Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence-Function Relationships.

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Biochemistry

• Publication date

  2016-11-11

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1021/ACS.BIOCHEM.6B00723PMID 27802036
• 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.

• Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies

  2016cited by this paper
• Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

  2016cited by this paper
• Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis.

  2016cited by this paper
• An Evolved Orthogonal Enzyme/Cofactor Pair.

  2016cited by this paper
• How mutational epistasis impairs predictability in protein evolution and design

  2016cited by this paper
• A new view of the tree of life

  2016cited by this paper
• The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism

  2016cited by this paper
• Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements

  2016cited by this paper
• Model-driven discovery of underground metabolic functions in Escherichia coli

  2015cited by this paper
• Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics

  2015cited by this paper
• Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution.

  2015cited by this paper
• Diversity in protein domain superfamilies

  2015cited by this paper
• Distinct Metal Isoforms Underlie Promiscuous Activity Profiles of Metalloenzymes.

  2015cited by this paper
• Panoramic view of a superfamily of phosphatases through substrate profiling

  2015cited by this paper
• Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria.

  2015cited by this paper
• The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions

  2015cited by this paper
• How do regulatory networks evolve and expand throughout evolution?

  2015cited by this paper
• Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.

  2015cited by this paper
• Cryptic genetic variation: evolution's hidden substrate

  2014cited by this paper
• Resilience of biochemical activity in protein domains in the face of structural divergence.

  2014cited by this paper
• Network-level architecture and the evolutionary potential of underground metabolism

  2014cited by this paper
• Metal Preferences and Metallation

  2014cited by this paper
• CATH: comprehensive structural and functional annotations for genome sequences

  2014cited by this paper
• Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network

  2014cited by this paper
• Strong epistatic interactions within a single protein.

  2014cited by this paper
• Metabolomic strategies for the identification of new enzyme functions and metabolic pathways

  2014cited by this paper
• Hopeful (protein InDel) monsters?

  2014cited by this paper
• Evolutionary relationship of two ancient protein superfolds.

  2014cited by this paper
• Dynamics and constraints of enzyme evolution.

  2014cited by this paper
• Connectivity between catalytic landscapes of the metallo-β-lactamase superfamily.

  2014cited by this paper
• Differential Effects of a Mutation on the Normal and Promiscuous Activities of Orthologs: Implications for Natural and Directed Evolution

  2014cited by this paper
• What can we learn from fitness landscapes?

  2014cited by this paper
• New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships*

  2014cited by this paper
• A high-throughput, multiplexed assay for superfamily-wide profiling of enzyme activity

  2014cited by this paper
• The Mismetallation of Enzymes during Oxidative Stress*

  2014cited by this paper
• Revealing the hidden functional diversity of an enzyme family.

  2014cited by this paper
• The evolutionary paths towards complexity: a metabolic perspective.

  2014cited by this paper
• Large-Scale Determination of Sequence, Structure, and Function Relationships in Cytosolic Glutathione Transferases across the Biosphere

  2014cited by this paper
• Discovery of new enzymes and metabolic pathways using structure and genome context

  2013cited by this paper
• Structure-guided discovery of new deaminase enzymes.

  2013cited by this paper
• The Structure–Function Linkage Database

  2013cited by this paper
• Evolutionary biochemistry: revealing the historical and physical causes of protein properties

  2013cited by this paper
• Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer.

  2013cited by this paper
• Functional and evolutionary implications of gene orthology

  2013cited by this paper
• A large-scale evaluation of computational protein function prediction

  2013cited by this paper
• Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

  2013cited by this paper
• Strategies for the discovery and engineering of enzymes for biocatalysis.

  2013cited by this paper
• Cofactor promiscuity among F 420 -dependent reductases enables them to catalyse both oxidation and reduction of the same substrate

  2012cited by this paper
• Evolution of the Chalcone Isomerase Fold from Fatty Acid-Binding to Stereospecific Enzyme

  2012cited by this paper
• Arabidopsis ETHE1 Encodes a Sulfur Dioxygenase That Is Essential for Embryo and Endosperm Development1[C][OA]

  2012cited by this paper
• Pythoscape: a framework for generation of large protein similarity networks

  2012cited by this paper
• The Rise of Chemodiversity in Plants

  2012cited by this paper
• Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

  2012cited by this paper
• Network Context and Selection in the Evolution to Enzyme Specificity

  2012cited by this paper
• Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study.

  2012cited by this paper
• Moonlighting is mainstream: Paradigm adjustment required

  2012cited by this paper
• Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones.

  2012cited by this paper
• Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates

  2012cited by this paper
• Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

  2012cited by this paper
• Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication

  2012cited by this paper
• Intramolecular Epistasis and the Evolution of a New Enzymatic Function

  2012cited by this paper
• Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling.

  2012cited by this paper
• Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

  2012cited by this paper
• Toward a Systems Biology Perspective on Enzyme Evolution*

  2011cited by this paper
• Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase*

  2011cited by this paper
• 3-Keto-5-aminohexanoate Cleavage Enzyme

  2011cited by this paper
• Divergent Evolution in Enolase Superfamily: Strategies for Assigning Functions*

  2011cited by this paper
• Iron-containing urease in a pathogenic bacterium

  2011cited by this paper
• Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies.

  2011cited by this paper
• The Enzyme Function Initiative.

  2011cited by this paper
• The Pfam protein families database

  2011cited by this paper
• Inference of Functional Properties from Large-scale Analysis of Enzyme Superfamilies*

  2011cited by this paper
• Enzyme promiscuity: a mechanistic and evolutionary perspective.

  2010cited by this paper
• Robustness and evolvability.

  2010cited by this paper
• Analyzing protein structure and function using ancestral gene reconstruction.

  2010cited by this paper
• The evolution of gene duplications: classifying and distinguishing between models

  2010cited by this paper
• Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli

  2010cited by this paper
• Pervasive Cryptic Epistasis in Molecular Evolution

  2010cited by this paper
• What makes an enzyme promiscuous?

  2010cited by this paper
• Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

  2009cited by this paper
• An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

  2009cited by this paper
• Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

  2009cited by this paper
• Protein promiscuity and its implications for biotechnology

  2009cited by this paper
• Enzyme activities and subcellular localization of members of the Arabidopsis glutathione transferase superfamily

  2009cited by this paper
• Docking and chemoinformatic screens for new ligands and targets.

  2009cited by this paper
• Exploring protein fitness landscapes by directed evolution

  2009cited by this paper
• Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

  2009cited by this paper
• From Kinase to Cyclase: An Unusual Example of Catalytic Promiscuity Modulated by Metal Switching

  2009cited by this paper
• Evolution of efficient pathways for degradation of anthropogenic chemicals.

  2009cited by this paper
• Protein Dynamism and Evolvability

  2009cited by this paper
• Cofactor-mediated protein promiscuity

  2009cited by this paper
• How do bacterial cells ensure that metalloproteins get the correct metal?

  2009cited by this paper
• Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms

  2008cited by this paper
• Activity-based protein profiling: from enzyme chemistry to proteomic chemistry.

  2008cited by this paper
• The pyrroloquinoline quinone biosynthesis pathway revisited: A structural approach

  2008cited by this paper
• A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities

  2008cited by this paper
• The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

  2008cited by this paper
• Neutralism and selectionism: a network-based reconciliation

  2008cited by this paper
• Neutral genetic drift can aid functional protein evolution

  2007cited by this paper
• Exploiting temperature-dependent substrate promiscuity for nucleoside analogue activation by thymidine kinase from Thermotoga maritima.

  2007cited by this paper

• Deciphering enzymatic potential in metagenomic reads through DNA language models

  2025cites this paper
• Exploring Large Protein Sequence Space through Homology- and Representation-based Hierarchical Clustering

  2025cites this paper
• Chlorpyrifos degrading potential of a novel Kosakonia sp. FYF33 isolated from agricultural drainage water

  2025cites this paper
• Rapid continuous evolution of gene libraries towards arbitrary functions

  2025cites this paper
• UDP-Glycosyltransferases Engineering Coupled with UDPG Regeneration Facilitate the Efficient Conversion of Mogroside V.

  2025cites this paper
• New insights into exploring new functional enzymes through the enzyme promiscuity.

  2025cites this paper
• Stability of multi-species consortia during microbial metabolic evolution

  2025cites this paper
• ANTIMICROBIAL ACTIVITY OF SPECIALISED METABOLITES OF SOIL STREPTOMYCETES-CHITINOLYTIC

  2024cites this paper
• Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction.

  2024cites this paper
• Multifunctionality of alkaline phosphatase in ecology and biotechnology.

  2024cites this paper
• Antimicrobial Activity of Specialized Metabolites of Soil Chitinolytic Streptomycetes

  2024cites this paper
• Molecular determinants of protein evolvability.

  2023cites this paper
• Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles

  2023cites this paper
• Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution

  2023cites this paper
• The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities

  2023cites this paper
• Adventures on the Routes of Protein Evolution—In Memoriam Dan Salah Tawfik (1955–2021)

  2022cites this paper
• Adventures on the routes of protein evolution - in memoriam Dan Salah Tawfik (1955 - 2021).

  2022cites this paper
• Using mechanism similarity to understand enzyme evolution

  2022cites this paper
• Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase

  2022cites this paper
• Unusual commonality in active site structural features of substrate promiscuous and specialist enzymes.

  2022cites this paper
• Altering the binding determinant on the interdigitating loop of mandelate racemase shifts specificity towards that of d-tartrate dehydratase.

  2022cites this paper
• Enzyme promiscuity in natural environments: alkaline phosphatase in the ocean

  2021cites this paper
• The Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase

  2021cites this paper
• Phthalate hydrolase: distribution, diversity and molecular evolution.

  2021cites this paper
• Contrastive Multiview Coding for Enzyme-Substrate Interaction Prediction

  2021cites this paper
• The Birth of Genomic Enzymology: Discovery of the Mechanistically Diverse Enolase Superfamily.

  2021cites this paper
• Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design.

  2021cites this paper
• Evolution of β-lactamases and enzyme promiscuity.

  2021cites this paper
• Machine learning differentiates enzymatic and non-enzymatic metals in proteins

  2021cites this paper
• Engineering the protein dynamics of an ancestral luciferase

  2020cites this paper
• Submergence response of pyruvate decarboxylase family genes in adzuki bean

  2020cites this paper
• Learning graph representations of biochemical networks and its application to enzymatic link prediction

  2020cites this paper
• Harnessing Conformational Plasticity to Generate Designer Enzymes

  2020cites this paper
• A mechanistic view of enzyme evolution

  2020cites this paper
• Biochemical characterization of 2-phosphinomethylmalate synthase from Streptomyces hygroscopicus: A member of the DRE-TIM metallolyase superfamily.

  2020cites this paper
• Dual activity of PNGM-1, a metallo-β-lactamase and tRNase Z, pinpoints the evolutionary origin of subclass B3 metallo-β-lactamases

  2019cites this paper
• A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases.

  2019cites this paper
• Dual activity of PNGM-1 pinpoints the evolutionary origin of subclass B3 metallo-β-lactamases: a molecular and evolutionary study

  2019cites this paper
• Characterization of alkaline phosphatase PhoK from Sphingomonas sp. BSAR-1 for phosphate monoester synthesis and hydrolysis.

  2019cites this paper
• Computational physical organic chemistry using the empirical valence bond approach

  2019cites this paper
• Efecto de medicamentos homeopáticos sobre crecimiento, supervivencia y microbiota gastrointestinal, en juveniles del pectínido Argopecten ventricosus

  2019cites this paper
• Functional Metagenomics Reveals a New Catalytic Domain, the Metallo-β-Lactamase Superfamily Domain, Associated with Phytase Activity

  2019cites this paper
• Functional Analysis of Enzyme Families Using Residue-Residue Coevolution Similarity Networks

  2019influential citation
• Horizontal transfer of promiscuous activity from non-photosynthetic bacteria contributed to evolution of chlorophyll degradation pathway.

  2019cites this paper
• Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions.

  2019cites this paper
• The Early Asexual Development Regulator fluG Codes for a Putative Bifunctional Enzyme

  2019cites this paper
• Enzyme Evolution

  2019cites this paper
• Following the Evolutionary Track of a Highly Specific l-Arginine Oxidase by Reconstruction and Biochemical Analysis of Ancestral and Native Enzymes

  2019cites this paper
• Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes

  2019cites this paper
• Functional Profiling and Crystal Structures of Isothiocyanate Hydrolases Found in Gut-Associated and Plant-Pathogenic Bacteria

  2018cites this paper
• Enzyme evolution: innovation is easy, optimization is complicated.

  2018cites this paper
• Evolutionary Effects on Bound Substrate p Ka in Dihydrofolate Reductase.

  2018cites this paper
• Ancestral diterpene cyclases show increased thermostability and substrate acceptance

  2018cites this paper
• Tailoring Proteins to Re-Evolve Nature: A Short Review

  2018cites this paper
• Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution

  2018cites this paper
• Metabolite-Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks.

  2018cites this paper
• Biochemical Profiling of DMSP Lyases.

  2018cites this paper
• Underground metabolism: network-level perspective and biotechnological potential.

  2018cites this paper
• Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein

  2018cites this paper
• Canine and Feline Differences in the Cytochrome P450 Transcriptome and Drug Metabolism

  2018cites this paper
• Machine Learning for Enzyme Promiscuity

  2018cites this paper
• Approach in Function Annotation to Enzymes

  2018cites this paper
• Discovery and analysis of a novel type of the serine biosynthetic enzyme phosphoserine phosphatase in Thermus thermophilus

  2018cites this paper
• CHARACTERIZATION AND MUTATION OF IODOTYROSINE DEIODINASE FROM Haliscomenobacter hydrossis FOR DETOXIFICATION OF IODOPHENOLS

  2017cites this paper
• Understanding enzyme function evolution from a computational perspective.

  2017cites this paper
• Crystal structures reveal metal-binding plasticity at the metallo-β-lactamase active site of PqqB from Pseudomonas putida

  2017cites this paper
• Evolution of an enzyme from a solute-binding protein

  2017cites this paper
• Artificial metalloenzymes as catalysts in non-natural compounds synthesis

  2017cites this paper
• Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution

  2017cites this paper
• Cryptic genetic variation defines the adaptive evolutionary potential of enzymes

  2017cites this paper
• Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence–Function Space and Genome Context to Discover Novel Functions

  2017cites this paper