Searching the Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
In order to understand the evolution of enzyme reactions and to gain an overview of biological catalysis we have combined sequence and structural data to generate phylogenetic trees in an analysis of 276 structurally defined enzyme superfamilies, and used these to study how enzyme functions have evolved. We describe in detail the analysis of two superfamilies to illustrate different paradigms of enzyme evolution. Gathering together data from all the superfamilies supports and develops the observation that they have all evolved to act on a diverse set of substrates, whilst the evolution of new chemistry is much less common. Despite that, by bringing together so much data, we can provide a comprehensive overview of the most common and rare types of changes in function. Our analysis demonstrates on a larger scale than previously studied, that modifications in overall chemistry still occur, with all possible changes at the primary level of the Enzyme Commission (E.C.) classification observed to a greater or lesser extent. The phylogenetic trees map out the evolutionary route taken within a superfamily, as well as all the possible changes within a superfamily. This has been used to generate a matrix of observed exchanges from one enzyme function to another, revealing the scale and nature of enzyme evolution and that some types of exchanges between and within E.C. classes are more prevalent than others. Surprisingly a large proportion (71%) of all known enzyme functions are performed by this relatively small set of 276 superfamilies. This reinforces the hypothesis that relatively few ancient enzymatic domain superfamilies were progenitors for most of the chemistry required for life.
Pubmed ID: 22396634
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
The Wellcome Trust is the largest charity in the UK. We fund innovative biomedical research, in the UK and internationally, spending over 600 million each year to support the brightest scientists with the best ideas. The Wellcome Trust is an independent charity funding research to improve human and animal health. Established in 1936 and with an endowment of around 13 billion, it is the UK's largest non-governmental source of funds for biomedical research. What we do We spend over 600 million every year both in the UK and internationally achieving our mission. Funding We support many different kinds of research and activities with the ultimate aim of protecting and improving human and animal health. This support is not restricted to UK researchers - we devote significant funding to international research too. Biomedical science Our biomedical science funding enables the investigation of health and disease in humans and animals. This includes funding for scientists, clinicians and veterinarians at different career stages. Technology transfer Our technology transfer funding supports the development of innovative, early-stage projects with potential medical applications. Medical humanities Our medical humanities funding supports research into biomedical ethics and the history of medicine. Public engagement Our public engagement funding promotes interest, excitement and debate around science and society. Capital funding Our capital funding is for large-scale construction or refurbishment projects in the UK that support science, public engagement, medical history, or the activities of learned societies. Strategic awards Our Strategic Awards provide flexible funding that adds value to excellent research groups. Managing a grant This area contains information and resources to help you manage a grant once it has been awarded, from the grant-start certificate to the end-of-grant report and beyond. Education Resources Teaching and education Resources to help promote contemporary science in the curriculum and to enable young people to engage with biomedical science. Tree of Life Darwin200 Big Picture Science Learning Centres Scientific animations Creative Encounters Courses and conferences Trust-run conferences, courses and workshops for scientists, historians, ethicists, social scientists, teachers, healthcare professionals and policymakers, held in the UK and overseas. Advanced Courses Scientific conferences Conference centres Retreats History of medicine Biomedical ethics Biomedical resources Tools, databases and information to support different areas of biomedical research, including genomics, post-genomics and developmental biology. Animal research Genomics Model organisms Microorganisms Post-genomics Tissues Researcher support Support and advice for all kinds of engagement activities to help you communicate your work in the most effective and rewarding way possible. About researcher support National opportunities Regional opportunities Highlights Publications Browse a wealth of publications covering all aspects of the work we fund. Wellcome Trust websites Explore a range of sites covering key biomedical topics and our public engagement activities.
View all literature mentionsThe UK''s leading funding agency for academic research and training in the non-clinical life sciences.
View all literature mentionsThe mission of the Department of Energy is to ensure America''s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. Goal 1: Transform our Energy Systems - Catalyze the timely, material, and efficient transformation of the nation''s energy system and secure U.S. leadership in clean energy technologies. Goal 2: The Science and Engineering Enterprise - Maintain a vibrant U.S. effort in science and engineering as a cornerstone of our economic prosperity, with clear leadership in strategic areas. Goal 3: Secure Our Nation - Enhance nuclear security through defense, nonproliferation, and environmental efforts. Goal 4: Management and Operational Excellence - Establish an operational and adaptable framework that combines the best wisdom of all Department stakeholders to maximize mission success.
View all literature mentionsCentral repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway.
View all literature mentionsSoftware package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
View all literature mentions