51
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Helmetag V, Samel SA, Thomas MG, Marahiel MA, Essen LO. Structural basis for the erythro-stereospecificity of the L-arginine oxygenase VioC in viomycin biosynthesis. FEBS J 2009; 276:3669-82. [PMID: 19490124 DOI: 10.1111/j.1742-4658.2009.07085.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nonheme iron oxygenase VioC from Streptomyces vinaceus catalyzes Fe(II)-dependent and alpha-ketoglutarate-dependent Cbeta-hydroxylation of L-arginine during the biosynthesis of the tuberactinomycin antibiotic viomycin. Crystal structures of VioC were determined in complexes with the cofactor Fe(II), the substrate L-arginine, the product (2S,3S)-hydroxyarginine and the coproduct succinate at 1.1-1.3 A resolution. The overall structure reveals a beta-helix core fold with two additional helical subdomains that are common to nonheme iron oxygenases of the clavaminic acid synthase-like superfamily. In contrast to other clavaminic acid synthase-like oxygenases, which catalyze the formation of threo diastereomers, VioC produces the erythro diastereomer of Cbeta-hydroxylated L-arginine. This unexpected stereospecificity is caused by conformational control of the bound substrate, which enforces a gauche(-) conformer for chi(1) instead of the trans conformers observed for the asparagine oxygenase AsnO and other members of the clavaminic acid synthase-like superfamily. Additionally, the substrate specificity of VioC was investigated. The side chain of the L-arginine substrate projects outwards from the active site by undergoing interactions mainly with the C-terminal helical subdomain. Accordingly, VioC exerts broadened substrate specificity by accepting the analogs L-homoarginine and L-canavanine for Cbeta-hydroxylation.
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Affiliation(s)
- Verena Helmetag
- Department of Chemistry, Philipps-University Marburg, Germany
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52
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Grove TL, Lee KH, St Clair J, Krebs C, Booker SJ. In vitro characterization of AtsB, a radical SAM formylglycine-generating enzyme that contains three [4Fe-4S] clusters. Biochemistry 2008; 47:7523-38. [PMID: 18558715 DOI: 10.1021/bi8004297] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sulfatases catalyze the cleavage of a variety of cellular sulfate esters via a novel mechanism that requires the action of a protein-derived formylglycine cofactor. Formation of the cofactor is catalyzed by an accessory protein and involves the two-electron oxidation of a specific cysteinyl or seryl residue on the relevant sulfatase. Although some sulfatases undergo maturation via mechanisms in which oxygen serves as an electron acceptor, AtsB, the maturase from Klebsiella pneumoniae, catalyzes the oxidation of Ser72 on AtsA, its cognate sulfatase, via an oxygen-independent mechanism. Moreover, it does not make use of pyridine or flavin nucleotide cofactors as direct electron acceptors. In fact, AtsB has been shown to be a member of the radical S-adenosylmethionine superfamily of proteins, suggesting that it catalyzes this oxidation via an intermediate 5'-deoxyadenosyl 5'-radical that is generated by a reductive cleavage of S-adenosyl- l-methionine. In contrast to AtsA, very little in vitro characterization of AtsB has been conducted. Herein we show that coexpression of the K. pneumoniae atsB gene with a plasmid that encodes genes that are known to be involved in iron-sulfur cluster biosynthesis yields soluble protein that can be characterized in vitro. The as-isolated protein contained 8.7 +/- 0.4 irons and 12.2 +/- 2.6 sulfides per polypeptide, which existed almost entirely in the [4Fe-4S] (2+) configuration, as determined by Mossbauer spectroscopy, suggesting that it contained at least two of these clusters per polypeptide. Reconstitution of the as-isolated protein with additional iron and sulfide indicated the presence of 12.3 +/- 0.2 irons and 9.9 +/- 0.4 sulfides per polypeptide. Subsequent characterization of the reconstituted protein by Mossbauer spectroscopy indicated the presence of only [4Fe-4S] clusters, suggesting that reconstituted AtsB contains three per polypeptide. Consistent with this stoichiometry, an as-isolated AtsB triple variant containing Cys --> Ala substitutions at each of the cysteines in its CX 3CX 2C radical SAM motif contained 7.3 +/- 0.1 irons and 7.2 +/- 0.2 sulfides per polypeptide while the reconstituted triple variant contained 7.7 +/- 0.1 irons and 8.4 +/- 0.4 sulfides per polypeptide, indicating that it was unable to incorporate an additional cluster. UV-visible and Mossbauer spectra of both samples indicated the presence of only [4Fe-4S] clusters. AtsB was capable of catalyzing multiple turnovers and exhibited a V max/[E T] of approximately 0.36 min (-1) for an 18-amino acid peptide substrate using dithionite to supply the requisite electron and a value of approximately 0.039 min (-1) for the same substrate using the physiologically relevant flavodoxin reducing system. Simultaneous quantification of formylglycine and 5'-deoxyadenosine as a function of time indicates an approximate 1:1 stoichiometry. Use of a peptide substrate in which the target serine is changed to cysteine also gives rise to turnover, supporting approximately 4-fold the activity of that observed with the natural substrate.
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Affiliation(s)
- Tyler L Grove
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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53
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Carlson BL, Ballister ER, Skordalakes E, King DS, Breidenbach MA, Gilmore SA, Berger JM, Bertozzi CR. Function and structure of a prokaryotic formylglycine-generating enzyme. J Biol Chem 2008; 283:20117-25. [PMID: 18390551 PMCID: PMC2459300 DOI: 10.1074/jbc.m800217200] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Type I sulfatases require an unusual co- or post-translational modification for their activity in hydrolyzing sulfate esters. In eukaryotic sulfatases, an active site cysteine residue is oxidized to the aldehyde-containing Cα-formylglycine residue by the formylglycine-generating enzyme (FGE). The machinery responsible for sulfatase activation is poorly understood in prokaryotes. Here we describe the identification of a prokaryotic FGE from Mycobacterium tuberculosis. In addition, we solved the crystal structure of the Streptomyces coelicolor FGE homolog to 2.1Å resolution. The prokaryotic homolog exhibits remarkable structural similarity to human FGE, including the position of catalytic cysteine residues. Both biochemical and structural data indicate the presence of an oxidized cysteine modification in the active site that may be relevant to catalysis. In addition, we generated a mutant M. tuberculosis strain lacking FGE. Although global sulfatase activity was reduced in the mutant, a significant amount of residual sulfatase activity suggests the presence of FGE-independent sulfatases in this organism.
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Affiliation(s)
- Brian L Carlson
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
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54
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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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55
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You Z, Omura S, Ikeda H, Cane DE, Jogl G. Crystal structure of the non-heme iron dioxygenase PtlH in pentalenolactone biosynthesis. J Biol Chem 2007; 282:36552-60. [PMID: 17942405 PMCID: PMC3010413 DOI: 10.1074/jbc.m706358200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The non-heme iron dioxygenase PtlH from the soil organism Streptomyces avermitilis is a member of the iron(II)/alpha-ketoglutarate-dependent dioxygenase superfamily and catalyzes an essential reaction in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. To investigate the structural basis for substrate recognition and catalysis, we have determined the x-ray crystal structure of PtlH in several complexes with the cofactors iron, alpha-ketoglutarate, and the non-reactive enantiomer of the substrate, ent-1-deoxypentalenic acid, in four different crystal forms to up to 1.31 A resolution. The overall structure of PtlH forms a double-stranded barrel helix fold, and the cofactor-binding site for iron and alpha-ketoglutarate is similar to other double-stranded barrel helix fold enzymes. Additional secondary structure elements that contribute to the substrate-binding site in PtlH are not conserved in other double-stranded barrel helix fold enzymes. Binding of the substrate enantiomer induces a reorganization of the monoclinic crystal lattice leading to a disorder-order transition of a C-terminal alpha-helix. The newly formed helix blocks the major access to the active site and effectively traps the bound substrate. Kinetic analysis of wild type and site-directed mutant proteins confirms a critical function of two arginine residues in substrate binding, while simulated docking of the enzymatic reaction product reveals the likely orientation of bound substrate.
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Affiliation(s)
- Zheng You
- Department of Chemistry, Brown University, Box H, Providence, RI 02912-9108, USA
| | - Satoshi Omura
- The Kitasato Institute, 9-1, Shirokane 5-chome, Minato-ku, Tokyo 108-8642, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1, Kitasato, Sagamihara, Kanagawa 228-8555, Japan
| | - David E. Cane
- Department of Chemistry, Brown University, Box H, Providence, RI 02912-9108, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G, Providence, RI 02912, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G, Providence, RI 02912, USA
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56
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Gadler P, Faber K. Highly Enantioselective Biohydrolysis ofsec-Alkyl Sulfate Esters with Inversion of Configuration Catalysed byPseudomonas spp. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700637] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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57
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Andreini C, Banci L, Bertini I, Elmi S, Rosato A. Non-heme iron through the three domains of life. Proteins 2007; 67:317-24. [PMID: 17286284 DOI: 10.1002/prot.21324] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Metalloproteins are proteins capable of binding one or more metal ions, which are often required for their biological function or for regulation of their activities or for structural purposes. In high-throughput genome-level protein investigation efforts, such as Structural Genomics, the systematic experimental characterization of metal-binding properties (i.e. the investigation of the metalloproteome) is not always pursued, and remains far from trivial. In the present work we have applied a bioinformatic approach to investigate the occurrence of (putative) non-heme iron-binding proteins in 57 different organisms spanning the entire tree of life. It is found that the non-heme iron-proteome constitutes between 1% and 10% of the entire proteome of an organism. However, the iron-proteome constitutes a higher fraction of the proteome in archaea (on average 7.1% +/- 2.1%) than in bacteria (3.9% +/- 1.6%) and in eukaryota (1.1% +/- 0.4%). The analysis of the function of each putative iron-protein identified suggests that extant organisms have inherited the large majority of their iron-proteome from the last common ancestor.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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58
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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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59
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Benjdia A, Dehò G, Rabot S, Berteau O. First evidences for a third sulfatase maturation system in prokaryotes fromE. coli aslBandydeMdeletion mutants. FEBS Lett 2007; 581:1009-14. [PMID: 17303125 DOI: 10.1016/j.febslet.2007.01.076] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 01/30/2007] [Accepted: 01/31/2007] [Indexed: 10/23/2022]
Abstract
To be active all known arylsulfatases undergo a unique post-translational modification leading to the conversion of an active site residue (serine or cysteine) into a C(alpha)-formylglycine. Although deprived of sulfatase activity, Escherichia coli K12 can efficiently mature heterologous Cys-type sulfatases. Three potential enzymes (AslB, YdeM and YidF) belonging to the anaerobic sulfatase maturating enzyme family (an SME) are present in its genome. Here we show that E. coli could mature Cys-type sulfatases only in aerobic conditions and that knocking-out of aslB, ydeM and yidF does not impair Cys-type sulfatase maturation. These findings demonstrate that these putative anSME are not involved in Cys-type sulfatase maturation and strongly support the existence of a second, oxygen-dependent and Cys-type specific sulfatase maturation system among prokaryotes.
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Affiliation(s)
- Alhosna Benjdia
- INRA, Unité d'Ecologie et Physiologie du Système Digestif, 78352 Jouy-en-Josas, France
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60
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Gadler P, Faber K. New enzymes for biotransformations: microbial alkyl sulfatases displaying stereo- and enantioselectivity. Trends Biotechnol 2007; 25:83-8. [PMID: 17150269 DOI: 10.1016/j.tibtech.2006.11.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 10/17/2006] [Accepted: 11/27/2006] [Indexed: 11/24/2022]
Abstract
The majority of hydrolytic enzymes used in white biotechnology for the production of non-natural compounds--such as carboxyl ester hydrolases, lipases and proteases--show a certain preference for a given enantiomer. However, they are unable to alter the stereochemistry of the substrate during catalysis with respect to inversion or retention of configuration. The latter can be achieved by (alkyl) sulfatases, which can be employed for the enantio-convergent transformation of racemic sulfate esters into a single stereoisomeric secondary alcohol, with a theoretical yield of 100%. This is a major improvement over traditional kinetic resolution processes, which yield both enantiomers, each at 50%.
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Affiliation(s)
- Petra Gadler
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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61
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de Visser SP. Can the peroxosuccinate complex in the catalytic cycle of taurine/α-ketoglutarate dioxygenase (TauD) act as an alternative oxidant? Chem Commun (Camb) 2007:171-3. [PMID: 17180236 DOI: 10.1039/b611273k] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional theoretical studies on the catalytic properties of the peroxosuccinate intermediate in the catalytic cycle of taurine/alpha-ketoglutarate dioxygenase suggest that it cannot act as a second oxidant.
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Affiliation(s)
- Sam P de Visser
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, 131 Princess Street, Manchester, M1 7DN, UK.
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62
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Müller TA, Zavodszky MI, Feig M, Kuhn LA, Hausinger RP. Structural basis for the enantiospecificities of R- and S-specific phenoxypropionate/alpha-ketoglutarate dioxygenases. Protein Sci 2006; 15:1356-68. [PMID: 16731970 PMCID: PMC2242530 DOI: 10.1110/ps.052059406] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
(R)- and (S)-dichlorprop/alpha-ketoglutarate dioxygenases (RdpA and SdpA) catalyze the oxidative cleavage of 2-(2,4-dichlorophenoxy)propanoic acid (dichlorprop) and 2-(4-chloro-2-methyl-phenoxy)propanoic acid (mecoprop) to form pyruvate plus the corresponding phenol concurrent with the conversion of alpha-ketoglutarate (alphaKG) to succinate plus CO2. RdpA and SdpA are strictly enantiospecific, converting only the (R) or the (S) enantiomer, respectively. Homology models were generated for both enzymes on the basis of the structure of the related enzyme TauD (PDB code 1OS7). Docking was used to predict the orientation of the appropriate mecoprop enantiomer in each protein, and the predictions were tested by characterizing the activities of site-directed variants of the enzymes. Mutant proteins that changed at residues predicted to interact with (R)- or (S)-mecoprop exhibited significantly reduced activity, often accompanied by increased Km values, consistent with roles for these residues in substrate binding. Four of the designed SdpA variants were (slightly) active with (R)-mecoprop. The results of the kinetic investigations are consistent with the identification of key interactions in the structural models and demonstrate that enantiospecificity is coordinated by the interactions of a number of residues in RdpA and SdpA. Most significantly, residues Phe171 in RdpA and Glu69 in SdpA apparently act by hindering the binding of the wrong enantiomer more than the correct one, as judged by the observed decreases in Km when these side chains are replaced by Ala.
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Affiliation(s)
- Tina A Müller
- Department of Microbiology, Michigan State University, East Lansing, Michigan 48824-4320, USA
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63
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Hagelueken G, Adams TM, Wiehlmann L, Widow U, Kolmar H, Tümmler B, Heinz DW, Schubert WD. The crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, defines a third class of sulfatases. Proc Natl Acad Sci U S A 2006; 103:7631-6. [PMID: 16684886 PMCID: PMC1472496 DOI: 10.1073/pnas.0510501103] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is both a ubiquitous environmental bacterium and an opportunistic human pathogen. A remarkable metabolic versatility allows it to occupy a multitude of ecological niches, including wastewater treatment plants and such hostile environments as the human respiratory tract. P. aeruginosa is able to degrade and metabolize biocidic SDS, the detergent of most commercial personal hygiene products. We identify SdsA1 of P. aeruginosa as a secreted SDS hydrolase that allows the bacterium to use primary sulfates such as SDS as a sole carbon or sulfur source. Homologues of SdsA1 are found in many pathogenic and some nonpathogenic bacteria. The crystal structure of SdsA1 reveals three distinct domains. The N-terminal catalytic domain with a binuclear Zn2+ cluster is a distinct member of the metallo-beta-lactamase fold family, the central dimerization domain ensures resistance to high concentrations of SDS, whereas the C-terminal domain provides a hydrophobic groove, presumably to recruit long aliphatic substrates. Crystal structures of apo-SdsA1 and complexes with substrate analog and products indicate an enzymatic mechanism involving a water molecule indirectly activated by the Zn2+ cluster. The enzyme SdsA1 thus represents a previously undescribed class of sulfatases that allows P. aeruginosa to survive and thrive under otherwise bacteriocidal conditions.
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Affiliation(s)
- Gregor Hagelueken
- *Division of Structural Biology, German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany
| | - Thorsten M. Adams
- Department of Molecular Genetics, Institute for Microbiology and Genetics, University of Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
- Klinische Forschergruppe OE 6711, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany; and
| | - Lutz Wiehlmann
- Klinische Forschergruppe OE 6711, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany; and
| | - Ute Widow
- *Division of Structural Biology, German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany
| | - Harald Kolmar
- Department of Molecular Genetics, Institute for Microbiology and Genetics, University of Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
- Clemens-Schoepf-Institute for Organic Chemistry and Biochemistry, Darmstadt University of Technology, Petersenstrasse 22, D-64287 Darmstadt, Germany
| | - Burkhard Tümmler
- Klinische Forschergruppe OE 6711, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany; and
| | - Dirk W. Heinz
- *Division of Structural Biology, German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany
| | - Wolf-Dieter Schubert
- *Division of Structural Biology, German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany
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64
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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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65
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Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF. Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature 2006; 439:879-84. [PMID: 16482161 DOI: 10.1038/nature04561] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Accepted: 01/05/2006] [Indexed: 11/08/2022]
Abstract
Nucleic acid damage by environmental and endogenous alkylation reagents creates lesions that are both mutagenic and cytotoxic, with the latter effect accounting for their widespread use in clinical cancer chemotherapy. Escherichia coli AlkB and the homologous human proteins ABH2 and ABH3 (refs 5, 7) promiscuously repair DNA and RNA bases damaged by S(N)2 alkylation reagents, which attach hydrocarbons to endocyclic ring nitrogen atoms (N1 of adenine and guanine and N3 of thymine and cytosine). Although the role of AlkB in DNA repair has long been established based on phenotypic studies, its exact biochemical activity was only elucidated recently after sequence profile analysis revealed it to be a member of the Fe-oxoglutarate-dependent dioxygenase superfamily. These enzymes use an Fe(II) cofactor and 2-oxoglutarate co-substrate to oxidize organic substrates. AlkB hydroxylates an alkylated nucleotide base to produce an unstable product that releases an aldehyde to regenerate the unmodified base. Here we have determined crystal structures of substrate and product complexes of E. coli AlkB at resolutions from 1.8 to 2.3 A. Whereas the Fe-2-oxoglutarate dioxygenase core matches that in other superfamily members, a unique subdomain holds a methylated trinucleotide substrate into the active site through contacts to the polynucleotide backbone. Amide hydrogen exchange studies and crystallographic analyses suggest that this substrate-binding 'lid' is conformationally flexible, which may enable docking of diverse alkylated nucleotide substrates in optimal catalytic geometry. Different crystal structures show open and closed states of a tunnel putatively gating O2 diffusion into the active site. Exposing crystals of the anaerobic Michaelis complex to air yields slow but substantial oxidation of 2-oxoglutarate that is inefficiently coupled to nucleotide oxidation. These observations suggest that protein dynamics modulate redox chemistry and that a hypothesized migration of the reactive oxy-ferryl ligand on the catalytic Fe ion may be impeded when the protein is constrained in the crystal lattice.
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Affiliation(s)
- Bomina Yu
- Department of Biological Sciences and Northeast Structural Genomics Consortium, 702A Fairchild Center, MC2434, Columbia University, New York, New York 10027, USA
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66
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Bollinger JM, Price JC, Hoffart LM, Barr EW, Krebs C. Mechanism of Taurine: α‐Ketoglutarate Dioxygenase (TauD) from
Escherichia coli. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200500476] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA, Fax: +1‐814‐863‐7024
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - John C. Price
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA, Fax: +1‐814‐863‐7024
| | - Lee M. Hoffart
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA, Fax: +1‐814‐863‐7024
| | - Eric W. Barr
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA, Fax: +1‐814‐863‐7024
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA, Fax: +1‐814‐863‐7024
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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67
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Abu-Omar MM, Loaiza A, Hontzeas N. Reaction mechanisms of mononuclear non-heme iron oxygenases. Chem Rev 2005; 105:2227-52. [PMID: 15941213 DOI: 10.1021/cr040653o] [Citation(s) in RCA: 447] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mahdi M Abu-Omar
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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Bitto E, Bingman CA, Allard STM, Wesenberg GE, Aceti DJ, Wrobel RL, Frederick RO, Sreenath H, Vojtik FC, Jeon WB, Newman CS, Primm J, Sussman MR, Fox BG, Markley JL, Phillips GN. The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:469-72. [PMID: 16511070 PMCID: PMC1952295 DOI: 10.1107/s1744309105011565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 04/13/2005] [Indexed: 11/10/2022]
Abstract
The crystal structure of the gene product of At3g21360 from Arabidopsis thaliana was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 19.3% (Rfree = 24.1%) at 2.4 A resolution. The crystal structure includes two monomers in the asymmetric unit that differ in the conformation of a flexible domain that spans residues 178-230. The crystal structure confirmed that At3g21360 encodes a protein belonging to the clavaminate synthase-like superfamily of iron(II) and 2-oxoglutarate-dependent enzymes. The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily.
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Affiliation(s)
- Eduard Bitto
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Craig A. Bingman
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Simon T. M. Allard
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Gary E. Wesenberg
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - David J. Aceti
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Russell L. Wrobel
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Ronnie O. Frederick
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Hassan Sreenath
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Frank C. Vojtik
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Won Bae Jeon
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Craig S. Newman
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - John Primm
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Michael R. Sussman
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - Brian G. Fox
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - John L. Markley
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
| | - George N. Phillips
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
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69
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Müller I, Stückl C, Wakeley J, Kertesz M, Usón I. Succinate Complex Crystal Structures of the α-Ketoglutarate-dependent Dioxygenase AtsK. J Biol Chem 2005; 280:5716-23. [PMID: 15542595 DOI: 10.1074/jbc.m410840200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The alkylsulfatase AtsK from Pseudomonas putida S-313 is a member of the non-heme iron(II)-alpha-ketoglutarate-dependent dioxygenase superfamily. In the initial step of their catalytic cycle, enzymes belonging to this widespread and versatile family coordinate molecular oxygen to the iron center in the active site. The subsequent decarboxylation of the cosubstrate alpha-ketoglutarate yields carbon dioxide, succinate, and a highly reactive ferryl (IV) species, which is required for substrate oxidation via a complex mechanism involving the transfer of radical species. Non-productive activation of oxygen may lead to harmful side reactions; therefore, such enzymes need an effective built-in protection mechanism. One of the ways of controlling undesired side reactions is the self-hydroxylation of an aromatic side chain, which leads to an irreversibly inactivated species. Here we describe the crystal structure of the alkylsulfatase AtsK in complexes with succinate and with Fe(II)/succinate. In the crystal structure of the AtsK-Fe(II)-succinate complex, the side chain of Tyr(168) is co-ordinated to the iron, suggesting that Tyr(168) is the target of enzyme self-hydroxylation. This is the first structural study of an Fe(II)-alpha-ketoglutarate-dependent dioxygenase that presents an aromatic side chain coordinated to the metal center, thus allowing structural insight into this protective mechanism of enzyme self-inactivation.
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Affiliation(s)
- Ilka Müller
- Lehrstuhl für Strukturchemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
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