- Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology
Marie Christine Daniel
Molecular Nanosciences and Catalysis Group, LCOO, UMR CNRS No 5802, Universite Bordeaux I, 33405 Talence Cedex, France
Chem Rev 104:293-346. 2004
- Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
Cell 121:1005-16. 2005
..RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand...
- A general two-metal-ion mechanism for catalytic RNA
T A Steitz
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
Proc Natl Acad Sci U S A 90:6498-502. 1993
..The mechanism postulates that chemical catalysis is facilitated by two divalent metal ions 3...
- Industrial biocatalysis today and tomorrow
Institute of Biotechnology, , , Switzerland
Nature 409:258-68. 2001
..As the use of biocatalysis for industrial chemical synthesis becomes easier, several chemical companies have begun to increase significantly the number and sophistication of the biocatalytic processes used in their synthesis operations...
- Pd-Pt bimetallic nanodendrites with high activity for oxygen reduction
Department of Biomedical Engineering, Washington University, St Louis, MO 63130, USA
Science 324:1302-5. 2009
..The Pd-Pt nanodendrites were two and a half times more active on the basis of equivalent Pt mass for the ORR than the state-of-the-art Pt/C catalyst and five times more active than the first-generation supportless Pt-black catalyst...
- Ligand effects in homogeneous Au catalysis
David J Gorin
Department of Chemistry, University of California, Berkeley, California 94720, USA
Chem Rev 108:3351-78. 2008
- Single-atom catalysis of CO oxidation using Pt1/FeOx
State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
Nat Chem 3:634-41. 2011
- Allosteric regulation and catalysis emerge via a common route
Nina M Goodey
Montclair State University, Department of Chemistry and Biochemistry, 1 Normal Avenue, Montclair, New Jersey 07043, USA
Nat Chem Biol 4:474-82. 2008
..In this review, conformational mobility as the common route between allosteric regulation and catalysis is discussed...
- Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase
Seung Seo Lee
Department of Chemistry, University of Oxford, Oxford, United Kingdom
Nat Chem Biol 7:631-8. 2011
..Together, these comprehensive, quantitative data substantiate this unusual enzymatic reaction mechanism. Its discovery should prompt useful reassessment of many biocatalysts and their substrates and inhibitors...
- Programming biomolecular self-assembly pathways
Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA
Nature 451:318-22. 2008
- Crystal structure of a self-spliced group II intron
Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Bass Building, New Haven, CT 06511, USA
Science 320:77-82. 2008
..coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a ..
- Generating disulfides enzymatically: reaction products and electron acceptors of the endoplasmic reticulum thiol oxidase Ero1p
Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 103:299-304. 2006
..In particular, Ero1p can catalyze reduction of exogenous FAD in solution. Free FAD is not required for the catalysis of dithiol oxidation by Ero1p, but it is sufficient to drive disulfide bond formation under anaerobic conditions...
- SU5416 is a potent and selective inhibitor of the vascular endothelial growth factor receptor (Flk-1/KDR) that inhibits tyrosine kinase catalysis, tumor vascularization, and growth of multiple tumor types
T A Fong
SUGEN, Inc, South San Francisco, California 94080, USA
Cancer Res 59:99-106. 1999
..These findings support that pharmacological inhibition of the enzymatic activity of the vascular endothelial growth factor receptor represents a novel strategy for limiting the growth of a wide variety of tumor types...
- Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
Justin B Siegel
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
Science 329:309-13. 2010
..Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry...
- The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants
Max Planck Institut fur molekulare Physiologie, Abteilung Strukturelle Biologie, Rheinlanddamm 201, 44139 Dortmund, Germany
Science 277:333-8. 1997
..thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl ..
- Improving enzymes by using them in organic solvents
A M Klibanov
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Nature 409:241-6. 2001
..Enzyme-catalysed reactions in organic solvents, and even in supercritical fluids and the gas phase, have found numerous potential applications, some of which are already commercialized...
- The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation
Yuri A Nedialkov
Department of Biochemistry and Molecular Biology, Michigan State University, E Lansing, MI 48824 1319, USA
Biochim Biophys Acta 1829:187-98. 2013
The bridge α-helix in the β' subunit of RNA polymerase (RNAP) borders the active site and may have roles in catalysis and translocation...
- Gold and platinum catalysis--a convenient tool for generating molecular complexity
Max Planck Institut fur Kohlenforschung, D 45470 Mulheim Ruhr, Germany
Chem Soc Rev 38:3208-21. 2009
This critical review intends to familiarize the reader with the essence of pi-acid catalysis, in particular with reactions or reaction cascades effected by gold and platinum complexes...
- Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
S D Bruner
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Nature 403:859-66. 2000
..One known mutation, R154H, converts hOGG1 to a promutator by relaxing the specificity of the enzyme for the base opposite oxoG...
- Catalysis of guanine nucleotide exchange on Ran by the mitotic regulator RCC1
F R Bischoff
Deutsches Krebsforschungszentrum, Heidelberg, Germany
Nature 354:80-2. 1991
..Here we show that RCC1 specifically catalyses the exchange of guanine nucleotides on the Ran protein but not on the protein c-Ha-ras p21 (p21ras)...
- The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
Craig T Porter
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 32:D129-33. 2004
..The CSA will be updated on a monthly basis to include homologous sites found in new PDBs, and new hand-annotated enzymes as and when their annotation is completed...
- Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions
Matthew W Powner
School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
Nature 459:239-42. 2009
..For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps...
- Enhanced hydrogen evolution catalysis from chemically exfoliated metallic MoS2 nanosheets
Mark A Lukowski
Department of Chemistry, University of Wisconsin Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
J Am Chem Soc 135:10274-7. 2013
..Here we report dramatically enhanced HER catalysis (an electrocatalytic current density of 10 mA/cm(2) at a low overpotential of -187 mV vs RHE and a Tafel slope ..
- Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093 0506, USA
Biochemistry 35:12742-61. 1996
..turn), and GXK corresponds to a part of the HhH motif that is proposed to be critical for DNA binding and catalysis for both enzymes...
- Alanine racemase from Tolypocladium inflatum: a key PLP-dependent enzyme in cyclosporin biosynthesis and a model of catalytic promiscuity
Martino L di Salvo
Dipartimento di Scienze Biochimiche A Rossi Fanelli, Sapienza Universita di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
Arch Biochem Biophys 529:55-65. 2013
..A three-dimensional model of T. inflatum alanine racemase was constructed on the basis of threonine aldolase crystal structure. The model helped rationalise the experimental data and explain the catalytic properties of the enzymes...
- Immobilization of MP-11 into a mesoporous metal-organic framework, MP-11@mesoMOF: a new platform for enzymatic catalysis
Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, USA
J Am Chem Soc 133:10382-5. 2011
..for the first time been successfully immobilized into a mesoporous metal-organic framework (MOF) consisting of nanoscopic cages and it demonstrates superior enzymatic catalysis performances compared to its mesoporous silica counterpart.
- Dioxygen activation at mononuclear nonheme iron active sites: enzymes, models, and intermediates
Departament de Quimica, Universitat de Girona, 17071, Girona, Spain
Chem Rev 104:939-86. 2004
- Dynamic personalities of proteins
Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
Nature 450:964-72. 2007
..This requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail...
- Iridium N-heterocyclic carbene complexes as efficient catalysts for magnetization transfer from para-hydrogen
Michael J Cowley
Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
J Am Chem Soc 133:6134-7. 2011
..Deuterium labeling yields an additional 60% improvement in signal, an observation that offers insight into strategies for optimizing this approach...
- An artificial di-iron oxo-protein with phenol oxidase activity
Department of Chemistry, University Federico II of Napoli, Complesso Universitario Monte S Angelo, Italy
Nat Chem Biol 5:882-4. 2009
..Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site...
- Multiple translational products from a five-nucleotide ribozyme
Rebecca M Turk
Department of Molecular, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309 0347, USA
Proc Natl Acad Sci U S A 107:4585-9. 2010
..Small size and minimal requirements for regiospecific translational activity strongly support the hypothesis that minuscule RNA enzymes participated in early forms of translation...
- Design and evolution of new catalytic activity with an existing protein scaffold
Hee Sung Park
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373 1, Kusung dong, Yusung Gu, Daejon 305 701, Korea
Science 311:535-8. 2006
..8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100...
- The antiquity of RNA-based evolution
Gerald F Joyce
Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Nature 418:214-21. 2002
..This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA...
- Hidden alternative structures of proline isomerase essential for catalysis
James S Fraser
Department of Molecular and Cell Biology QB3, University of California, Berkeley, California 94720 3220, USA
Nature 462:669-73. 2009
A long-standing challenge is to understand at the atomic level how protein dynamics contribute to enzyme catalysis. X-ray crystallography can provide snapshots of conformational substates sampled during enzymatic reactions, while NMR ..
- Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis
Jill D Dombrauckas
Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA
Biochemistry 44:9417-29. 2005
- Diverse effects of pathogenic mutations of Parkin that catalyze multiple monoubiquitylation in vitro
Laboratory of Frontier Science, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613
J Biol Chem 281:3204-9. 2006
- Physiological and biochemical aspects of hydroxylations and demethylations catalyzed by human 2-oxoglutarate oxygenases
Chemistry Research Laboratory and the Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
Trends Biochem Sci 36:7-18. 2011
..The combination of new molecular biological and analytical techniques is likely to reveal further roles for oxygenase-mediated modifications to biomacromolecules...
- Accurate sequence-based prediction of catalytic residues
College of Mathematical Science and LPMC, Nankai University, Tianjin, PRC
Bioinformatics 24:2329-38. 2008
..We propose a sequence-based catalytic residue predictor that provides predictions with quality comparable to modern structure-based methods and that exceeds quality of state-of-the-art sequence-based methods...
- Product-assisted catalysis in base-excision DNA repair
J Christopher Fromme
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Nat Struct Biol 10:204-11. 2003
..reveal that the enzyme sequesters the excised lesion base and exploits it as a cofactor to participate in catalysis. To our knowledge, the present example represents the first documented case of product-assisted catalysis in an ..
- HIV-2 and SIVmac accessory virulence factor Vpx down-regulates SAMHD1 enzyme catalysis prior to proteasome-dependent degradation
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
J Biol Chem 288:19116-26. 2013
- O-GlcNAc transferase invokes nucleotide sugar pyrophosphate participation in catalysis
College of Life Sciences, University of Dundee, Dundee, UK
Nat Chem Biol 8:969-74. 2012
..This mechanism seems to be a unique evolutionary solution to the spatial constraints imposed by a bulky protein acceptor substrate and explains the unexpected specificity of a recently reported metabolic OGT inhibitor...
- Gold catalysis in total synthesis--an update
Organisch Chemisches Institut, Universitat Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
Chem Soc Rev 41:2448-62. 2012
In this critical review, the strongly increasing amount of new applications of gold catalysis in total synthesis is summarised and, for the new developed methods, the mode of activation of the substrate by the gold catalyst is discussed (..
- Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase
Kirsten R Wolthers
Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, United Kingdom
J Biol Chem 285:13942-50. 2010
..different catalytic states that together demonstrate unusual stability of the AdoCbl Co-C bond and that radical catalysis is coupled to large-scale domain motion. The 2...
- Taking Ockham's razor to enzyme dynamics and catalysis
David R Glowacki
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
Nat Chem 4:169-76. 2012
The role of protein dynamics in enzyme catalysis is a matter of intense current debate...
- Characterization of purified human Bact spliceosomal complexes reveals compositional and morphological changes during spliceosome activation and first step catalysis
Department of Cellular Biochemistry, MPI of Biophysical Chemistry, D 37077 Gottingen, Germany
RNA 16:2384-403. 2010
..The overall architecture of the human and S. cerevisiae B(act) complex is similar, suggesting that many of the higher order interactions among spliceosomal components, as well as their dynamics, are also largely conserved...
- Crystallographic evidence that the dinuclear copper center of tyrosinase is flexible during catalysis
Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
J Biol Chem 281:8981-90. 2006
..Our crystallographic study shows evidence that the tyrosinase active center formed by dinuclear coppers is flexible during catalysis.
- Highly enantioselective relay catalysis in the three-component reaction for direct construction of structurally complex heterocycles
Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
Org Lett 12:2266-9. 2010
- Structural insights into phosphoinositide 3-kinase catalysis and signalling
E H Walker
MRC Laboratory of Molecular Biology, MRC Centre, Cambridge, UK
Nature 402:313-20. 1999
- Structural plasticity and catalysis regulation of a thermosensor histidine kinase
Institut Pasteur, Unité de Biochimie Structurale and Plateforme de Cristallogenèse et Diffraction de Rayons X, URA 2185 Centre National de la Recherche Scientifique, Paris 75015, France
Proc Natl Acad Sci U S A 106:16185-90. 2009
- The interplay of catalysis and toxicity by amyloid intermediates on lipid bilayers: insights from type II diabetes
James A Hebda
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
Annu Rev Biophys 38:125-52. 2009
..Remarkably, the precursors of these fibers are intrinsically disordered, and yet catalysis of beta-sheet formation appears to be mediated by the stabilization of alpha-helical states...
- Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility
Pablo E Tomatis
Instituto de Biologia Molecular y Celular de Rosario IBR, Consejo Nacional de Investigaciones Cientificas y Tecnicas de Argentina, Biophysics Section, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Suipacha
Proc Natl Acad Sci U S A 105:20605-10. 2008
..Directed evolution aided by a thorough characterization of the selected proteins can be successfully used to predict future evolutionary events and design inhibitors with an evolutionary perspective...
- RNA folding and catalysis mediated by iron (II)
Shreyas S Athavale
School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
PLoS ONE 7:e38024. 2012
..and experiment to evaluate Fe²⁺ in the absence of free oxygen as a replacement for Mg²⁺ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg²⁺ in RNA ..
- Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate
D J Vocadlo
Protein Engineering Network of Centres of Excellence and the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
Nature 412:835-8. 2001
..We formulate a general catalytic mechanism for all retaining beta-glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate...
- Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
C W Muller
Institut fur Organische Chemie und Biochemie, 79104 Freiburg im Breisgau, Germany
Structure 4:147-56. 1996
..Because these changes have been studied by comparison of structures from different species, which share approximately one-third of their residues, only rough descriptions have been possible to date...
- In situ formation of an oxygen-evolving catalyst in neutral water containing phosphate and Co2+
Matthew W Kanan
Department of Chemistry, 6 335, Massachusetts Institute of Technology, Cambridge, MA 02139 4307, USA
Science 321:1072-5. 2008
..This catalyst not only forms in situ from earth-abundant materials but also operates in neutral water under ambient conditions...
- Alternative synthetic methods through new developments in catalysis by gold
Department of Chemistry, Chemical Engineering and Materials, University of L Aquila, Via Vetoio, 67010 Coppito AQ, Italy
Chem Rev 108:3266-325. 2008
- Engineering entropy-driven reactions and networks catalyzed by DNA
David Yu Zhang
Computation and Neural Systems, California Institute of Technology, MC 136 93, 1200 East California Boulevard, Pasadena, CA91125, USA
Science 318:1121-5. 2007
..We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics...
- Weak coordination as a powerful means for developing broadly useful C-H functionalization reactions
Keary M Engle
Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
Acc Chem Res 45:788-802. 2012
- Biochemical activities of highly purified, catalytically active human APOBEC3G: correlation with antiviral effect
Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, Bethesda, MD 20892 2780, USA
J Virol 80:5992-6002. 2006
..In contrast, deamination is associated exclusively with the second zinc finger. Moreover, zinc finger two is more important than finger one for the antiviral effect, demonstrating a correlation between deaminase and antiviral activities...
- Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii
National Institute of Bioscience and Human Technology, Tsukuba, Ibaraki 305, Japan
J Biol Chem 276:27376-83. 2001
..Furthermore we determined the molecular mass of the recombinant enzyme by gel filtration and proposed a heterotetrameric structure for this enzyme...
- A convenient catalyst for aqueous and protein Suzuki-Miyaura cross-coupling
Justin M Chalker
Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
J Am Chem Soc 131:16346-7. 2009
..The convenience and activity of this catalyst prompts use in both general synthesis and bioconjugation...
- Enzymes for chemical synthesis
K M Koeller
Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
Nature 409:232-40. 2001
..Enzyme-catalysed chemical transformations are now widely recognized as practical alternatives to traditional (non-biological) organic synthesis, and as convenient solutions to certain intractable synthetic problems...
- Catalysis of cis/trans isomerization in native HIV-1 capsid by human cyclophilin A
Daryl A Bosco
Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
Proc Natl Acad Sci U S A 99:5247-52. 2002
..In addition, conformational changes in CA(N) distal to the CypA binding loop are observed on CypA binding and catalysis. The results provide experimental evidence for efficient CypA catalysis on a natively folded and biologically ..
- DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
EMBO J 19:758-66. 2000
..The structure of the AlkA-DNA complex offers the first glimpse of a helix-hairpin-helix (HhH) glycosylase complexed to DNA. Modeling studies suggest that other HhH glycosylases can bind to DNA in a similar manner...
- Catalysis of electron transfer during activation of O2 by the flavoprotein glucose oxidase
Justine P Roth
Department of Chemistry and, University of California, Berkeley, 94720, USA
Proc Natl Acad Sci U S A 100:62-7. 2003
..0 kcal.mol(-1) (0.26 eV). Within the context of Marcus theory, catalysis of electron transfer is attributed to a 19-kcal.mol(-1) (0...
- Critical residues for structure and catalysis in short-chain dehydrogenases/reductases
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
J Biol Chem 277:25677-84. 2002
..emphasize the critical role of residues Thr-12, Asp-60, Asn-86, Asn-87, and Ala-88 in coenzyme binding and catalysis. The data also demonstrate essential interactions of Asn-111 with active site residues...
- Catalysis in the nitrilase superfamily
Structural Biology and Bioinformatics Program, Kimmel Cancer Center, Philadelphia, PA 19107, USA
Curr Opin Struct Biol 12:775-82. 2002
..Recent experimental results confirm the essentiality of the catalytic triad residues and specify the biochemical functions of additional branches and sub-branches of the nitrilase superfamily...
- Characterization of NocL involved in thiopeptide nocathiacin I biosynthesis: a [4Fe-4S] cluster and the catalysis of a radical S-adenosylmethionine enzyme
State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
J Biol Chem 286:21287-94. 2011
..Furthermore, a free radical was observed by EPR during the catalysis, which is in good agreement with the hypothesis of a glycyl radical intermediate...
- Snapshots of enzymatic Baeyer-Villiger catalysis: oxygen activation and intermediate stabilization
Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
J Biol Chem 286:29284-91. 2011
..analogs, we have captured several snapshots along the catalytic cycle which highlight key features in enzyme catalysis. After acting as electron donor, the enzyme-bound NADP(H) forms an H-bond with the flavin cofactor...
- The protein kinase family: conserved features and deduced phylogeny of the catalytic domains
S K Hanks
Molecular Biology Laboratory, Salk Institute for Biological Studies, San Diego, CA 92138
Science 241:42-52. 1988
..Phylogenetic mapping of the conserved protein kinase catalytic domains can serve as a useful first step in the functional characterization of these newly identified family members...
- Key role of cysteine residues in catalysis and subcellular localization of sulfur oxygenase-reductase of Acidianus tengchongensis
Zhi Wei Chen
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People s Republic of China
Appl Environ Microbiol 71:621-8. 2005
..We tentatively propose that these enzymes are located in close proximity on the membrane to catalyze sulfur oxidation in A. tengchongensis...
- Role of the RNA polymerase trigger loop in catalysis and pausing
Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
Nat Struct Mol Biol 17:99-104. 2010
..However, the roles of the TL/TH in transcript cleavage, catalysis, substrate selectivity and pausing remain ill defined...
- Crystal structure of the catalytic portion of human HMG-CoA reductase: insights into regulation of activity and catalysis
E S Istvan
Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, TX 75235 9050, USA
EMBO J 19:819-30. 2000
..The active site architecture of human HMGR is different from that of bacterial HMGR; this may explain why binding of HMGR inhibitors to bacterial HMGRs has not been reported...
- PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis
Departments of Molecular and Cellular Biology, and Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 107:2467-72. 2010
..PR65-dominated fluctuations of PP2A have the effect of opening and closing the enzyme's substrate binding/catalysis interface, as well as altering the positions of certain catalytic residues...
- Triple-helix structure in telomerase RNA contributes to catalysis
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Campus Box 215, University of Colorado, Boulder, Colorado 80309 0215, USA
Nat Struct Mol Biol 15:634-40. 2008
..Instead, 2'-OH groups protruding from the triple helix participate in both yeast and human telomerase catalysis; they may orient the primer-template relative to the active site in a manner analogous to group I ribozymes...
- Structural basis for Ca(2+)-induced activation of human PAD4
Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
Nat Struct Mol Biol 11:777-83. 2004
..Our findings identify a novel mechanism for enzyme activation by Ca(2+) ions, and are important for understanding the mechanism of protein citrullination and for developing PAD-inhibiting drugs for the treatment of rheumatoid arthritis...
- Kemp elimination catalysts by computational enzyme design
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
Nature 453:190-5. 2008
..biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse ..
- Flexibility, diversity, and cooperativity: pillars of enzyme catalysis
Gordon G Hammes
Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
Biochemistry 50:10422-30. 2011
This brief review discusses our current understanding of the molecular basis of enzyme catalysis. A historical development is presented, beginning with steady state kinetics and progressing through modern fast reaction methods, nuclear ..
- Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
EMBO J 25:1924-33. 2006
In two-metal catalysis, metal ion A has been proposed to activate the nucleophile and metal ion B to stabilize the transition state. We recently reported crystal structures of RNase H-RNA/DNA substrate complexes obtained at 1.5-2...
- Electrostatic basis for enzyme catalysis
Department of Chemistry, University of Southern California, SGM Building 418, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
Chem Rev 106:3210-35. 2006
- Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair
Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
Nat Struct Mol Biol 11:945-9. 2004
A fundamental question is how enzymes can accelerate chemical reactions. Catalysis is not only defined by actual chemical steps, but also by enzyme structure and dynamics...
- Network of coupled promoting motions in enzyme catalysis
Pratul K Agarwal
Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
Proc Natl Acad Sci U S A 99:2794-9. 2002
..This type of network has broad implications for an expanded role of the protein fold in catalysis as well as ancillaries such as the engineering of altered protein function and the action of drugs distal to the ..
- Molecular recognition and catalysis in translation termination complexes
Bruno P Klaholz
IGBMC Institute of Genetics and of Molecular and Cellular Biology, Department of Structural Biology and Genomics, Illkirch, France
Trends Biochem Sci 36:282-92. 2011
..Moreover, ongoing research also promises to reveal the structure-function relations of class-II RFs...
- A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance
Department of Biology, University of Padova, Via U Bassi 58 B, Padua 35131, Italy
Nucleic Acids Res 36:5635-44. 2008
..To understand the contribution of this residue in drug resistance, we have studied the effect on hTop1p catalysis and CPT sensitivity of four different substitutions in the Thr729 position (Thr729Ala, Thr729Glu, Thr729Lys and ..
- Similar enzyme activation and catalysis in hemocyanins and tyrosinases
Institut für Molekulare Biophysik, Johannes Gutenberg Universitat, 55099 Mainz, Germany
Gene 398:183-91. 2007
..In spite of these differences a common mechanism of activation and catalysis seems to have been preserved throughout evolution...
- Crystal structures of fructose 1,6-bisphosphatase: mechanism of catalysis and allosteric inhibition revealed in product complexes
J Y Choe
Department of Biochemistry, Iowa State University, Ames 50011, USA
Biochemistry 39:8565-74. 2000
..Development of negative charge on the 1-oxygen of F6P is stabilized by its coordination to the Mg(2+) at site 1...
- Polytriazoles as copper(I)-stabilizing ligands in catalysis
Timothy R Chan
Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, USA
Org Lett 6:2853-5. 2004
..The C3-symmetric derivative, TBTA, was shown to be a powerful stabilizing ligand for copper(I), protecting it from oxidation and disproportionation, while enhancing its catalytic activity...
- Mechanism of cysteine desulfurase Slr0387 from Synechocystis sp. PCC 6803: kinetic analysis of cleavage of the persulfide intermediate by chemical reductants
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Biochemistry 43:12220-6. 2004
..the persulfide intermediate, and it has been suggested that persulfide cleavage is the rate-limiting step for catalysis. In this study, the kinetics and mechanisms of cleavage of the persulfide intermediate in Slr0387 (CD-0387), a ..
- Click chemistry with DNA
Afaf H El-Sagheer
School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
Chem Soc Rev 39:1388-405. 2010
..In this critical review we describe some of the pioneering work that has been carried out in this area (78 references)...
- Palladium-catalyzed oxidative diarylating carbocyclization of enynes
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE 106 91 Stockholm, Sweden
Org Lett 14:3538-41. 2012
..Control experiments suggest that the reaction starts with an arylpalladation of the alkyne, followed by carbocyclization, transmetalation, and reductive elimination to afford the diarylated product...
- Evolution of the protein repertoire
Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Science 300:1701-3. 2003
..Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes...
- Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases
Institut de Biologie et Chimie des Proteines, UMR 5086, Laboratoire de Bio Cristallographie, CNRS et Université Claude Bernard Lyon I, Lyon, France
Proteins 50:636-47. 2003
..Finally, the active site is more accessible due to deletions occurring in surrounding loop regions...
- Free-energy landscape of enzyme catalysis
Stephen J Benkovic
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Biochemistry 47:3317-21. 2008
..Experimental and theoretical evidence is presented to support this concept...
- Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme
Timothy J Wilson
Cancer Research United Kingdom Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
Proc Natl Acad Sci U S A 107:11751-6. 2010
..satellite (VS) ribozyme accelerates the cleavage of a specific phosphodiester bond using general acid-base catalysis. The key functionalities are the nucleobases of adenine 756 in helix VI of the ribozyme, and guanine 638 in the ..
- Investigations of the esterase, phosphatase, and sulfatase activities of the cytosolic mammalian carbonic anhydrase isoforms I, II, and XIII with 4-nitrophenyl esters as substrates
Universita degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm 188, Via della Lastruccia 3, I 50019 Sesto Fiorentino, Firenze, Italy
Bioorg Med Chem Lett 18:2267-71. 2008
..CA XIII was the most effective esterase and phosphatase. CA XIII might catalyze other physiological reactions than CO(2) hydration, based on its relevant phosphatase activity...
- Interrupted catalysis: the EF4 (LepA) effect on back-translocation
Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
J Mol Biol 396:1043-52. 2010
..EF4 may be thought of as performing an interrupted catalysis of back-translocation, stopping at the formation of I(3) rather than catalyzing the complete process of back-..
- Mechanistic analysis of the immunomodulatory effects of a catalytic antioxidant on antigen-presenting cells: implication for their use in targeting oxidation-reduction reactions in innate immunity
Hubert M Tse
Diabetes Institute, Division of Immunogenetics, Department of Pediatrics, Children s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213 3205, USA
Free Radic Biol Med 36:233-47. 2004
- Palladium-catalyzed oxidative carbocyclization/arylation of enallenes
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE 10691, Stockholm, Sweden
Org Lett 13:5838-41. 2011
..The reaction shows wide tolerance toward highly functionalized arylboronic acids and results in a cis addition of two carbon moieties to an olefin in good to excellent yields...
- Bioconjugation with strained alkenes and alkynes
Marjoke F Debets
Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, The Netherlands
Acc Chem Res 44:805-15. 2011
..In the search for bioorthogonal reactions, cycloadditions of cyclic alkenes and alkynes have now established themselves as powerful tools in reagent-free bioconjugations...
- Analysis of proanthocyanidin cleavage products following acid-catalysis in the presence of excess phloroglucinol
J A Kennedy
Department of Horticulture, Viticulture and Oenology, University of Adelaide, Waite Campus, PMB 1, Glen Osmond, South Australia 5064, Australia
J Agric Food Chem 49:1740-6. 2001
The analysis of proanthocyanidin cleavage products after acid-catalysis in the presence of excess phloroglucinol was investigated. In the developed analytical method, a solution of 0...
- A natural ribozyme with 3',5' RNA ligase activity
Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309 0215, USA
Nat Chem Biol 5:97-9. 2009
..In the process, this ribozyme forms a unique circular RNA that incorporates the exogenous guanosine cofactor added during self-splicing. This finding may have relevance to a prebiotic RNA world and to modern biology...