Structures and Analysis of Highly Homologous Psychrophilic, Mesophilic, and Thermophilic Adenylate Kinases*

The crystal structures of adenylate kinases from the psychrophile Bacillus globisporus and the mesophile Bacillus subtilis have been solved and compared with that from the thermophile Bacillus stearothermophilus. This is the first example we know of where a trio of protein structures has been solved that have the same number of amino acids and a high level of identity (66–74%) and yet come from organisms with different operating temperatures. The enzymes were characterized for their own thermal denaturation and inactivation, and they exhibited the same temperature preferences as their source organisms. The structures of the three highly homologous, dynamic proteins with different temperature-activity profiles provide an opportunity to explore a molecular mechanism of cold and heat adaptation. Their analysis suggests that the maintenance of the balance between stability and flexibility is crucial for proteins to function at their environmental temperatures, and it is achieved by the modification of intramolecular interactions in the process of temperature adaptation.

• Publication year

  2004

• Venue

  Journal of Biological Chemistry

• Publication date

  2004-07-02

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1074/jbc.M401865200PMID 15100224
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Ribbons.

  2019cited by this paper
• SOMoRe: a multi-dimensional search and optimization approach to molecular replacement.

  2003cited by this paper
• The Structure of a Cold-adapted Family 8 Xylanase at 1.3 Å Resolution

  2003cited by this paper
• Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus.

  2003cited by this paper
• Activity-Stability Relationships in Extremophilic Enzymes*

  2003cited by this paper
• The Hydrophobic Effect: A New Insight from Cold Denaturation and a Two-State Water Structure

  2002cited by this paper
• Contribution of hydrogen bonding to protein stability estimated from isotope effects.

  2002cited by this paper
• Molecular basis of cold adaptation.

  2002cited by this paper
• Comparative structural analysis of psychrophilic and meso‐ and thermophilic enzymes

  2002cited by this paper
• Psychrophiles and polar regions.

  2002cited by this paper
• Small-scale batch crystallization of proteins revisited: an underutilized way to grow large protein crystals.

  2002cited by this paper
• Review: Protein function at thermal extremes: balancing stability and flexibility.

  2001cited by this paper
• Life in extreme environments

  2001cited by this paper
• Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability

  2001cited by this paper
• Enzymes from extremophiles.

  2001cited by this paper
• Thermozymes and their applications

  2001cited by this paper
• Approaches for deciphering the structural basis of low temperature enzyme activity.

  2000cited by this paper
• Psychrophilic enzymes: revisiting the thermodynamic parameters of activation may explain local flexibility.

  2000cited by this paper
• Two exposed amino acid residues confer thermostability on a cold shock protein

  2000cited by this paper
• Effect of Temperature on Stability and Activity of Elongation Factor 2 Proteins from Antarctic and Thermophilic Methanogens

  2000cited by this paper
• Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey.

  2000cited by this paper
• Toward a molecular understanding of cold activity of enzymes from psychrophiles

  2000cited by this paper
• Structural Basis for Cold Adaptation

  1999cited by this paper
• Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products.

  1999cited by this paper
• XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density.

  1999cited by this paper
• Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.

  1998cited by this paper
• Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+

  1998cited by this paper
• The stability of proteins in extreme environments.

  1998cited by this paper
• Analysis of zinc binding sites in protein crystal structures

  1998cited by this paper
• Crystallography & NMR system: A new software suite for macromolecular structure determination.

  1998cited by this paper
• The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins.

  1998cited by this paper
• Processing of X-ray diffraction data collected in oscillation mode.

  1997cited by this paper
• [20] Processing of X-ray diffraction data collected in oscillation mode.

  1997cited by this paper
• New compatible solutes related to Di-myo-inositol-phosphate in members of the order Thermotogales

  1996cited by this paper
• Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 25 Angstroms Resolution.

  1996cited by this paper
• Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding.

  1996cited by this paper
• Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases.

  1995cited by this paper
• Zinc, a structural component of adenylate kinases from gram-positive bacteria

  1994cited by this paper
• Cold adaption of enzymes: Structural comparison between salmon and bovine trypsins

  1994cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994cited by this paper
• Zinc chelation and structural stability of adenylate kinase from Bacillus subtilis.

  1994cited by this paper
• Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers.

  1993cited by this paper
• PROCHECK: a program to check the stereochemical quality of protein structures

  1993cited by this paper
• Zinc, a novel structural element found in the family of bacterial adenylate kinases.

  1992cited by this paper
• 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.

  1992cited by this paper
• Cold denaturation of proteins.

  1990cited by this paper
• Cold Denaturation of Protein

  1990cited by this paper
• WHAT IF: a molecular modeling and drug design program.

  1990cited by this paper
• Bergey's Manual of Systematic Bacteriology

  1989cited by this paper
• Thermoadaptation of methanogenic bacteria by intracellular ion concentration

  1988cited by this paper
• Structural and functional relationships in the adenylate kinase family.

  1987cited by this paper
• 8 Adenylate Kinase

  1973cited by this paper

• Evolutionary-scale enzymology enables exploration of a rugged catalytic landscape.

  2025cites this paper
• Cold-active enzymes from deep marine psychrophiles: harnessing their potential in enhanced food production and sustainability

  2025cites this paper
• Conformational flexibility associated with remote residues regulates the kinetic properties of glutamate dehydrogenase

  2025cites this paper
• Magnesium induced structural reorganization in the active site of adenylate kinase

  2024cites this paper
• Conformational dynamics of adenylate kinase in crystals

  2024cites this paper
• MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability

  2023cites this paper
• The biochemical impact of extracting an embedded adenylate kinase domain using circular permutation

  2023influential citation
• Facile method for high-throughput identification of stabilizing mutations.

  2023cites this paper
• Conformation-Stabilized Amorphous Nanocoating for Rational Design of Long-Term Thermostable Viral Vaccines.

  2022cites this paper
• Structural features, temperature adaptation and industrial applications of microbial lipases from psychrophilic, mesophilic and thermophilic origins.

  2022cites this paper
• Disentanglement of Entropy and Coevolution using Spectral Regularization

  2022cites this paper
• Structure-function relationship of extremozymes

  2022cites this paper
• A meta-analysis of the activity, stability, and mutational characteristics of temperature-adapted enzymes

  2021cites this paper
• Adaptations for Pressure and Temperature in Dihydrofolate Reductases

  2021cites this paper
• Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis

  2021cites this paper
• Investigation of cold-active and mesophilic cellulases: opportunities awaited

  2021cites this paper
• Insights on Rigidity and Flexibility at the Global and Local Levels of Protein Structures and Their Roles in Homologous Psychrophilic, Mesophilic, and Thermophilic Proteins: A Computational Study

  2021cites this paper
• Structural and Functional Characterisation of a Cold-Active Yet Heat-Tolerant Dehydroquinase From Glaciozyma antarctica PI12.

  2021cites this paper
• Biological wastewater treatment plants (WWTPs) for industrial wastewater

  2021cites this paper
• Thermal destabilization mechanism of cytochrome c' from psychrophilic Shewanella violacea.

  2021cites this paper
• CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus

  2021cites this paper
• High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels

  2020cites this paper
• Quantifying the Relationship between Conformational Dynamics and Enzymatic Activity in Ribonuclease HI Homologues.

  2020cites this paper
• Time Resolved Diffraction Studies of Structural Changes in Sensory Rhodopsin

  2019cites this paper
• Distinct roles of an ionic interaction holding an alpha-helix with catalytic Asp and a beta-strand with catalytic His in a hyperthermophilic esterase EstE1 and a mesophilic esterase rPPE

  2019cites this paper
• Structural and mutational analyses of psychrophilic and mesophilic adenylate kinases highlight the role of hydrophobic interactions in protein thermal stability

  2019cites this paper
• Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase

  2019cites this paper
• Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica

  2019cites this paper
• Family permutation profiling identifies a dynamic protein domain as functionally tolerant to increased conformational entropy

  2019cites this paper
• Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts.

  2019influential citation
• Nucleation of an Activating Conformational Change by a Cation-π Interaction.

  2019cites this paper
• Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica

  2019cites this paper
• Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms.

  2018cites this paper
• Enzymatic characteristics of two adenylate kinases, AdkA and AdkB, from Myxococcus xanthus

  2018cites this paper
• The Role of Critical Ion Pairs in the Evolution of a Novel Enzyme in Tomato

  2018cites this paper
• Substrate inhibition imposes fitness penalty at high protein stability

  2018cites this paper
• Combining crystallogenesis methods to produce diffraction-quality crystals of a psychrophilic tRNA-maturation enzyme.

  2018cites this paper
• Molecular Docking Evaluation of (E)-5-arylidene-2-thioxothiazolidin-4-one Derivatives as Selective Bacterial Adenylate Kinase Inhibitors

  2018cites this paper
• Temperature dependent dynamics in highly homologous adenylate kinases

  2018influential citation
• Roles of Active-Site Aromatic Residues in Cold Adaptation of Sphingomonas glacialis Esterase EstSP1

  2017cites this paper
• Psychrophilic Microorganisms as Important Source for Biotechnological Processes

  2017cites this paper
• Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H

  2017cites this paper
• Structural analyses of adenylate kinases from Antarctic and tropical fishes for understanding cold adaptation of enzymes

  2017cites this paper
• Exploring protein dynamics using graph theory and single-molecule spectroscopy

  2017cites this paper
• Evolutionary drivers of thermoadaptation in enzyme catalysis

  2017cites this paper
• Expression and structural investigation of acid tolerant arsenite oxidase with biosensor potential

  2017cites this paper
• Allosteric communication networks and enzymatic regulation as mediated by conformational dynamics in the cyclophilin family of peptidyl-prolyl isomerases

  2017cites this paper
• Thermodynamic and Structural Adaptation Differences between the Mesophilic and Psychrophilic Lactate Dehydrogenases.

  2017cites this paper
• Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation.

  2017cites this paper
• The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation.

  2016cites this paper
• Conserved tyrosine 182 residue in hyperthermophilic esterase EstE1 plays a critical role in stabilizing the active site

  2016cites this paper
• Structural Optimization for Thermal Stabilization of Adenylate Kinases

  2016cites this paper
• Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii

  2016cites this paper
• Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes

  2016cites this paper
• Corrigendum: Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii

  2016cites this paper
• Crystal structure of fuculose aldolase from the Antarctic psychrophilic yeast Glaciozyma antarctica PI12.

  2016cites this paper
• Comparing the thermal, chemical and mechanical stabilities of extremophilic cold shock protein variants

  2016cites this paper
• Draft Genome Sequence of Sporosarcina globispora W 25T (DSM 4), a Psychrophilic Bacterium Isolated from Soil and River Water

  2015cites this paper
• Improving the Thermostability and Activity of a Thermophilic Subtilase by Incorporating Structural Elements of Its Psychrophilic Counterpart

  2015cites this paper
• Enhanced functionality and stabilization of a cold active laccase using nanotechnology based activation-immobilization.

  2015cites this paper
• Structural features determining thermal adaptation of esterases

  2015cites this paper
• Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case.

  2015cites this paper
• Conformational preferences underlying reduced activity of a thermophilic ribonuclease H.

  2015cites this paper
• Structure and Dynamics of GeoCyp: A Thermophilic Cyclophilin with a Novel Substrate Binding Mechanism That Functions Efficiently at Low Temperatures.

  2015cites this paper
• Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations

  2015cites this paper
• Structural Basis Underlying the Binding Preference of Human Galectins-1, -3 and -7 for Galβ1-3/4GlcNAc

  2015cites this paper
• Bioinformatics-Driven Enzyme Engineering: Work On Adenylate Kinase

  2015influential citation
• Molecular dynamics simulation of a psychrophilic adenylate kinase

  2015cites this paper
• Leveraging the Mechanism of Oxidative Decay for Adenylate Kinase to Design Structural and Functional Resistances.

  2015cites this paper
• Correction: Role of Key Salt Bridges in Thermostability of G. thermodenitrificans EstGtA2: Distinctive Patterns within the New Bacterial Lipolytic Enzyme Family XV

  2015cites this paper
• Nanotechnology based activation-immobilization of psychrophilic pectate lyase: A novel approach towards enzyme stabilization and enhanced activity

  2015cites this paper
• Polar Microbiology: Recent Advances and Future Perspectives

  2014cites this paper
• Adenylate kinase from Streptococcus pneumoniae is essential for growth through its catalytic activity

  2014cites this paper
• Expression and Thermostability study of Triose Phosphate Isomerase (TIM) from Pseudomonas π9, a Psychrophilic Bacterium

  2014cites this paper
• Life in the cold biosphere: The ecology of psychrophile communities, genomes, and genes

  2014cites this paper
• Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12

  2014cites this paper
• Circular Dichroism and Fluorescence Spectroscopy of Cysteinyl-tRNA Synthetase from Halobacterium salinarum ssp. NRC-1 Demonstrates that Group I Cations Are Particularly Effective in Providing Structure and Stability to This Halophilic Protein

  2014cites this paper
• Cold growth behaviour and genetic comparison of Canadian and Swiss Listeria monocytogenes strains associated with the food supply chain and human listeriosis cases.

  2014cites this paper
• Engineering lipase A from mesophilic Bacillus subtilis for activity at low temperatures.

  2014cites this paper
• Structural and denaturation studies of two mutants of a cold adapted superoxide dismutase point to the importance of electrostatic interactions in protein stability.

  2014cites this paper
• Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases

  2014cites this paper
• Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

  2014cites this paper
• Effect of chemical oxidation on the sorption tendency of dissolved organic matter to a model hydrophobic surface.

  2014cites this paper
• Crystal structures of thermally stable adenylate kinase mutants designed by local structural entropy optimization and structure-guided mutagenesis

  2014cites this paper
• An integrated approach for thermal stabilization of a mesophilic adenylate kinase

  2014cites this paper
• Understanding thermal adaptation of enzymes through the multistate rational design and stability prediction of 100 adenylate kinases.

  2014cites this paper
• Psychrophily and Catalysis

  2013cites this paper
• Thermodynamic Stability of Psychrophilic and Mesophilic Pheromones of the Protozoan Ciliate Euplotes

  2013cites this paper
• Psychrophilic Enzymes: From Folding to Function and Biotechnology

  2013cites this paper
• Protein Adaptations in Archaeal Extremophiles

  2013cites this paper
• Role of Key Salt Bridges in Thermostability of G. thermodenitrificans EstGtA2: Distinctive Patterns within the New Bacterial Lipolytic Enzyme Family XV

  2013cites this paper
• Thermal Adaptation of Conformational Dynamics in Ribonuclease H

  2013cites this paper
• Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis

  2013cites this paper
• Inhibition of Streptococcus pneumoniae adenylate kinase by some 5-arylidene-thiazolidin-4-on-2-thione derivates

  2013cites this paper
• Energetics of protein stability at extreme environmental temperatures in bacterial trigger factors.

  2013cites this paper
• Effect of dimerization on dihydrofolate reductase catalysis.

  2013cites this paper
• Role of lysine during protein modification by HOCl and HOBr: halogen-transfer agent or sacrificial antioxidant?

  2013cites this paper
• Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism

  2013cites this paper
• Insights into Adenylate Kinase Mechanism and Evolution on the Molecular Level

  2013cites this paper
• Thermal unfolding studies of cold adapted uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). A comparative study with human UNG.

  2012cites this paper