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The FEBS Journal

Cover image for Vol. 280 Issue 13

Special Issue: Catalytic Mechanisms by Biological Systems

July 2013

Volume 280, Issue 13

Pages i–iii, 2947–3177

  1. Front Cover

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Special Issue
    5. Author index
    6. Table of Contents
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      Front Cover (page i)

      Version of Record online: 18 JUN 2013 | DOI: 10.1111/j.1742-4658.2013.08784.x

      Thumbnail image of graphical abstract

      The picture is an artistic impression of the protease papain (representing one of the first crystal structures, solved in Groningen in 1968 by Jan Drenth et al.) containing a cysteinyl-linked flavin cofactor derivative (one of first artificial enzymes engineered by the Kaiser group in the 70's). This figure was provided by Special Issue coordinator M.W. Fraaije.

  2. Editorial Information

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Special Issue
    5. Author index
    6. Table of Contents
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      Editorial Information (pages ii–iii)

      Version of Record online: 18 JUN 2013 | DOI: 10.1111/j.1742-4658.2013.08784_1.x

  3. Special Issue

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Special Issue
    5. Author index
    6. Table of Contents
    1. You have free access to this content
      Special issue: Catalytic mechanisms by biological systems : Introduction (page 2947)

      Marco W. Fraaije and Nigel S. Scrutton

      Version of Record online: 3 JUN 2013 | DOI: 10.1111/febs.12317

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      Research on enzyme mechanisms is advancing knowledge of the chemistry and biochemistry of catalytic mechanisms by biological systems. The structural-dynamical properties of enzymes are of key importance. Advanced methodological approaches and new insights into enzyme functioning, and new emerging approaches for the redesign/design of enzymes or artificial biocatalysts, were discussed at the EMBO conference on Catalytic Mechanisms by Biological Systems.

    2. Review Articles

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      Computational design gains momentum in enzyme catalysis engineering (pages 2948–2960)

      Hein J. Wijma and Dick B. Janssen

      Version of Record online: 3 JUN 2013 | DOI: 10.1111/febs.12324

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      Computational protein design is becoming a powerful tool for tailoring enzymes for specific biotechnological applications. Compared to established protein engineering methods, computational design allows much larger jumps in sequence space. Recent advances in the computational design toolbox, which include new backbone redesign methods and the use of molecular dynamics simulations, will increase the possibilities for computational enzyme engineering.

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      To get what we aim for – progress in diversity generation methods (pages 2961–2978)

      Anna J. Ruff, Alexander Dennig and Ulrich Schwaneberg

      Version of Record online: 5 JUN 2013 | DOI: 10.1111/febs.12325

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      Methodological advancements and novel concepts of the three diversity generation strategies (I. Focused mutagenesis, II. Random mutagenesis, and III. Gene recombination) in directed enzyme evolution are summarized. Advancements are discussed in respect to the state of the art in diversity generation and high throughput screening capabilities as well as robustness and simplicity in use.

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      Reporter-based screening and selection of enzymes (pages 2979–2996)

      Teunke van Rossum, Servé W. M. Kengen and John van der Oost

      Version of Record online: 29 APR 2013 | DOI: 10.1111/febs.12281

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      The biotech industry is continuously seeking for new or improved biocatalysts. These efforts are, however, often hampered by the lack of an efficient high-throughput screening assay. This review discusses different in vivo screening and selection strategies, with as main focus reporter-based systems in which the activity of the reporter is controlled by the activity of the enzyme of interest.

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      Relating localized protein motions to the reaction coordinate in coenzyme B12-dependent enzymes (pages 2997–3008)

      Alex R. Jones, Colin Levy, Sam Hay and Nigel S. Scrutton

      Version of Record online: 21 MAR 2013 | DOI: 10.1111/febs.12223

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      Coenzyme B12-dependent enzymes have remarkable catalytic power and unique properties that enable detailed analysis of the reaction chemistry and associated protein dynamics. Here we discuss recent developments that are beginning to provide atomistic insight of how coenzyme B12-dependent enzymes steer reactants along the reaction coordinate. Such insight will ultimately generate ‘movies’ of the catalytic process across all relevant timescales.

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      The substrate oxidation mechanism of pyranose 2-oxidase and other related enzymes in the glucose–methanol–choline superfamily (pages 3009–3027)

      Thanyaporn Wongnate and Pimchai Chaiyen

      Version of Record online: 10 MAY 2013 | DOI: 10.1111/febs.12280

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      This review surveys recent discoveries about the reaction mechanisms of pyranose 2-oxidase and other members of the glucose-methanol-choline (GMC) oxidoreductase superfamily. These enzymes are flavoenzymes that catalyze the oxidation of alcohol moiety to aldehyde. Most current research finds that GMC enzymes use the hydride transfer mechanism, but the modes by which substrates are activated to facilitate the hydride transfer reaction appear to differ.

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      The chitinolytic machinery of Serratia marcescens – a model system for enzymatic degradation of recalcitrant polysaccharides (pages 3028–3049)

      Gustav Vaaje-Kolstad, Svein J. Horn, Morten Sørlie and Vincent G. H. Eijsink

      Version of Record online: 7 MAR 2013 | DOI: 10.1111/febs.12181

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      The chitinolytic machinery of Serratia marcescens is one of the best known enzyme systems for the conversion of insoluble polysaccharides. This machinery includes three chitinases, a lytic polysaccharide monooxygenases and an N-acetylhexosaminidase. In this review we discuss the catalytic mechanisms of these enzymes as well as the structural basis of each enzyme's specific role in the chitin-degradation process.

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      Adenosine-5′-phosphosulfate – a multifaceted modulator of bifunctional 3′-phospho-adenosine-5′-phosphosulfate synthases and related enzymes (pages 3050–3057)

      Jonathan W. Mueller and Naeem Shafqat

      Version of Record online: 17 APR 2013 | DOI: 10.1111/febs.12252

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      The activation of the stable oxyanion sulfate via the formation of the sulfonucleotides adenosine-5′-phosphosulfate (APS) and 3′-phospho-adenosine-5′-phosphosulfate (PAPS) is vital for sulfur metabolism. Here we review the various inhibitory, regulatory and stabilising effects of APS and related nucleotides on sulfate-activating enzymes. For bifunctional PAPS synthases of metazoans, APS can be regarded as a key modulator of function.

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      H2-driven cofactor regeneration with NAD(P)+-reducing hydrogenases (pages 3058–3068)

      Lars Lauterbach, Oliver Lenz and Kylie A. Vincent

      Version of Record online: 17 APR 2013 | DOI: 10.1111/febs.12245

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      Many industrially relevant enzymes depend upon expensive nicotinamide cofactors which must be recycled for enzyme applications to be economically viable. Here we review the state of development of H2-driven enzymatic cofactor regeneration which has 100% atom efficiency and uses H2 as a cheap reducing agent. We show the O2 tolerant NAD+-reducing hydrogenase from Ralstonia eutropha to be an attractive candidate.

    10. Hypothesis

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      The solution of nitrogen inversion in amidases (pages 3069–3083)

      Per-Olof Syrén

      Version of Record online: 12 APR 2013 | DOI: 10.1111/febs.12241

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      As discussed during the last decades, nitrogen inversion is required during enzyme catalyzed amide bond hydrolysis. Herein it is demonstrated that one general solution to the inversion problem is to stabilize the transition state of inversion by hydrogen bond formation, another is to introduce a concerted proton shuttle mechanism that avoids inversion and hence relieves the stereoelectronic penalties during catalysis.

    11. Original Articles

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      Use of ‘small but smart’ libraries to enhance the enantioselectivity of an esterase from Bacillus stearothermophilus towards tetrahydrofuran-3-yl acetate (pages 3084–3093)

      Alberto Nobili, Markus G. Gall, Ioannis V. Pavlidis, Mark L. Thompson, Marlen Schmidt and Uwe T. Bornscheuer

      Version of Record online: 14 FEB 2013 | DOI: 10.1111/febs.12137

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      A semi-rational approach was applied for the enhancement of the enantioselectivity of an esterase from Bacillus stearothermophilus towards the industrially interesting substrate tetrahydrofuran-3-yl acetate, based on data derived from structural alignment. The design of ‘small but smart’ libraries led to a 2.4-fold increase of (S)-selectivity compared to wild type enzyme, while some mutants with marginal (R)-selectivity were found.

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      Double site saturation mutagenesis of the human cytochrome P450 2D6 results in regioselective steroid hydroxylation (pages 3094–3108)

      Martina Geier, Andreas Braun, Patrik Fladischer, Piotr Stepniak, Florian Rudroff, Christian Hametner, Marko D. Mihovilovic and Anton Glieder

      Version of Record online: 3 MAY 2013 | DOI: 10.1111/febs.12270

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      400 cytochrome P450 2D6 (CYP2D6) variants representing all possible amino acid exchanges at two important enzyme's residues were expressed and individually analyzed to investigate their influence on regioselective steroid hydroxylation. Steroids represent a substrate class atypical for wildtype CYP2D6. Employing this strategy CYP2D6 variants with improved activity and variants with altered region-preference were identified and characterized.

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      Evaluation of the fluorescent probes Nile Red and 25-NBD-cholesterol as substrates for steroid-converting oxidoreductases using pure enzymes and microorganisms (pages 3109–3119)

      Yaroslav V. Faletrov, Nina S. Frolova, Hanna V. Hlushko, Elena V. Rudaya, Irina P. Edimecheva, Stephan Mauersberger and Vladimir M. Shkumatov

      Version of Record online: 29 APR 2013 | DOI: 10.1111/febs.12265

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      Docking simulations show that fluorescent substances Nile Red and 25-NBD-cholesterol fit well the substrate-binding sites of CYP17A1 and the cholesterol oxidase (CHOX), respectively. Recombinant yeasts, expressing CYP17A1, as well as pure CYP17A1 catalyze the Nile Red conversion into N-dealkylated derivatives. 25-NBD-cholesterol is converted into its 4-en-3-one derivative by the CHOX and cholesterol dehydrogenase as well as by bacteria Pseudomonas aeruginosa.

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      QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis (pages 3120–3131)

      Marc W. van der Kamp, Robin Chaudret and Adrian J. Mulholland

      Version of Record online: 27 FEB 2013 | DOI: 10.1111/febs.12158

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      Ketosteroid isomerase is a highly efficient enzyme involved in the formation of hormones such as testosterone. We show, using high-level QM/MM potential energy profiles and semi-empirical QM/MM dynamics simulations, that the catalytic cycle involves active site closure, desolvation of the catalytic base, isomerization and reopening of the active site. Closure of the active site is essential for efficient catalysis.

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      Evolutionary and mechanistic insights into substrate and product accommodation of CTP:phosphocholine cytidylyltransferase from Plasmodium falciparum (pages 3132–3148)

      Gergely N. Nagy, Lívia Marton, Balázs Krámos, Julianna Oláh, Ágnes Révész, Károly Vékey, Frédéric Delsuc, Éva Hunyadi-Gulyás, Katalin F. Medzihradszky, Marina Lavigne, Henri Vial, Rachel Cerdan and Beáta G. Vértessy

      Version of Record online: 24 MAY 2013 | DOI: 10.1111/febs.12282

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      CTP:phosphocholine cytidylyltransferase (CCT) is essential in lipid biosynthesis of Plasmodia, presenting a promising antimalarial target. We identified two independent gene duplication events of CCT within Apicomplexa and characterized a dimeric truncated construct of Plasmodium falciparum CCT. Catalytic mechanism of PfCCT may involve conformational changes affecting the choline subsite of the enzyme whereas Mg2+ cofactor is dispensable for CTP substrate binding.

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      The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 (pages 3149–3159)

      Khomaini Hasan, Artur Gora, Jan Brezovsky, Radka Chaloupkova, Hana Moskalikova, Andrea Fortova, Yuji Nagata, Jiri Damborsky and Zbynek Prokop

      Version of Record online: 8 APR 2013 | DOI: 10.1111/febs.12238

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      The newly-isolated haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 possesses a unique halide-stabilising tyrosine residue, Y109, in place of the conventional tryptophan. This is the first natural haloalkane dehalogenase that stabilises its substrate in the active site using only a single hydrogen bond, which is a new paradigm in catalysis by this enzyme family.

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      The isomerase and hydratase reaction mechanism of the crotonase active site of the multifunctional enzyme (type-1), as deduced from structures of complexes with 3S-hydroxy-acyl-CoA (pages 3160–3175)

      Prasad Kasaragod, Werner Schmitz, Jukka K. Hiltunen and Rik K. Wierenga

      Version of Record online: 15 FEB 2013 | DOI: 10.1111/febs.12150

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      Protein crystallographic studies of multifunctional enzyme, type-1 (MFE1) are reported. MFE1 catalyses two reactions of the β-oxidation pathway, being a hydratase active site (provided by the crotonase domain) and a dehydrogenase active site (provided by the HAD domain). The studies focus on the catalytic properties of the hydratase active site, elucidating the mode of binding of the hydrated product molecules.

  4. Author index

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Special Issue
    5. Author index
    6. Table of Contents
    1. You have free access to this content
      Author index (page 3176)

      Version of Record online: 18 JUN 2013 | DOI: 10.1111/j.1742-4658.2013.08783.x

  5. Table of Contents

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Special Issue
    5. Author index
    6. Table of Contents
    1. You have free access to this content
      Table of Contents (page 3177)

      Version of Record online: 18 JUN 2013 | DOI: 10.1111/febs.12381

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