adk

Summary

Gene Symbol: adk
Description: adenylate kinase
Alias: ECK0468, JW0463, dnaW, plsA
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. pmc Many local motions cooperate to produce the adenylate kinase conformational transition
    Michael D Daily
    Department of Chemistry, University of Wisconsin Madison, 1101 University Avenue, Madison, WI 53706, USA
    J Mol Biol 400:618-31. 2010
  2. pmc Cloning and sequencing of the adenylate kinase gene (adk) of Escherichia coli
    M Brune
    Nucleic Acids Res 13:7139-51. 1985
  3. ncbi The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP
    M B Berry
    W M Keck Center for Computational Biology, Rice University, Houston, Texas 77251 1892
    Proteins 19:183-98. 1994
  4. ncbi Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop
    C W Muller
    Institut für Organische Chemie und Biochemie der Universität, Freiburg im Breisgau, Federal Republic of Germany
    Proteins 15:42-9. 1993
  5. ncbi Domain closure in adenylate kinase
    M A Sinev
    Department of Life Sciences, Bar Ilan University, Ramat Gan, Israel
    Biochemistry 35:6425-37. 1996
  6. ncbi 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
  7. ncbi Backbone dynamics of escherichia coli adenylate kinase at the extreme stages of the catalytic cycle studied by (15)N NMR relaxation
    Y E Shapiro
    Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel, Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Biochemistry 39:6634-44. 2000
  8. pmc Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data
    N Alpay Temiz
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
    Proteins 57:468-80. 2004
  9. ncbi Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates
    Harini Krishnamurthy
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48224 1322, USA
    Proteins 58:88-100. 2005
  10. ncbi Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase
    Paul Maragakis
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, USA
    J Mol Biol 352:807-22. 2005

Research Grants

Scientific Experts

  • Martin Willemoes
  • Tiziana Gigliobianco
  • Lucia L Nemoy
  • H Munier-Lehmann
  • Yury E Shapiro
  • ROBERT CUKIER
  • Paul Maragakis
  • Tomer Orevi
  • V Ratner
  • E Haas
  • Elisha Haas
  • Dan Amir
  • Hongfeng Lou
  • S Burlacu-Miron
  • Eldad Ben Ishay
  • A M Gilles
  • Y Lin
  • Michael D Daily
  • E Kahana
  • Yaping Feng
  • R Potestio
  • Louise Rundqvist
  • George N Phillips
  • O Barzu
  • Marcus B Kubitzki
  • Rory M Watt
  • Paul C Whitford
  • Katherine A Henzler-Wildman
  • Catherine Snow
  • Michael B Berry
  • V Perrier
  • Juhyun Kim
  • Harini Krishnamurthy
  • Varda Ittah
  • N Alpay Temiz
  • Eva Meirovitch
  • C W Muller
  • Mayan Ben Dalak
  • Sivan Levin Gershanov
  • M A Sinev
  • Vitali Tugarinov
  • Q Ruan
  • V Ittah
  • M Glaser
  • M Sinev
  • B D Nageswara Rao
  • Qiang Cui
  • Robert L Jernigan
  • C Micheletti
  • Menachem Pirchi
  • F Pontiggia
  • Lei Yang
  • Magnus Wolf-Watz
  • Jörgen Adén
  • Andrzej Kloczkowski
  • Maik H Jacob
  • G E Schulz
  • Ulrika Olsson
  • Tobias Sparrman
  • Marcus Wallgren
  • C T Craescu
  • Bert L de Groot
  • Dorothee Kern
  • Depei Liu
  • Osamu Miyashita
  • S Jordan Kerns
  • Jose N Onuchic
  • Ming Lei
  • Yaakov Levy
  • Steven Hayward
  • Vu Thai
  • Jian Dong Huang
  • Martin Karplus
  • Meikid Leong
  • Hsiang Fu Kung
  • Kathryn S E Cheah
  • Antoine Danchin
  • Jing Wang
  • Guoying Qi
  • Michael Glaser
  • Tim R Bilderback
  • Euiyoung Bae
  • Claire Vieille
  • Michael C Olcott
  • Christopher K Mathews
  • Adam Kimple
  • Indira Rajagopal
  • D Amir
  • Rongkun Shen
  • Ivet Bahar

Detail Information

Publications89

  1. pmc Many local motions cooperate to produce the adenylate kinase conformational transition
    Michael D Daily
    Department of Chemistry, University of Wisconsin Madison, 1101 University Avenue, Madison, WI 53706, USA
    J Mol Biol 400:618-31. 2010
    ..Finally, the analytical approach and the insights derived from this work may inform the rational design of flexibility and allostery in proteins...
  2. pmc Cloning and sequencing of the adenylate kinase gene (adk) of Escherichia coli
    M Brune
    Nucleic Acids Res 13:7139-51. 1985
    Adenylate kinase, the product of the adk locus in Escherichia coli K12, catalyzes the conversion of AMP and ATP to two molecules of ADP. The gene has been cloned by complementation of an adk temperature sensitive mutation...
  3. ncbi The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP
    M B Berry
    W M Keck Center for Computational Biology, Rice University, Houston, Texas 77251 1892
    Proteins 19:183-98. 1994
    ..Finally, a comparison is made between the present structure and the structure of the heavy chain of muscle myosin...
  4. ncbi Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop
    C W Muller
    Institut für Organische Chemie und Biochemie der Universität, Freiburg im Breisgau, Federal Republic of Germany
    Proteins 15:42-9. 1993
    ....
  5. ncbi Domain closure in adenylate kinase
    M A Sinev
    Department of Life Sciences, Bar Ilan University, Ramat Gan, Israel
    Biochemistry 35:6425-37. 1996
    ..The data confirmed the proposed stepwise manner of the domain closure of the enzyme and revealed the presence of multiple conformations of E. coli AK in solution...
  6. ncbi 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...
  7. ncbi Backbone dynamics of escherichia coli adenylate kinase at the extreme stages of the catalytic cycle studied by (15)N NMR relaxation
    Y E Shapiro
    Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel, Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Biochemistry 39:6634-44. 2000
    ..The hypothesis of energetic counter balancing of substrate binding based on crystallographic data is strongly supported by the solution NMR results. Correlations between backbone dynamics and domain displacement are established...
  8. pmc Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data
    N Alpay Temiz
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
    Proteins 57:468-80. 2004
    ..It is shown that NMR/SRLS and GNM/ANM analyses can be advantageously synthesized to provide insights into the molecular mechanisms that control biological function...
  9. ncbi Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates
    Harini Krishnamurthy
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48224 1322, USA
    Proteins 58:88-100. 2005
    ....
  10. ncbi Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase
    Paul Maragakis
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, USA
    J Mol Biol 352:807-22. 2005
    ..0 A of the pathway, which corresponds to a conformational change between two end structures that differ by a C(alpha)-atom root-mean-squared deviation of 7.1A...
  11. ncbi Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase
    Michael B Berry
    W M Keck Center for Computational Biology, Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA
    Proteins 62:555-6. 2006
  12. pmc Conformational transitions of adenylate kinase: switching by cracking
    Paul C Whitford
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA
    J Mol Biol 366:1661-71. 2007
    ..We further characterize the conformational transitions with a new measure Phi(Func), and demonstrate that local unfolding may be due, in part, to competing intra-protein interactions...
  13. ncbi Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions
    Catherine Snow
    School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
    Proteins 67:325-37. 2007
    ..In general though it appears a bias toward keeping the unliganded enzyme in the open-domain conformation may be a common feature of domain enzymes...
  14. ncbi A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    Katherine A Henzler-Wildman
    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
    Nature 450:913-6. 2007
    ..The connection between different timescales and the corresponding amplitudes of motions in adenylate kinase and their linkage to catalytic function is likely to be a general characteristic of protein energy landscapes...
  15. doi The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study
    Marcus B Kubitzki
    Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    Structure 16:1175-82. 2008
    ..molecular dynamics simulation of the complete conformational transition of Escherichia coli adenylate kinase (ADK) using the recently developed TEE-REX algorithm...
  16. ncbi Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state
    C W Muller
    Institut für Organische Chemie und Biochemie der Universität, Freiburg, Germany
    J Mol Biol 224:159-77. 1992
    ..The mutants were classified. The concomitant increase of the Michaelis constants for ATP and AMP in the group of mutants that modify only the ATP-binding site cannot be explained...
  17. pmc Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits
    R Potestio
    Scuola Internazionale Superiore di Studi Avanzati SISSA, Trieste, Italy
    Biophys J 96:4993-5002. 2009
    ..The known catalytic site of these enzymes is found to be preferentially located close to the boundary separating the two primary dynamical subdomains...
  18. ncbi Molecular dynamics of apo-adenylate kinase: a principal component analysis
    Hongfeng Lou
    Department of Chemistry and the Quantitative Biology Modeling Initiative, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 110:12796-808. 2006
    ..A pair of residues is suggested for labeling that would be useful for monitoring distance fluctuations by energy transfer experiments...
  19. ncbi Applications of time-resolved resonance energy transfer measurements in studies of the molecular crowding effect
    Varda Ittah
    Faculty of life sciences Bar Ilan University, Ramat Gan 52900, Israel
    J Mol Recognit 17:448-55. 2004
    ..Networks of pairs of labeled sites can be prepared and tr-RET experiments can be performed in order to search for the segments of the protein molecules, which respond to the presence of inert macromolecules in their environment...
  20. ncbi A general strategy for site-specific double labeling of globular proteins for kinetic FRET studies
    V Ratner
    Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
    Bioconjug Chem 13:1163-70. 2002
    ..The procedure described herein is a general outline of procedures, which can meet the double challenge of both site specificity and large-scale preparation of doubly labeled proteins...
  21. ncbi Characterization of metal and nucleotide liganded forms of adenylate kinase by electrospray ionization mass spectrometry
    G Briand
    Laboratoire d Application de Spectrométrie de Masse, Universite de Lille II, Lille Cedex, 59045, France
    Arch Biochem Biophys 339:291-7. 1997
    ..coli adenylate kinase, was proposed to stabilize the nucleotide.Mg2+ complex via water molecules...
  22. pmc Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes
    Rory M Watt
    Open Laboratory of Chemical Biology, The Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
    Nucleic Acids Res 35:e37. 2007
    ..Our results show that E. coli has an organized and dynamic proteome, and demonstrate that this approach is applicable for tagging and (co-) localizing CDSs on a genome-wide scale...
  23. doi Fast closure of N-terminal long loops but slow formation of β strands precedes the folding transition state of Escherichia coli adenylate kinase
    Tomer Orevi
    The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
    Biochemistry 53:3169-78. 2014
    ..The study of subdomain folding in situ suggests a hierarchic ordered folding mechanism, in which early and rapid cross-linking by hydrophobic loop closure provides structural stabilization at the initiation of the folding pathway. ..
  24. ncbi Circular dichroism investigation of Escherichia coli adenylate kinase
    M Monnot
    J Biol Chem 262:2502-6. 1987
    ..When mixed, C1 and C2 fragments reassociated into structures resembling native, uncleaved adenylate kinase. The recovery of ordered structures, indicated by CD spectroscopy, paralleled the recovery of catalytic activity...
  25. ncbi Structural and catalytic role of arginine 88 in Escherichia coli adenylate kinase as evidenced by chemical modification and site-directed mutagenesis
    J Reinstein
    Max Planck Institut fur medizinische Forschung, Abteilung Biophysik, Heidelberg, West Germany
    J Biol Chem 264:8107-12. 1989
    ..It possibly stabilizes the transferable gamma-phosphate group from ATP to AMP in the transition state...
  26. ncbi Structure of the complex of adenylate kinase from Escherichia coli with the inhibitor P1,P5-di(adenosine-5'-)pentaphosphate
    C W Muller
    Institut für Organische Chemie und Biochemie der Universität, Freiburg i Br, F R G
    J Mol Biol 202:909-12. 1988
    ..The final R-factor is 35.9%. The corresponding model is given as backbone tracing. The structure will be used for protein-engineering studies...
  27. ncbi Complexes of Escherichia coli adenylate kinase and nucleotides: 1H NMR studies of the nucleotide sites in solution
    I R Vetter
    Department of Biophysics, Max Planck Institute for Medical Research, Heidelberg, FRG
    Biochemistry 29:7459-67. 1990
    ..4) The ATP.Mg2+ adenine in the AKEC.AP5A.Mg2+ complex is located close to His134 and Phe19. (5) The AKEC "G-loop" with bound ATP.Mg2+ is structurally highly homologous to the loop region in the oncogene product p21 with bound GTP.Mg2+...
  28. pmc Identification of valine/leucine/isoleucine and threonine/alanine/glycine proton-spin systems of Escherichia coli adenylate kinase by selective deuteration and selective protonation
    I Bock-Möbius
    Max Planck Institut fur medizinische Forschung, Abteilung Biophysik, Heidelberg, Federal Republic of Germany
    Biochem J 273:311-6. 1991
    ..Use of these proteins enabled identification of the spin systems of these amino acid residues in the n.m.r. spectra of the protein...
  29. ncbi Isolation and characterization of visible light-sensitive mutants of Escherichia coli K12
    K Miyamoto
    Department of Biophysics, Faculty of Science, Kyoto University, Japan
    J Mol Biol 219:393-8. 1991
    ..A possible mechanism for the killing of the visA mutant bacteria is discussed...
  30. ncbi Structural characterization of adenine nucleotides bound to Escherichia coli adenylate kinase. 2. 31P and 13C relaxation measurements in the presence of cobalt(II) and manganese(II)
    Y Lin
    Department of Physics, Indiana University Purdue University Indianapolis, Indiana 46202 3273, USA
    Biochemistry 39:3647-55. 2000
    ..These conformations differ significantly from the nucleotide conformations in crystals of AKe. AP(5)A and AKe.AMP.AMPPNP as determined by X-ray crystallography...
  31. ncbi Structural and catalytic characteristics of Escherichia coli adenylate kinase
    I Saint Girons
    J Biol Chem 262:622-9. 1987
    The adk gene encoding adenylate kinase in Escherichia coli was cloned in pBR322. Adenylate kinase represented about 4% of total proteins in extracts of cells containing the pBR322:adk plasmid...
  32. ncbi Protein folding pathways of adenylate kinase from E. coli: hydrostatic pressure and stopped-flow studies
    Q Ruan
    Laboratory of Fluorescence Dynamics, Department of Biochemistry, University of Illinois at Urbana Champaign, 61801, USA
    Biochemistry 40:14706-14. 2001
    ..The results suggest that the differences in regional folding rates of AKe are not derived from the specific denaturation methods, but rather are inherent in the structural organization of the protein...
  33. ncbi A novel view of domain flexibility in E. coli adenylate kinase based on structural mode-coupling (15)N NMR relaxation
    Vitali Tugarinov
    Faculty of Life Sciences, Bar Ilan University, Ramat Gan, 52900, Israel
    J Mol Biol 315:155-70. 2002
    ..A powerful new model of protein flexibility/domain motion has been established. Conformational exchange (R(ex)) processes accompany the tau( perpendicular) mode. The SRLS analysis is compared with the conventional model-free analysis...
  34. ncbi Domain flexibility in ligand-free and inhibitor-bound Escherichia coli adenylate kinase based on a mode-coupling analysis of 15N spin relaxation
    Yury E Shapiro
    Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
    Biochemistry 41:6271-81. 2002
    ..The other flexible AKeco*AP(5)A loops may relate to domain motion toward product release...
  35. ncbi The natively helical chain segment 169-188 of Escherichia coli adenylate kinase is formed in the latest phase of the refolding transition
    V Ratner
    Department of Life Sciences, Bat Ilan University, Ramat Gan, Israel
    J Mol Biol 320:1135-45. 2002
    ..The helical conformation of this segment is established only in the second, much slower, refolding phase, simultaneously with the completion of the native structure...
  36. ncbi The binding of ATP and AMP to Escherichia coli adenylate kinase investigated by 1H and 15N NMR spectroscopy
    J Glushka
    Rockefeller University, N Y, N Y 10021
    Biochem Biophys Res Commun 172:432-8. 1990
    ....
  37. ncbi Fluorescence and NMR investigations on the ligand binding properties of adenylate kinases
    J Reinstein
    Abteilung Biophysik, Max Planck Institut fur medizinische Forschung, Heidelberg, West Germany
    Biochemistry 29:7440-50. 1990
    ..coli (AKec) and 36 of AK1 are situated in a comparable environment and are not essential for catalytic activity...
  38. ncbi Adenylate kinase of Escherichia coli, a component of the phage T4 dNTP synthetase complex
    Juhyun Kim
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331 7305, USA
    J Biol Chem 280:28221-9. 2005
    ....
  39. ncbi Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase
    V Ratner
    Faculty of Life Sciences, Bar Ilan University, 52900 Ramat Gan, Israel
    J Mol Biol 352:683-99. 2005
    ..The AK molecules undergo fast collapse to an ensemble of compact structures where the local environment of surface probes seems to be native-like but the two labeled secondary structure elements remain unfolded...
  40. ncbi Nucleoside triphosphate synthesis catalysed by adenylate kinase is ADP dependent
    Martin Willemoes
    Department of Biological Chemistry, Institute of Molecular Biology and Physiology, University of Copenhagen, Sølvgade 83H DK 1307, Denmark
    Arch Biochem Biophys 444:195-9. 2005
    Adenylate kinase (Adk) that catalyses the synthesis of ADP from ATP and AMP has also been shown to perform an ATP dependent phosphorylation of ribo- and deoxynucleoside diphosphates to their corresponding nucleoside triphosphate; ATP+(d)..
  41. ncbi Activation energy of catalysis-related domain motion in E. coli adenylate kinase
    Yury E Shapiro
    Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
    J Phys Chem B 110:11519-24. 2006
    ..However, the latter process clearly facilitates important mechanical aspects such as steric recognition and capturing of the AMP and ATP substrates, their proper positioning for phosphorylation, and the release of the ADP product...
  42. ncbi Design consideration and probes for fluorescence resonance energy transfer studies
    M Sinev
    Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
    Bioconjug Chem 11:352-62. 2000
    ..General considerations for design of charged probes and site-directed labeling for applications of FRET methods in studies of protein structure and dynamics are presented...
  43. ncbi Structural and catalytic properties of a deletion derivative (delta 133-157) of Escherichia coli adenylate kinase
    T Rose
    Unité de Biochimie des Régulations Cellulaires, Institut Pasteur, Paris, France
    J Biol Chem 266:10781-6. 1991
    ..Removal of 25 codons in the corresponding adk gene resulted in expression of a modified form of adenylate kinase (delta 133-157 AKe) which still conserved 7% of ..
  44. ncbi Assignment of the nucleotide binding sites and the mechanism of substrate inhibition of Escherichia coli adenylate kinase
    P Liang
    Department of Biochemistry, University of Illinois, Urbana 61801
    Proteins 9:28-36. 1991
    ..The fluorescence results are consistent with the kinetic studies, and also suggest that AMP substrate inhibition is caused by the formation of an abortive complex that prevents the release of product...
  45. pmc Adenylate kinase-independent thiamine triphosphate accumulation under severe energy stress in Escherichia coli
    Tiziana Gigliobianco
    Center for Cellular and Molecular Neurobiology, University of Liege, Liege, Belgium
    BMC Microbiol 8:16. 2008
    ..However, it is also known that vertebrate adenylate kinase 1 catalyzes ThTP synthesis at a very low rate and it has been postulated that this enzyme is responsible for ThTP synthesis in vivo...
  46. ncbi Structural and functional consequences of amino acid substitutions in the second conserved loop of Escherichia coli adenylate kinase
    T Rose
    Unité de Biochimie des Régulations Cellulaires, Institut Pasteur, Paris, France
    J Biol Chem 266:23654-9. 1991
    ..The two remaining residues probed in this study, Gly85 and Phe86, belong to a beta-turn which appears to play a major role in stabilizing the three-dimensional structure of adenylate kinase...
  47. doi Early closure of a long loop in the refolding of adenylate kinase: a possible key role of non-local interactions in the initial folding steps
    Tomer Orevi
    The E Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
    J Mol Biol 385:1230-42. 2009
    ..We conclude that a specific network of non-local interactions, the closure of one or several loops, can play an important role in determining the protein folding pathway at its early phases...
  48. doi Apo adenylate kinase encodes its holo form: a principal component and varimax analysis
    Robert I Cukier
    Department of Chemistry and the Quantitative Biology Modeling Initiative, Michigan State University, East Lansing, Michigan 48824, USA
    J Phys Chem B 113:1662-72. 2009
    ..In this sense, apo AKE does encode in its fluctuations information about holo-like conformations...
  49. doi Noncooperative folding of subdomains in adenylate kinase
    Louise Rundqvist
    Department of Chemistry, Umea University, SE 901 87 Umea, Sweden
    Biochemistry 48:1911-27. 2009
    ..Adenylate kinase (Adk) is composed of three subdomains: CORE, ATPlid, and AMPbd...
  50. pmc The energy profiles of atomic conformational transition intermediates of adenylate kinase
    Yaping Feng
    Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University Ames, Iowa 50011 0320, USA
    Proteins 77:551-8. 2009
    ..1998;11:739-747) and the k-means clustering algorithm are then used to show that known PDB structures closely resemble computed intermediates along the transition pathway...
  51. doi Domain mobility in proteins from NMR/SRLS
    Yury E Shapiro
    The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
    J Phys Chem B 113:12050-60. 2009
    ..94; the main ordering axis, Z(M), lies along N-H, <c(2)(0)> approximately = 16 (c(2)(2) = 0); and the slow local motional correlation time lies at the low end of the nanosecond time scale...
  52. pmc Role of adenylate kinase in the regulation of macromolecular biosynthesis in a putative mutant of Escherichia coli defective in membrane phospholipid biosynthesis
    M Glaser
    J Bacteriol 123:128-36. 1975
    ..Adenylate kinase, therefore, is a key enzyme in controlling the rate of cell growth. The nature of the possible relationship between adenylate kinase and glycerol-3-phosphate acyltransferase is discussed...
  53. ncbi Multinuclear magnetic resonance studies of Escherichia coli adenylate kinase in free and bound forms. Resonance assignment, secondary structure and ligand binding
    S Burlacu-Miron
    INSERM U350, Institut Curie Recherche, Orsay, France
    Eur J Biochem 264:765-74. 1999
    ..1H/2H exchange experiments performed on free and Ap5A-bound enzymes showed a general decrease of the structural flexibility in the complex which is accompanied by a local increased flexibility on the N-side of the parallel beta-sheet...
  54. pmc Eukaryotic Mr 83,000 heat shock protein has a homologue in Escherichia coli
    J C Bardwell
    Proc Natl Acad Sci U S A 84:5177-81. 1987
    ..The gene encoding C62.5 (named htpG) is located between the dnaZ and adk genes at 11.1 minutes on the E. coli chromosome. The htpG gene appears to be a newly identified locus...
  55. ncbi Nucleotide sequence and deduced amino acid sequence of Escherichia coli adenine phosphoribosyltransferase and comparison with other analogous enzymes
    H V Hershey
    Gene 43:287-93. 1986
    ..All PRTs, including E. coli adenine PRT (APRT), have a strongly conserved 13-aa sequence, as well as other regions of aa sequence or structural similarity. E. coli APRT is remarkably similar to the mouse enzyme...
  56. ncbi Inactivation and proteolysis of heat-sensitive adenylate kinase of Escherichia coli CR341 T28
    N Guiso
    J Biol Chem 259:8713-7. 1984
    ..ATP, P1, P5-di(adenosine 5')-pentaphosphate, and anti-adenylate kinase antibodies protected the thermosensitive adenylate kinase in crude extracts against denaturation and proteolysis at 40 degrees C...
  57. pmc Genetic analysis of Escherichia coli mutants defective in adenylate kinase and sn-glycerol 3-phosphate acyltransferase
    B E Esmon
    J Bacteriol 141:405-8. 1980
    ..The results suggest that the adk (plsA) locus is the structural gene for adenylate kinase.
  58. ncbi Simple and fast purification of Escherichia coli adenylate kinase
    O Barzu
    FEBS Lett 153:280-4. 1983
    ..1 microM in the case of mutant enzyme). After denaturation in 6 M guanidinium hydrochloride both mutant and parent adenylate kinase returned rapidly to the native, active state by dilution of guanidinium hydrochloride...
  59. ncbi Identification and purification of an adenylate kinase-associated protein that influences the thermolability of adenylate kinase from a temperature-sensitive adk mutant of Escherichia coli
    R J Huss
    J Biol Chem 258:13370-6. 1983
    Adenylate kinase prepared from a temperature-sensitive adk mutant of Escherichia coli was thermolabile at 40 degrees C while the wild type enzyme was stable...
  60. ncbi Nucleotide-binding properties of adenylate kinase from Escherichia coli: a molecular dynamics study in aqueous and vacuum environments
    P Kern
    Department of Pharmacy, ETH, Zurich, Switzerland
    J Comput Aided Mol Des 8:367-88. 1994
    ..Reliable results were achieved only if water was explicitly included in the stimulation...
  61. ncbi Mutations in the nucleotide binding loop of adenylate kinase of Escherichia coli
    J Reinstein
    Max Planck Institut fur medizinische Forschung, Abteilung Biophysik, Heidelberg, West Germany
    Biochemistry 27:4712-20. 1988
    The adk gene of Escherichia coli has been used to overexpress the adenylate kinase protein in two ways: (1) by cloning the adk gene with its own promoter into pEMBL plasmids, which have an increased copy number, and (2) by deleting the ..
  62. ncbi Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers
    M Gerstein
    MRC Laboratory of Molecular Biology, Cambridge, U K
    J Mol Biol 229:494-501. 1993
    ..This jointed domain closure mechanism is contrasted with the shear mechanisms found in other enzymes...
  63. ncbi Structural characterization of adenine nucleotides bound to Escherichia coli adenylate kinase. 1. Adenosine conformations by proton two-dimensional transferred nuclear Overhauser effect spectroscopy
    Y Lin
    Department of Physics, Indiana University Purdue University Indianapolis IUPUI, Indiana 46202 3273, USA
    Biochemistry 39:3636-46. 2000
    ..N. , Jr. (1994) Proteins: Struct., Funct., Genet. 19, 183-198], showed that polarization transfer to the protein protons does not produce significant errors in the structures determined by considering the ligand NOEs alone...
  64. ncbi Crystallization and preliminary X-ray analysis of Escherichia coli adenylate kinase
    S Althoff
    J Mol Biol 199:665-6. 1988
  65. ncbi 1H, 13C and 15N backbone resonance assignment of Escherichia coli adenylate kinase, a 23.6 kDa protein
    S Burlacu-Miron
    J Biomol NMR 13:93-4. 1999
  66. ncbi Genetically engineered zinc-chelating adenylate kinase from Escherichia coli with enhanced thermal stability
    V Perrier
    Laboratoire de Chimie Structurale des Macromolecules, Institut Pasteur, 75724 Paris Cedex 15, France
    J Biol Chem 273:19097-101. 1998
    ..Moreover, the quadruple mutant exhibited a remarkably high thermal stability as compared with the wild-type form with preservation of the kinetic parameters of the parent enzyme...
  67. ncbi Investigation of adenylate kinase from Escherichia coli and its interaction with nucleotides by Fourier transform infrared spectroscopy
    J L Arrondo
    Department of Biochemistry, University of the Basque Country, Bilbao, Spain
    Biochem Cell Biol 67:327-31. 1989
    ..The effect of protein denaturing agents and conditions (temperature, high pH, sodium dodecyl sulfate) on changes in the protein conformation as revealed by the conformation-sensitive amide I bands is discussed...
  68. pmc Adenylate kinase complements nucleoside diphosphate kinase deficiency in nucleotide metabolism
    Q Lu
    Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
    Proc Natl Acad Sci U S A 93:5720-5. 1996
    ..Among the nucleoside monophosphate kinases tested, only adenylate kinase was found to have NDP kinase activity. To our knowledge, this is the first report of NDP kinase activity associated with adenylate kinase...
  69. ncbi Conservative replacement of methionine by norleucine in Escherichia coli adenylate kinase
    A M Gilles
    Unité de Chimie des Protéines, Institut Pasteur, Paris, France
    J Biol Chem 263:8204-9. 1988
    ..Bacteria, transformed by recombinant plasmid pIPD37 carrying the adk gene and grown under limiting methionine and excess norleucine, synthesize 16-20% of adenylate kinase molecules ..
  70. ncbi Modified nucleotides as substrates and inhibitors of adenylate kinase from different sources
    J S Skoblov
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
    FEBS Lett 395:283-5. 1996
    ..3'-Azido-2',3'-dideoxythymidine and its phosphorus derivatives did not inhibit the adenylate kinase reaction...
  71. ncbi Towards a mechanism of AMP-substrate inhibition in adenylate kinase from Escherichia coli
    M A Sinev
    Department of Life Sciences, Bar Ilan University, Ramat Gan, Israel
    FEBS Lett 397:273-6. 1996
    ..Closure of the LID domain in response to AMP binding may be a possible reason for the strong AMP-substrate inhibition known for E. coli AK...
  72. pmc The recR locus of Escherichia coli K-12: molecular cloning, DNA sequencing and identification of the gene product
    A A Mahdi
    Department of Genetics, University of Nottingham, Queens Medical Centre, UK
    Nucleic Acids Res 17:6781-94. 1989
    ..It encodes a polypeptide with a predicted molecular weight of 21,965 Daltons that migrates on SDS gels as a 26 kDa protein. The first gene of the operon encodes a polypeptide of 12,015 daltons. Its function is not known...
  73. ncbi A new subfamily of short bacterial adenylate kinases with the Mycobacterium tuberculosis enzyme as a model: A predictive and experimental study
    H Munier-Lehmann
    Laboratoire de Chimie Structurale des Macromolecules, Institut Pasteur, France
    Proteins 36:238-48. 1999
    The adk gene from Mycobacterium tuberculosis codes for an enzyme of 181 amino acids. A sequence comparison with 52 different forms of adenylate kinases (AK) suggests that the enzyme from M...
  74. pmc The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame
    A M Flower
    Nucleic Acids Res 14:8091-101. 1986
    ..Both the promoters and ribosome binding sites are predicted to be weak, perhaps contributing to the low expression of these genes...
  75. pmc Nucleotide sequence of the Escherichia coli replication gene dnaZX
    K C Yin
    Nucleic Acids Res 14:6541-9. 1986
    ..The dnaZX sequence contains a region homologous to ATP binding sites, suggesting that these replication factors are adenine nucleotide binding proteins...
  76. pmc Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold
    J E Walker
    EMBO J 1:945-51. 1982
    ....
  77. ncbi Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
    C Vonrhein
    Institut fur Organische Chemie und Biochemie, Albert Ludwigs Universitat, Freiburg im Breisgau, Germany
    Structure 3:483-90. 1995
    ..These are concentrated in two chain segments, or domains, of 30 and 38 residues that are involved in binding of the substrates N1TP and N2MP (nucleoside tri- and monophosphates with bases N1 and N2), respectively...
  78. pmc The gamma subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting
    A M Flower
    Department of Biochemistry, Biophysics and Genetics, University of Colorado Health Sciences Center, Denver 80262
    Proc Natl Acad Sci U S A 87:3713-7. 1990
    ..Comparison of the expression of lacZ fused to dnaX distal to the site of frameshifting in the -1 and 0 reading frames indicates that the efficiency of frameshifting is approximately 40%...
  79. ncbi Induced-fit movements in adenylate kinases
    G E Schulz
    Institut fur Organische Chemie und Biochemie, Universitat, Freiburg, F R G
    J Mol Biol 213:627-30. 1990
    ..6 A) but also the 38 residue domain (C alpha shifts up to 32.3 A). Taken together, these observations yield a three-picture "moving film" of the induced-fit...
  80. pmc Multilocus sequence typing versus pulsed-field gel electrophoresis for characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolates
    Lucia L Nemoy
    Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, MSTF Building, Room 9 34, 10 South Pine Street, Baltimore, MD 21201, USA
    J Clin Microbiol 43:1776-81. 2005
    ..MLST has clear utility in studies of ESBL-producing E. coli, based on a greater discriminatory ability and reproducibility than PFGE and the ability to a priori define genetically related bacterial strains...
  81. pmc Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme
    Z Tsuchihashi
    Department of Biochemistry, Stanford University, CA 94305 5307
    Proc Natl Acad Sci U S A 87:2516-20. 1990
    ..e., about 80% in an overproducing cell) and the striking structural similarity to the frameshifting signal responsible for expression of the pol and pro genes in many retroviruses...
  82. pmc Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame
    A L Blinkowa
    Department of Microbiology, University of Texas, Austin 78712
    Nucleic Acids Res 18:1725-9. 1990
    ....

Research Grants1

  1. Proton-coupled electron translocation in metalloenzymes
    ROBERT CUKIER; Fiscal Year: 2006
    ..Contemporaneously, we will explore PTR by simulation methodologies that we are developing, which combine quantum mechanics and molecular dynamics to quantitatively describe proton translocation. ..