Ulrich Ermler

Max Planck Institute of Biophysics, Frankfurt, Hesse, Germany

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Publications (114)656.48 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Isoprenoid biosynthesis in many bacteria, plant chloroplasts and parasitic protozoa but not in humans proceeds via the mevalonate independent 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. Its penultimate reaction step is catalyzed by (E)-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate (HMBPP) synthase (GcpE/IspG) which transforms 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate (MEcPP) to HMBPP. In this report we present the structure of GcpE of Thermus thermophiles in complex with its product HMBPP at a resolution of 1.65 Å. The GcpE-HMBPP like the GcpE-MEcPP structure is found in a closed, the ligand-free GcpE structure in an open enzyme state. Imposed by the rigid protein scaffold inside the active site funnel, linear HMBPP and circular MEcPP adopt highly similar conformations. The confined space also determines the conformational freedom of transition state intermediates and the design of anti-infective drugs. The apical Fe of the [4Fe-4S] cluster is coordinated to MEcPP in the GcpE-MEcPP complex and to a hydroxyl/water ligand but not to HMBPP in the GcpE-HMBPP complex. The GcpE-HMBPP structure can be attributed to one step in the currently proposed GcpE reaction cycle. Copyright © 2015 Elsevier Inc. All rights reserved.
    Biochemical and Biophysical Research Communications 02/2015; DOI:10.1016/j.bbrc.2015.01.088 · 2.28 Impact Factor
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    ABSTRACT: Nature developed a special protein that stores Mo as compact polyoxomolybdate (POM) clusters. The 1.35 Å X-ray structure revealed reliable electron density for two new POM cluster ensembles along the threefold axis. The protein template wraps the new POM clusters, thereby determines their complementary structure and suppresses their hydrolysis.
    Journal of Inorganic Biochemistry 09/2014; DOI:10.1016/j.jinorgbio.2014.05.009 · 3.27 Impact Factor
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics 07/2014; 1837:e83. DOI:10.1016/j.bbabio.2014.05.087 · 4.83 Impact Factor
  • Takashi Fujishiro, Ulrich Ermler, Seigo Shima
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    ABSTRACT: HcgD, a homolog of the ubiquitous Nif3-like protein family, is found in a gene cluster involved in the biosynthesis of the iron-guanylylpyridinol (FeGP) cofactor of [Fe]-hydrogenase. The presented crystal structure and biochemical analyses indicated that HcgD has a dinuclear iron-center, which provides a pronounced binding site for anionic ligands. HcgD contains a stronger and a weaker bound iron; the latter being removable by chelating reagents preferentially in the oxidized state. Therefore, we propose HcgD as an iron chaperon in FeGP cofactor biosynthesis, which might also stimulate investigations on the functionally unknown but physiologically important eukaryotic Nif3-like protein family members.
    FEBS Letters 06/2014; 588(17). DOI:10.1016/j.febslet.2014.05.059 · 3.34 Impact Factor
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    ABSTRACT: The reversible redox reaction between coenzyme F420 and H2 to F420H2 is catalyzed by a F420-reducing [NiFe]-hydrogenase (FrhABG) which is an enzyme of the energy metabolism of methanogenic archaea. FrhABG is a group 3 [NiFe]-hydrogenase with a dodecameric quaternary structure of 1.25 MDa as recently revealed by high resolution cryo electron microscopy. We report on the crystal structure of FrhABG from Methanothermobacter marburgensis at 1.7Å resolution and compare it with the structures of group 1 [NiFe]-hydrogenases, the only group structurally characterized yet. FrhA is similar to the large subunit of group 1 [NiFe]-hydrogenases regarding its core structure and the embedded [NiFe]-center but different because of the truncation of ca. 160 residues which results in similar but modified H2- and proton- transport pathways and in suitable interfaces for oligomerization. The small subunit FrhG is composed of a N-terminal domain related to group 1 enzymes and a new C-terminal ferredoxin-like domain carrying the distal and medial [4Fe-4S] clusters. FrhB adopts a novel fold, binds one [4Fe-4S] cluster as well as one FAD in a U-shaped conformation and provides the F420-binding site at the Si-face of the isoalloxazine ring. Similar electrochemical potentials of both catalytic reactions and the electron-transferring [4Fe-4S] clusters, determined to be E°' ≈ -400mV, are in full agreement with the equalized forward and backward rates of the FrhABG reaction. The protein might contribute to balanced redox potentials by the aspartate coordination of the proximal [4Fe-4S] cluster, the new ferredoxin module and a rather negatively charged FAD surrounding.
    Journal of Molecular Biology 05/2014; 426(15). DOI:10.1016/j.jmb.2014.05.024 · 3.96 Impact Factor
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    ABSTRACT: The cbb3 cytochrome c oxidases are distant members of the superfamily of heme copper oxidases. These terminal oxidases couple O2 reduction with proton transport across the plasma membrane and, as a part of the respiratory chain, contribute to the generation of an electrochemical proton gradient. Compared with other structurally characterized members of the heme copper oxidases, the recently determined cbb3 oxidase structure at 3.2 Å resolution revealed significant differences in the electron supply system, the proton conducting pathways and the coupling of O2 reduction to proton translocation. In this paper, we present a detailed report on the key steps for structure determination. Improvement of the protein quality was achieved by optimization of the number of lipids attached to the protein as well as the separation of two cbb3 oxidase isoenzymes. The exchange of n-dodecyl-β-d-maltoside for a precisely defined mixture of two α-maltosides and decanoylsucrose as well as the choice of the crystallization method had a most profound impact on crystal quality. This report highlights problems frequently encountered in membrane protein crystallization and offers meaningful approaches to improve crystal quality. © 2014 The Protein Society.
    Protein Science 04/2014; 23(4). DOI:10.1002/pro.2423 · 2.86 Impact Factor
  • Takashi Fujishiro, Ulrich Ermler, Seigo Shima
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    ABSTRACT: HcgD and HcgD bind by X-ray crystallography (View interaction)
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    ABSTRACT: Electron bifurcation is a fundamental strategy of energy coupling originally discovered in the Q-cycle of many organisms. Recently a flavin-based electron bifurcation has been detected in anaerobes, first in clostridia and later in acetogens and methanogens. It enables anaerobic bacteria and archaea to reduce the two [4Fe-4S] cluster-containing ferredoxin, an energy rich compound that is used to conduct difficult reductions as well as to increase the efficiency of substrate level and electron transport phosphorylations (SLP and ETP). Here we characterize the bifurcating electron transferring flavoprotein (EtfAf) and butyryl-CoA dehydrogenase (BcdAf) from Acidaminococcus fermentans which couple the exergonic reduction of crotonyl-CoA to butyryl-CoA to the endergonic reduction of ferredoxin both with NADH. EtfAf contains one FAD (α-FAD) in subunit α and a second FAD (β-FAD) in subunit β. The distance between the two isoalloxazine rings is 18 Angstrom. The EtfAf-NAD+ complex structure revealed β-FAD as acceptor of the hydride of NADH. The formed β-FADH- is considered as the bifurcating electron donor. Due to a conformational change, α-FAD is able to approach β-FADH- by ca. 5 Angstrom and take up one electron yielding a stable anionic semiquinone, α-FAD-, which due to a second conformational change donates this electron further to FAD of BcdAf. The remaining non-stabilized neutral semiquinone, β-FADH, immediately reduces ferredoxin. Repetition of this process affords a second reduced ferredoxin and FADH- of BcdAf that converts crotonyl-CoA to butyryl-CoA.
    Journal of Biological Chemistry 12/2013; 289(8). DOI:10.1074/jbc.M113.521013 · 4.60 Impact Factor
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    ABSTRACT: Ein Reaktionsschritt der Biosynthese des [Fe]‐Hydrogenase‐Cofaktors wurde von S. Shima et al. in ihrer Zuschrift auf S. 12787 ff. aufgeklärt. Mithilfe struktureller Genomik in Kombination mit Modellreaktionen und gründlicher Produktanalyse durch Röntgenkristallographie von Protein‐Produkt‐Komplexen wurde gefunden, dass HcgB das Enzym ist, das die Guanylylpyridinolbildung aus einem 2,4‐Dihydroxypyridinderivat und Guanosintriphosphat katalysiert.
    Angewandte Chemie 11/2013; 125(48). DOI:10.1002/ange.201308951
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    ABSTRACT: [Fe]-Hydrogenase requires the iron guanylylpyridinol (FeGP) cofactor for activity. The function of HcgB, an enzyme in the biosynthesis of the FeGP cofactor, was predicted by structural genomics and confirmed by model reactions and various analytical methods: HcgB catalyzes the terminal guanylyltransferase reaction for the formation of guanylylpyridinol. GMP=guanosine monophosphate.
    Angewandte Chemie International Edition 11/2013; 52(48):12555-8. DOI:10.1002/anie.201306745 · 11.34 Impact Factor
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    ABSTRACT: One reaction step of the biosynthesis of [Fe]‐hydrogenase‐cofactor is elucidated by S. Shima et al. in their Communication on page 12555 ff. A structural genomics approach, in combination with model reactions and thorough product analysis by X‐ray crystallography of the protein–product complexes, revealed that HcgB is the enzyme that catalyzes guanylylpyridinol formation from a 2,4‐dihydroxypyridine derivative and guanosine triphosphate.
    Angewandte Chemie International Edition 11/2013; 52(48). DOI:10.1002/anie.201308951 · 11.34 Impact Factor
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    ABSTRACT: Terpenoid precursor biosynthesis occurs in human and many pathogenic organisms via the mevalonate and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, respectively. We determined the X-ray structure of the Fe/S containing (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase (LytB) of the pathogenic protozoa Plasmodium falciparum which catalyzes the terminal step of the MEP pathway. The cloverleaf fold and the active site of P. falciparum LytB corresponds to those of the Aquifex aeolicus and Escherichia coli enzymes. Its distinct electron donor [2Fe-2S] ferredoxin was modeled to its binding site by docking calculations. The presented structural data provide a platform for a rational search of anti-malarian drugs.
    FEBS letters 11/2013; 587(24). DOI:10.1016/j.febslet.2013.10.029 · 3.54 Impact Factor
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    ABSTRACT: ATP sulfurylase (ATPS) catalyzes a key reaction in the global sulfur cycle by reversibly converting inorganic sulfate (SO4 (2-)) with ATP to adenosine 5'-phosphosulfate (APS) and pyrophosphate (PPi). In this work we report on the sat encoded dissimilatory ATP sulfurylase from the sulfur-oxidizing purple sulfur bacterium Allochromatium vinosum. In this organism, the sat gene is located in one operon and co-transcribed with the aprMBA genes for membrane-bound APS reductase. Like APS reductase, Sat is dispensible for growth on reduced sulfur compounds due to the presence of an alternate, so far unidentified sulfite-oxidizing pathway in A. vinosum. Sulfate assimilation also proceeds independently of Sat by a separate pathway involving a cysDN-encoded assimilatory ATP sulfurylase. We produced the purple bacterial sat-encoded ATP sulfurylase as a recombinant protein in E. coli, determined crucial kinetic parameters and obtained a crystal structure in an open state with a ligand-free active site. By comparison with several known structures of the ATPS-APS complex in the closed state a scenario about substrate-induced conformational changes was worked out. Despite different kinetic properties ATPS involved in sulfur-oxidizing and sulfate-reducing processes are not distinguishable on a structural level presumably due to the interference between functional and evolutionary processes.
    PLoS ONE 10/2013; 8(9):e74707. DOI:10.1371/journal.pone.0074707 · 3.53 Impact Factor
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    ABSTRACT: Heterodisulfide reductase (Hdr) is a key enzyme in the energy metabolism of methanogenic archaea. The enzyme catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) to the thiol coenzymes M (CoM-SH) and B (CoB-SH). Cleavage of CoM-S-S-CoB at an unusual FeS cluster reveals unique substrate chemistry. The cluster is fixed by cysteines of two cysteine-rich CCG domain sequence motifs (CX31-39CCX35-36CXXC) of subunit HdrB of the Methanothermobacter marburgensis HdrABC complex. We report on Q-band (34 GHz) (57)Fe electron-nuclear double resonance (ENDOR) spectroscopic measurements on the oxidized form of the cluster found in HdrABC and in two other CCG-domain-containing proteins, recombinant HdrB of Hdr from M. marburgensis and recombinant SdhE of succinate: quinone reductase from Sulfolobus solfataricus P2. The spectra at 34 GHz show clearly improved resolution arising from the absence of proton resonances and polarization effects. Systematic spectral simulations of 34 GHz data combined with previous 9 GHz data allowed the unambiguous assignment of four (57)Fe hyperfine couplings to the cluster in all three proteins. (13)C Mims ENDOR spectra of labelled CoM-SH were consistent with the attachment of the substrate to the cluster in HdrABC, whereas in the other two proteins no substrate is present. (57)Fe resonances in all three systems revealed unusually large (57)Fe ENDOR hyperfine splitting as compared to known systems. The results infer that the cluster's unique magnetic properties arise from the CCG binding motif.
    European Journal of Biochemistry 09/2013; DOI:10.1007/s00775-013-1037-x · 3.16 Impact Factor
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    ABSTRACT: Inhibition mechanism: Isocyanides strongly inhibit [Fe]-hydrogenase. X-ray crystallography and X-ray absorption spectroscopy revealed that the isocyanide binds to the trans position, versus the acyl carbon of the Fe center, and is covalently bound to the pyridinol hydroxy oxygen. These results also indicated that the hydroxy group is essential for H2 activation.
    Angewandte Chemie International Edition 07/2013; 52(37). DOI:10.1002/anie.201305089 · 11.34 Impact Factor
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    ABSTRACT: Autotrophic members of the Sulfolobales (crenarchaeota) use the 3-hydroxypropionate/4-hydroxybutyrate cycle to assimilate CO2 into cell material. The product of the initial acetyl-CoA carboxylation with CO2, malonyl-CoA, is further reduced to malonic semialdehyde by an NADPH-dependent malonyl-CoA reductase (MCR); the enzyme also catalyzes the reduction of succinyl-CoA to succinic semialdehyde onwards in the cycle. Here, we present the crystal structure of Sulfolobus tokodaii malonyl-CoA reductase in the substrate-free state and in complex with NADP+ and CoA. Structural analysis revealed an unexpected reaction cycle in which NADP+ and CoA successively occupy identical binding sites. Both coenzymes are pressed into a S-shaped, nearly superimposable structure imposed by a fixed and preformed binding site. The template-governed cofactor shaping implicates the same binding site for the 3- and 2- ribose phosphate group of CoA and NADP+, respectively, but a different one for the common ADP part: the β-phosphate of CoA aligns with the α-phosphate of NADP+. Evolution from an NADP+ to a bispecific NADP+ and CoA binding site involves many amino acid exchanges within a complex process by which constraints of the CoA structure also influence NADP+ binding. Based on the paralogous aspartate-semialdehyde dehydrogenase structurally characterized with a covalent Cys-aspartyl adduct, a malonyl/succinyl group can be reliably modelled into MCR and discussed regarding its binding mode, the malonyl/succinyl specificity, and the catalyzed reaction. The modified polypeptide surrounding around the absent ammonium group in malonate/succinate compared to aspartate provides the structural basis for engineering a methylmalonyl-CoA reductase applied for biotechnical polyester building block synthesis.
    Journal of Biological Chemistry 01/2013; 288(9). DOI:10.1074/jbc.M112.421263 · 4.60 Impact Factor
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    ABSTRACT: Sulfate-reducing bacteria and archaea are important players in the biogeochemical sulfur cycle. ATP sulfurylase, adenosine 5'-phosphosulfate reductase and dissimilatory sulfite reductase are the key enzymes in the energy conserving process of SO(4)(2-) → H(2)S reduction. This review summarizes recent advances in our understanding of the activation of sulfate to adenosine 5'-phosphosulfate, the following reductive cleavage to SO(3)(2-) and AMP, and the final six-electron reduction of SO(3)(2-) to H(2)S in the hyperthermophilic archaeon Archaeoglobus fulgidus. Structure based mechanisms will be discussed for these three enzymes which host unique metal centers at their catalytic sites.
    Metallomics 01/2013; DOI:10.1039/c2mt20225e · 4.10 Impact Factor
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    ABSTRACT: Flavohemoglobins (flavoHbs) serve various microorganisms as the major protective enzymes against NO(•) - mediated toxicity. FlavoHbs dominantly function as a NO• dioxygenase (O(2) +NO→ NO(3) (-) ) the required electron being shuttled from NAD(P)H via FAD to the heme iron. The X-ray structures of the flavoHb from Saccharomyces cerevisae presented in complex with an unknown small ligand (Yhb) and with econazole (Yhb(E) ) at 2.1 Å and 3.0 Å resolutions, respectively, reveal a high architectural accordance between prokaryotic and eukaryotic family members. The active site is characterized by a proximal heme side with a strictly conserved histidine, glutamate and tyrosine triad and a highly variable distal heme side with helix shifts up to 10 Å mainly dependent on the presence/absence and size of the bound ligand. In yeast flavoHb, the small heme iron ligand adjusts a catalytically productive active site geometry that reliably suggests the NO and O(2) binding site. O(2) is activated by its ligation to an electron-rich heme iron and a hydrogen bond to Tyr29 and Gln53. High active site similarities between eukaryotic Yhb and bacterial single-domain globins argue for identical biochemical reactions. Binding of the bulky econazole implies a large-scale induced-fit process concerning, in particular, an outwards shift of helices B and E to increase the active site pocket. Yeast Yhb and Ralstonia eutropha flavoHb both structurally studied in complex with econazole indicate conformational differences between both the inhibitors and the polypeptide primarily caused by stable binding of a phospholipid to the latter and by distinct loop D structures. © 2012 The Authors Journal compilation © 2012 FEBS.
    FEBS Journal 10/2012; DOI:10.1111/febs.12043 · 3.99 Impact Factor
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    ABSTRACT: Methenyltetrahydromethanopterin (methenyl-H(4)MPT(+)) cyclohydrolase (Mch) catalyzes the interconversion of methenyl-H(4)MPT(+) and formyl-H(4)MPT in the one-carbon energy metabolism of methanogenic, methanotrophic, and sulfate-reducing archaea and of methylotrophic bacteria. To understand the catalytic mechanism of this reaction, we kinetically characterized site-specific variants of Mch from Archaeoglobus fulgidus (aMch) and determined the X-ray structures of the substrate-free aMch(E186Q), the aMch:H(4)MPT complex, and the aMch(E186Q):formyl-H(4)MPT complex. (Formyl-)H(4)MPT is embedded inside a largely preformed, interdomain pocket of the homotrimeric enzyme with the pterin and benzyl rings being oriented nearly perpendicular to each other. The active site is primarily built up by the segment 93:95, Arg183 and Glu186 that either interact with the catalytic water attacking methenyl-H(4)MPT(+) or with the formyl oxygen of formyl-H(4)MPT. The catalytic function of the strictly conserved Arg183 and Glu186 was substantiated by the low enzymatic activities of the E186A, E186D, E186N, E186Q, R183A, R183Q, R183E, R183K, and R183E-E186Q variants. Glu186 most likely acts as a general base. Arg183 decisively influences the pK(a) value of Glu186 and the proposed catalytic water mainly by its positive charge. In addition, Glu186 appears to be also responsible for product specificity by donating a proton to the directly neighbored N(10) tertiary amine of H(4)MPT. Thus, N(10) becomes a better leaving group than N(5) which implies the generation of N(5)-formyl-H(4)MPT. For comparison, methenyltetrahydrofolate (H(4)F) cyclohydrolase produces N(10)-formyl-H(4)F in an analogous reaction. An enzymatic mechanism of Mch is postulated and compared with that of other cyclohydrolases.
    Biochemistry 09/2012; 51(42):8435-43. DOI:10.1021/bi300777k · 3.38 Impact Factor
  • Ingo Rekittke, Hassan Jomaa, Ulrich Ermler
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    ABSTRACT: Isoprenoid precursor biosynthesis occurs through the mevalonate or the methylerythritol phosphate (MEP) pathway, used i.e., by humans and by many human pathogens, respectively. In the MEP pathway, 2-C-methyl-d-erythritol-2,4-cyclo-diphosphate (MEcPP) is converted to (E)-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate (HMBPP) by the iron-sulfur cluster enzyme HMBPP synthase (GcpE). The presented X-ray structure of the GcpE-MEcPP complex from Thermus thermophilus at 1.55Å resolution provides valuable information about the catalytic mechanism and for rational inhibitor design. MEcPP binding inside the TIM-barrel funnel induces a 60° rotation of the [4Fe-4S] cluster containing domain onto the TIM-barrel entrance. The apical iron of the [4Fe-4S] cluster ligates with the C3 oxygen atom of MEcPP.
    FEBS letters 08/2012; 586(19):3452-7. DOI:10.1016/j.febslet.2012.07.070 · 3.54 Impact Factor

Publication Stats

4k Citations
656.48 Total Impact Points

Institutions

  • 1993–2014
    • Max Planck Institute of Biophysics
      • Department of Molecular Membrane Biology
      Frankfurt, Hesse, Germany
  • 2012
    • French National Centre for Scientific Research
      Lutetia Parisorum, Île-de-France, France
  • 2011
    • University of Freiburg
      • Institute of Biology I
      Freiburg, Lower Saxony, Germany
  • 2009–2011
    • Max Planck Institute for Terrestrial Microbiology
      Marburg, Hesse, Germany
  • 2006–2011
    • Universität Konstanz
      • Faculty of Sciences
      Constance, Baden-Württemberg, Germany
  • 2010
    • Goethe-Universität Frankfurt am Main
      Frankfurt, Hesse, Germany
  • 1997–2004
    • Philipps-Universität Marburg
      • Fachbereich Biologie
      Marburg an der Lahn, Hesse, Germany
  • 2001
    • Universität Regensburg
      • Lehrstuhl für Mikrobiologie
      Ratisbon, Bavaria, Germany