in mechanistically related dioxygenases, which are rapidly inactivated by chlorinated substrate analogues, such as 3-hydroxyanthranilate dioxygenase by 4-Cl 3-hydroxyanthranilate.
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Key Words
- alkaptonuria
- dioxygenase
- enzymology
- homogentisate
- inhibition
- tyrosine catabolism
- c23o, catechol 2,3-dioxygenase
- dhb, 2,3-dihydroxybiphenyl
- dhbd, 2,3-dihydroxybiphenyl 1,2-dioxygenase
- dtt, dithiothreitol
- go, gentisate 1,2-dioxygenase
- had, 3-hydroxyanthranilate dioxygenase
- hga, homogentisate
- hgo, homogentisate 1,2-dioxygenase
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Affiliation(s)
- Edwin J. A. Veldhuizen
- *Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Blvd, Vancouver, BC, Canada V6T 1Z3
| | - Frédéric H. Vaillancourt
- †Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Cheryl J. Whiting
- *Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Blvd, Vancouver, BC, Canada V6T 1Z3
| | - Marvin M.-Y. Hsiao
- †Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Geneviève Gingras
- ‡Department of Chemistry, Université Laval, Quebec City, QC, Canada G1K 7P4
| | - Yufang Xiao
- ‡Department of Chemistry, Université Laval, Quebec City, QC, Canada G1K 7P4
| | - Robert M. Tanguay
- §Laboratoire de Génétique Cellulaire et Développementale, Département de Médecine, Pavillon Marchand, Université Laval, Quebec City, QC, Canada G1K 7P4
| | - John Boukouvalas
- ‡Department of Chemistry, Université Laval, Quebec City, QC, Canada G1K 7P4
| | - Lindsay D. Eltis
- *Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Blvd, Vancouver, BC, Canada V6T 1Z3
- †Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
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