315 results on '"Ermler, Ulrich"'
Search Results
302. Reaction cycle of the dissimilatory sulfite reductase from Archaeoglobus fulgidus.
- Author
-
Parey K, Warkentin E, Kroneck PM, and Ermler U
- Subjects
- Catalytic Domain, Crystallography, X-Ray, Electrons, Structure-Activity Relationship, Substrate Specificity, Archaeal Proteins chemistry, Archaeoglobus fulgidus enzymology, Hydrogensulfite Reductase chemistry, Sulfites chemistry
- Abstract
A vital process in the biogeochemical sulfur cycle is the dissimilatory sulfate reduction pathway in which sulfate (SO₄⁻²) is converted to hydrogen sulfide (H₂S). Dissimilatory sulfite reductase (dSir), its key enzyme, hosts a unique siroheme-[4Fe-4S] cofactor and catalyzes the six-electron reduction of sulfite (SO₃²⁻) to H₂S. To explore this reaction, we determined the X-ray structures of dSir from the archaeon Archaeoglobus fulgidus in complex with sulfite, sulfide (S²⁻) carbon monoxide (CO), cyanide (CN⁻), nitrite (NO₂⁻), nitrate (NO₃⁻), and phosphate (PO₄³⁻). Activity measurements indicated that dSir of A. fulgidus reduces, besides sulfite and nitrite, thiosulfate (S₂O₃²⁻) and trithionate (S₃O₆²⁻) and produces the latter two compounds besides sulfide. On this basis, a three-step mechanism was proposed, each step consisting of a two-electron transfer, a two-proton uptake, and a dehydration event. In comparison, the related active site structures of the assimilatory sulfite reductase (aSir)- and dSir-SO₃²⁻complexes reveal different conformations of Argα170 and Lysα211 both interacting with the sulfite oxygens (its sulfur atom coordinates the siroheme iron), a sulfite rotation of ~60° relative to each other, and different access of solvent molecules to the sulfite oxygens from the active site cleft. Therefore, solely in dSir a further sulfite molecule can be placed in van der Waals contact with the siroheme-ligated sulfite or sulfur-oxygen intermediates necessary for forming thiosulfate and trithionate. Although reported for dSir from several sulfate-reducing bacteria, the in vivo relevance of their formation is questionable.
- Published
- 2010
- Full Text
- View/download PDF
303. The structure of cbb3 cytochrome oxidase provides insights into proton pumping.
- Author
-
Buschmann S, Warkentin E, Xie H, Langer JD, Ermler U, and Michel H
- Subjects
- Amino Acid Sequence, Catalytic Domain, Crystallography, X-Ray, Cytoplasm metabolism, Electron Transport, Heme chemistry, Histidine chemistry, Hydrogen Bonding, Models, Molecular, Molecular Sequence Data, Oxidation-Reduction, Oxygen metabolism, Periplasm metabolism, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Tyrosine chemistry, Electron Transport Complex IV chemistry, Electron Transport Complex IV metabolism, Proton Pumps chemistry, Proton Pumps metabolism, Protons, Pseudomonas stutzeri enzymology
- Abstract
The heme-copper oxidases (HCOs) accomplish the key event of aerobic respiration; they couple O2 reduction and transmembrane proton pumping. To gain new insights into the still enigmatic process, we structurally characterized a C-family HCO--essential for the pathogenicity of many bacteria--that differs from the two other HCO families, A and B, that have been structurally analyzed. The x-ray structure of the C-family cbb3 oxidase from Pseudomonas stutzeri at 3.2 angstrom resolution shows an electron supply system different from families A and B. Like family-B HCOs, C HCOs have only one pathway, which conducts protons via an alternative tyrosine-histidine cross-link. Structural differences around hemes b and b3 suggest a different redox-driven proton-pumping mechanism and provide clues to explain the higher activity of family-C HCOs at low oxygen concentrations.
- Published
- 2010
- Full Text
- View/download PDF
304. Structure at 1.5 A resolution of cytochrome c(552) with its flexible linker segment, a membrane-anchored protein from Paracoccus denitrificans.
- Author
-
Rajendran C, Ermler U, Ludwig B, and Michel H
- Subjects
- Amino Acid Sequence, Binding Sites, Cell Membrane metabolism, Crystallography, X-Ray, Cytochromes c metabolism, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Structure, Secondary, Protein Structure, Tertiary, Zinc chemistry, Zinc metabolism, Cell Membrane chemistry, Cytochromes c chemistry, Paracoccus denitrificans enzymology
- Abstract
Electron transfer (ET) between the large membrane-integral redox complexes in the terminal part of the respiratory chain is mediated either by a soluble c-type cytochrome, as in mitochondria, or by a membrane-anchored cytochrome c, as described for the ET chain of the bacterium Paracoccus denitrificans. Here, the structure of cytochrome c(552) from P. denitrificans with the linker segment that attaches the globular domain to the membrane anchor is presented. Cytochrome c(552) including the linker segment was crystallized and its structure was determined by molecular replacement. The structural features provide functionally important information. The prediction of the flexibility of the linker region [Berry & Trumpower (1985), J. Biol. Chem. 260, 2458-2467] was confirmed by our crystal structure. The N-terminal region from residues 13 to 31 is characterized by poor electron density, which is compatible with high mobility of this region. This result indicates that this region is highly flexible, which is functionally important for this protein to shuttle electrons between complexes III and IV in the respiratory chain. Zinc present in the crystallization buffer played a key role in the successful crystallization of this protein. It provided rigidity to the long negatively charged flexible loop by coordinating negatively charged residues from two different molecules and by enhancing the crystal contacts.
- Published
- 2010
- Full Text
- View/download PDF
305. The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration.
- Author
-
Marcia M, Ermler U, Peng G, and Michel H
- Subjects
- Flavin-Adenine Dinucleotide metabolism, Models, Molecular, Protein Conformation, Quinone Reductases chemistry, Substrate Specificity, Bacteria enzymology, Inactivation, Metabolic, Oxygen metabolism, Quinone Reductases metabolism, Sulfides metabolism
- Abstract
Sulfide:quinone oxidoreductase (SQR) is a flavoprotein with homologues in all domains of life except plants. It plays a physiological role both in sulfide detoxification and in energy transduction. We isolated the protein from native membranes of the hyperthermophilic bacterium Aquifex aeolicus, and we determined its X-ray structure in the "as-purified," substrate-bound, and inhibitor-bound forms at resolutions of 2.3, 2.0, and 2.9 A, respectively. The structure is composed of 2 Rossmann domains and 1 attachment domain, with an overall monomeric architecture typical of disulfide oxidoreductase flavoproteins. A. aeolicus SQR is a surprisingly trimeric, periplasmic integral monotopic membrane protein that inserts about 12 A into the lipidic bilayer through an amphipathic helix-turn-helix tripodal motif. The quinone is located in a channel that extends from the si side of the FAD to the membrane. The quinone ring is sandwiched between the conserved amino acids Phe-385 and Ile-346, and it is possibly protonated upon reduction via Glu-318 and/or neighboring water molecules. Sulfide polymerization occurs on the re side of FAD, where the invariant Cys-156 and Cys-347 appear to be covalently bound to polysulfur fragments. The structure suggests that FAD is covalently linked to the polypeptide in an unusual way, via a disulfide bridge between the 8-methyl group and Cys-124. The applicability of this disulfide bridge for transferring electrons from sulfide to FAD, 2 mechanisms for sulfide polymerization and channeling of the substrate, S(2-), and of the product, S(n), in and out of the active site are discussed.
- Published
- 2009
- Full Text
- View/download PDF
306. Carbon monoxide as intrinsic ligand to iron in the active site of [fe]-hydrogenase.
- Author
-
Shima S, Thauer RK, and Ermler U
- Abstract
Structural and spectroscopic studies on [Fe]-hydrogenase revealed an active site mononuclear low spin iron coordinated by the Cys176 sulfur, two CO, and the sp(2) hybridized nitrogen of a 2-pyridinol compound with back bonding properties similar to those of cyanide. Thus, [Fe]-hydrogenases are endowed with an iron-ligation pattern related to that found in the active site of [NiFe]- and [FeFe]-hydrogenases although the three hydrogenases and the enzymes involved in their posttranslational maturation have evolved independently and although CO and cyanide ligands are not found in any other metallo-enzymes. Obviously, low-spin iron complexed with thiolate(s), CO, and cyanide or a cyanide functional analogue plays an essential role in H(2) activation.
- Published
- 2009
- Full Text
- View/download PDF
307. The crystal structure of an [Fe]-hydrogenase-substrate complex reveals the framework for H2 activation.
- Author
-
Hiromoto T, Warkentin E, Moll J, Ermler U, and Shima S
- Subjects
- Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Binding, Protein Conformation, Pterins metabolism, Hydrogenase chemistry, Hydrogenase metabolism, Iron-Sulfur Proteins chemistry, Iron-Sulfur Proteins metabolism, Methanococcales enzymology, Pterins chemistry
- Published
- 2009
- Full Text
- View/download PDF
308. Structure of (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, the terminal enzyme of the non-mevalonate pathway.
- Author
-
Rekittke I, Wiesner J, Röhrich R, Demmer U, Warkentin E, Xu W, Troschke K, Hintz M, No JH, Duin EC, Oldfield E, Jomaa H, and Ermler U
- Subjects
- Amino Acid Sequence, Animals, Bacteria metabolism, Catalysis, Evolution, Molecular, Hemiterpenes chemistry, Models, Chemical, Molecular Conformation, Molecular Sequence Data, Organophosphorus Compounds chemistry, Plasmodium falciparum metabolism, Sequence Homology, Amino Acid, Terpenes chemistry, Mevalonic Acid metabolism, Oxidoreductases chemistry
- Abstract
Molecular evolution has evolved two metabolic routes for isoprenoid biosynthesis: the mevalonate and the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. The MEP pathway is used by most pathogenic bacteria and some parasitic protozoa (including the malaria parasite, Plasmodium falciparum) as well as by plants, but is not present in animals. The terminal reaction of the MEP pathway is catalyzed by (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) reductase (LytB), an enzyme that converts HMBPP into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Here, we present the structure of Aquifex aeolicus LytB, at 1.65 A resolution. The protein adopts a cloverleaf or trefoil-like structure with each monomer in the dimer containing three alpha/beta domains surrounding a central [Fe3S4] cluster ligated to Cys13, Cys96, and Cys193. Two highly conserved His (His 42 and His 124) and a totally conserved Glu (Glu126) are located in the same central site and are proposed to be involved in ligand binding and catalysis. Substrate access is proposed to occur from the front-side face of the protein, with the HMBPP diphosphate binding to the two His and the 4OH of HMBPP binding to the fourth iron thought to be present in activated clusters, while Glu126 provides the protons required for IPP/DMAPP formation.
- Published
- 2008
- Full Text
- View/download PDF
309. Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O.
- Author
-
Seedorf H, Hagemeier CH, Shima S, Thauer RK, Warkentin E, and Ermler U
- Subjects
- Archaea enzymology, Catalysis, Flavin Mononucleotide metabolism, Flavoproteins metabolism, Models, Molecular, Oxidation-Reduction, Oxidoreductases metabolism, Protein Binding, Protein Conformation, Archaea metabolism, Flavoproteins chemistry, Oxidoreductases chemistry, Oxygen metabolism, Water metabolism
- Abstract
The di-iron flavoprotein F(420)H(2) oxidase found in methanogenic Archaea catalyzes the four-electron reduction of O(2) to 2H(2)O with 2 mol of reduced coenzyme F(420)(7,8-dimethyl-8-hydroxy-5-deazariboflavin). We report here on crystal structures of the homotetrameric F(420)H(2) oxidase from Methanothermobacter marburgensis at resolutions of 2.25 A, 2.25 A and 1.7 A, respectively, from which an active reduced state, an inactive oxidized state and an active oxidized state could be extracted. As found in structurally related A-type flavoproteins, the active site is formed at the dimer interface, where the di-iron center of one monomer is juxtaposed to FMN of the other. In the active reduced state [Fe(II)Fe(II)FMNH(2)], the two irons are surrounded by four histidines, one aspartate, one glutamate and one bridging aspartate. The so-called switch loop is in a closed conformation, thus preventing F(420) binding. In the inactive oxidized state [Fe(III)FMN], the iron nearest to FMN has moved to two remote binding sites, and the switch loop is changed to an open conformation. In the active oxidized state [Fe(III)Fe(III)FMN], both irons are positioned as in the reduced state but the switch loop is found in the open conformation as in the inactive oxidized state. It is proposed that the redox-dependent conformational change of the switch loop ensures alternate complete four-electron O(2) reduction and redox center re-reduction. On the basis of the known Si-Si stereospecific hydride transfer, F(420)H(2) was modeled into the solvent-accessible pocket in front of FMN. The inactive oxidized state might provide the molecular basis for enzyme inactivation by long-term O(2) exposure observed in some members of the FprA family.
- Published
- 2007
- Full Text
- View/download PDF
310. Towards biological supramolecular chemistry: a variety of pocket-templated, individual metal oxide cluster nucleations in the cavity of a mo/w-storage protein.
- Author
-
Schemberg J, Schneider K, Demmer U, Warkentin E, Müller A, and Ermler U
- Subjects
- Oxides, Protein Conformation, Protein Folding, Azotobacter vinelandii, Bacterial Proteins chemistry, Metalloproteins chemistry, Molybdenum chemistry, Tungsten chemistry
- Published
- 2007
- Full Text
- View/download PDF
311. Reaction mechanism of the iron-sulfur flavoenzyme adenosine-5'-phosphosulfate reductase based on the structural characterization of different enzymatic states.
- Author
-
Schiffer A, Fritz G, Kroneck PM, and Ermler U
- Subjects
- Adenosine Monophosphate chemistry, Adenosine Monophosphate metabolism, Adenosine Phosphosulfate metabolism, Binding Sites, Flavin-Adenine Dinucleotide chemistry, Flavin-Adenine Dinucleotide metabolism, Models, Molecular, Oxidation-Reduction, Protein Binding, Protein Structure, Secondary, Structure-Activity Relationship, Sulfites chemistry, Sulfites metabolism, Adenosine Phosphosulfate chemistry, Iron-Sulfur Proteins chemistry
- Abstract
The iron-sulfur flavoenzyme adenosine-5'-phosphosulfate (APS) reductase catalyzes a key reaction of the global sulfur cycle by reversibly transforming APS to sulfite and AMP. The structures of the dissimilatory enzyme from Archaeoglobus fulgidus in the reduced state (FAD(red)) and in the sulfite adduct state (FAD-sulfite-AMP) have been recently elucidated at 1.6 and 2.5 A resolution, respectively. Here we present new structural features of the enzyme trapped in four different catalytically relevant states that provide us with a detailed picture of its reaction cycle. In the oxidized state (FAD(ox)), the isoalloxazine moiety of the FAD cofactor exhibits a similarly bent conformation as observed in the structure of the reduced enzyme. In the APS-bound state (FAD(ox)-APS), the substrate APS is embedded into a 17 A long substrate channel in such a way that the isoalloxazine ring is pushed toward the channel bottom, thereby producing a compressed enzyme-substrate complex. A clamp formed by residues ArgA317 and LeuA278 to fix the adenine ring and the curved APS conformation appear to be key factors to hold APS in a strained conformation. This energy-rich state is relaxed during the attack of APS on the reduced FAD. A relaxed FAD-sulfite adduct is observed in the structure of the FAD-sulfite state. Finally, a FAD-sulfite-AMP1 state with AMP within van der Waals distance of the sulfite adduct could be characterized. This structure documents how adjacent negative charges are stabilized by the protein matrix which is crucial for forming APS from AMP and sulfite in the reverse reaction.
- Published
- 2006
- Full Text
- View/download PDF
312. X-ray structure of the gamma-subunit of a dissimilatory sulfite reductase: fixed and flexible C-terminal arms.
- Author
-
Mander GJ, Weiss MS, Hedderich R, Kahnt J, Ermler U, and Warkentin E
- Subjects
- Amino Acid Sequence, Archaeal Proteins genetics, Crystallography, X-Ray, Hydrogensulfite Reductase, Models, Molecular, Molecular Sequence Data, Oxidoreductases Acting on Sulfur Group Donors genetics, Protein Structure, Tertiary, Sequence Alignment, Archaeal Proteins chemistry, Archaeoglobus fulgidus enzymology, Oxidoreductases Acting on Sulfur Group Donors chemistry, Protein Subunits chemistry
- Abstract
The X-ray structure of the gamma-subunit of the dissimilatory sulfite reductase (DsrC) from Archaeoglobus fulgidus was determined at 1.12 and 2.1A resolution, in the two crystal forms named DsrC(nat) and DsrC(ox) the latter being cocrystallized with the oxidizing agent tert-butyl hydroperoxide. The fold corresponds to that of the homologous protein from Pyrobaculum aerophilum but is significantly more compact. The most interesting, highly conserved C-terminal arm adopts a well-defined conformation in A. fulgidus DsrC in contrast to the completely disordered conformation in P. aerophilum DsrC. The functional relevance of both conformations and of a potentially redox-active disulfide bond between the strictly invariant Cys103 and Cys114 are discussed.
- Published
- 2005
- Full Text
- View/download PDF
313. Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide containing bacterial luciferase family.
- Author
-
Aufhammer SW, Warkentin E, Ermler U, Hagemeier CH, Thauer RK, and Shima S
- Subjects
- Alcohol Oxidoreductases chemistry, Alcohol Oxidoreductases genetics, Alcohol Oxidoreductases metabolism, Amino Acid Sequence, Bacterial Proteins genetics, Bacterial Proteins metabolism, Binding Sites, Catalysis, Crystallography, X-Ray, Flavin Mononucleotide chemistry, Flavin Mononucleotide metabolism, Flavins, Luciferases genetics, Luciferases metabolism, Methanobacterium enzymology, Methanobacterium genetics, Methanobacterium metabolism, Models, Molecular, Molecular Sequence Data, Oxidoreductases Acting on CH-NH Group Donors genetics, Peptides genetics, Peptides metabolism, Proline chemistry, Proline genetics, Proline metabolism, Protein Binding, Protein Conformation, Riboflavin chemistry, Riboflavin metabolism, Sequence Homology, Amino Acid, Bacterial Proteins chemistry, Luciferases chemistry, Oxidoreductases Acting on CH-NH Group Donors chemistry, Oxidoreductases Acting on CH-NH Group Donors metabolism, Peptides chemistry, Riboflavin analogs & derivatives
- Abstract
Methylenetetratetrahydromethanopterin reductase (Mer) is involved in CO(2) reduction to methane in methanogenic archaea and catalyses the reversible reduction of methylenetetrahydromethanopterin (methylene-H(4)MPT) to methyl-H(4)MPT with coenzyme F(420)H(2), which is a reduced 5'-deazaflavin. Mer was recently established as a TIM barrel structure containing a nonprolyl cis-peptide bond but the binding site of the substrates remained elusive. We report here on the crystal structure of Mer in complex with F(420) at 2.6 A resolution. The isoalloxazine ring is present in a pronounced butterfly conformation, being induced from the Re-face of F(420) by a bulge that contains the non-prolyl cis-peptide bond. The bindingmode of F(420) is very similar to that in F(420)-dependent alcohol dehydrogenase Adf despite the low sequence identity of 21%. Moreover, binding of F(420) to the apoenzyme was only associated with minor conformational changes of the polypeptide chain. These findings allowed us to build an improved model of FMN into its binding site in bacterial luciferase, which belongs to the same structural family as Mer and Adf and also contains a nonprolyl cis-peptide bond in an equivalent position.
- Published
- 2005
- Full Text
- View/download PDF
314. The structure of F420-dependent methylenetetrahydromethanopterin dehydrogenase: a crystallographic 'superstructure' of the selenomethionine-labelled protein crystal structure.
- Author
-
Warkentin E, Hagemeier CH, Shima S, Thauer RK, and Ermler U
- Subjects
- Crystallography, X-Ray, Protein Conformation, Oxidoreductases Acting on CH-NH Group Donors chemistry, Selenomethionine chemistry
- Abstract
The diffraction pattern of native protein crystals of F(420)-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri shows weak additional reflections compared with the selenomethionine-labelled protein crystals, indicating a doubled c unit-cell parameter. These reflections indicate small reorientations of the hexameric structural units, breaking the translational symmetry. TLS refinement of the selenomethionine-labelled protein structure at 1.55 A resolution revealed an anisotropic rigid-body libration of the hexameric units. The anisotropy is consistent with the static reorientation in the native protein crystals. These results are discussed as related to the crystal packing. The relation between the two structures suggests an analogy to structural changes during certain kinds of phase transitions that have been well studied in inorganic structural chemistry.
- Published
- 2005
- Full Text
- View/download PDF
315. Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship.
- Author
-
Mamat B, Roth A, Grimm C, Ermler U, Tziatzios C, Schubert D, Thauer RK, and Shima S
- Subjects
- Crystallography, X-Ray, Environment, Hydroxymethyl and Formyl Transferases classification, Hydroxymethyl and Formyl Transferases genetics, Models, Molecular, Phylogeny, Protein Structure, Quaternary, Protein Subunits, Temperature, Ultracentrifugation, Archaeoglobus fulgidus enzymology, Euryarchaeota enzymology, Evolution, Molecular, Hydroxymethyl and Formyl Transferases chemistry, Hydroxymethyl and Formyl Transferases metabolism, Methanosarcina barkeri enzymology
- Abstract
Formyltransferase catalyzes the reversible formation of formylmethanofuran from N(5)-formyltetrahydromethanopterin and methanofuran, a reaction involved in the C1 metabolism of methanogenic and sulfate-reducing archaea. The crystal structure of the homotetrameric enzyme from Methanopyrus kandleri (growth temperature optimum 98 degrees C) has recently been solved at 1.65 A resolution. We report here the crystal structures of the formyltransferase from Methanosarcina barkeri (growth temperature optimum 37 degrees C) and from Archaeoglobus fulgidus (growth temperature optimum 83 degrees C) at 1.9 A and 2.0 A resolution, respectively. Comparison of the structures of the three enzymes revealed very similar folds. The most striking difference found was the negative surface charge, which was -32 for the M. kandleri enzyme, only -8 for the M. barkeri enzyme, and -11 for the A. fulgidus enzyme. The hydrophobic surface fraction was 50% for the M. kandleri enzyme, 56% for the M. barkeri enzyme, and 57% for the A. fulgidus enzyme. These differences most likely reflect the adaptation of the enzyme to different cytoplasmic concentrations of potassium cyclic 2,3-diphosphoglycerate, which are very high in M. kandleri (>1 M) and relatively low in M. barkeri and A. fulgidus. Formyltransferase is in a monomer/dimer/tetramer equilibrium that is dependent on the salt concentration. Only the dimers and tetramers are active, and only the tetramers are thermostable. The enzyme from M. kandleri is a tetramer, which is active and thermostable only at high concentrations of potassium phosphate (>1 M) or potassium cyclic 2,3-diphosphoglycerate. Conversely, the enzyme from M. barkeri and A. fulgidus already showed these properties, activity and stability, at much lower concentrations of these strong salting-out salts.
- Published
- 2002
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.