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MACiE: a database of enzyme reaction mechanisms

G. L. Holliday, G. J. Bartlett, D. E. Almonacid, N. M. O'Boyle, P. Murray-Rust, J. M. Thornton, J. B. O. Mitchell
2005 Bioinformatics  
MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme  ...  catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bti693 pmid:16188925 pmcid:PMC2748267 fatcat:2uya3zgehzhhrj2bkhkngudwwy

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

António J M Ribeiro, Gemma L Holliday, Nicholas Furnham, Jonathan D Tyzack, Katherine Ferris, Janet M Thornton
2017 Nucleic Acids Research  
M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic  ...  M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at thornton-srv/m-csa.  ...  CONTENT UPDATE Merging CSA and MACiE MACiE (22-24) was a database of enzyme mechanisms that primarily annotated individual mechanism reaction steps with 2D curly arrow schemes, the roles of catalytic  ... 
doi:10.1093/nar/gkx1012 pmid:29106569 pmcid:PMC5753290 fatcat:sep5alggufdb7msnnlsx47dlmq

MACiE: exploring the diversity of biochemical reactions

Gemma L. Holliday, Claudia Andreini, Julia D. Fischer, Syed Asad Rahman, Daniel E. Almonacid, Sophie T. Williams, William R. Pearson
2011 Nucleic Acids Research  
MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from MACiE/.  ...  This version of MACiE represents a shift in emphasis for new entries, from nonhomologous representatives covering EC reaction space to enzymes with mechanisms of interest to our users and collaborators  ...  We are also starting a long-term collaboration with the SFLD, a database of 'promiscuous' enzyme superfamilies, so that all reactions in that database that fulfil the criteria for inclusion into MACiE  ... 
doi:10.1093/nar/gkr799 pmid:22058127 pmcid:PMC3244993 fatcat:byhlceunrncahhkl6jvj2ufohu

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms

G. L. Holliday, D. E. Almonacid, G. J. Bartlett, N. M. O'Boyle, J. W. Torrance, P. Murray-Rust, J. B. O. Mitchell, J. M. Thornton
2007 Nucleic Acids Research  
MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource.  ...  This paper presents the first release of a web-based search tool to explore enzyme reaction mechanisms in MACiE.  ...  DATABASE FEATURES The original release of MACiE contained static images and annotation for the overall reaction and each step associated with the mechanism; it also included an animated reaction mechanism  ... 
doi:10.1093/nar/gkl774 pmid:17082206 pmcid:PMC1634735 fatcat:h7j6f74pbbcj5mya7ntcnvas6m

Co-culturing experiments reveal the uptake of myo-inositol phosphate synthase (EC in an inositol auxotroph of Saccharomyces cerevisiae

Erika Steele, Hana D. Alebous, Macy Vickers, Mary E. Harris, Margaret D. Johnson
2021 Microbial Cell Factories  
of inositol isolated from S. cerevisiae cells containing either wild-type enzyme (Wt-MIP), no MIP enzyme, auxotroph (Aux), or a green fluorescent protein (GFP) tagged reporter enzyme (MIP- GFP) in co-  ...  These findings revealed previously unknown functions, suggesting that the enzyme can: (1) move into and out of intercellular space, (2) traverse cell walls, and (3) act as a growth factor to promote cellular  ...  Consequently, we can now employ new experimental approaches to define mechanisms that regulate the complex metabolic flux of inositol phosphate biosynthesis and delineate the role of an essential enzyme  ... 
doi:10.1186/s12934-021-01610-6 pmid:34281557 pmcid:PMC8287684 fatcat:cah4dyagirh3bfqrksh5ehj3ve

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

Nicholas Furnham, Gemma L. Holliday, Tjaart A. P. de Beer, Julius O. B. Jacobsen, William R. Pearson, Janet M. Thornton
2013 Nucleic Acids Research  
To ease the transfer of CSA annotations to other resources a new ontology has been developed: the Enzyme Mechanism Ontology, which has permitted the transfer of annotations to Mechanism, Annotation and  ...  Classification in Enzymes (MACiE) and UniProt Knowledge Base (UniProtKB) resources.  ...  ACKNOWLEDGEMENTS The authors would like to thank the efforts of the many annotators who have contributed to the curated entries in the CSA. We would also like to thank Dr Syed A.  ... 
doi:10.1093/nar/gkt1243 pmid:24319146 pmcid:PMC3964973 fatcat:jb465gitcjdgxkrr3lw3drfa6m

The nitration of τ protein in neurone-like PC12 cells

Graziella Cappelletti, Gabriella Tedeschi, Maria G. Maggioni, Armando Negri, Simona Nonnis, Rosalba Maci
2004 FEBS Letters  
Tyrosine nitration of proteins is emerging as a posttranslational modi¢cation playing a role in physiological conditions.  ...  This paper supplies the ¢rst evidence that nitration of d d occurs in a physiological process and suggests that it could play a role in neuronal di¡erentiation.  ...  Looking for mechanisms of d regulation in neuronal cells, activation of protein kinases and phosphatases plays a primary role [20] .  ... 
doi:10.1016/s0014-5793(04)00173-5 pmid:15043998 fatcat:rq7zd6x6yvcornj22h4mjqc3fm

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt, Christine A. Orengo
2010 PLoS Computational Biology  
their EC codes) from the MACiE database.  ...  Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of  ...  Sunil Ojha for fruitful discussions about enzyme reaction mechanisms and enzyme evolution, and Dr. Gemma Holliday for providing MACiE version 2.3.9 data in RDF format and pictures in CDX format.  ... 
doi:10.1371/journal.pcbi.1000700 pmid:20300652 pmcid:PMC2837397 fatcat:gzf6fvbshzh6xcg5xuxargqs4i

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis

Gemma L. Holliday, Julia D. Fischer, John B. O. Mitchell, Janet M. Thornton
2011 The FEBS Journal  
MACiE [8, 9, 10] ( databases/MACiE), a database of distinct enzyme mechanisms, was thus created in order to enable a better understanding of how enzymes perform this  ...  enzymes (MACiE M0052 and M0222, EC, in which a cyclic permutation changes the mechanism of the reaction, but not the overall reaction]; and (b) the domain combination of the enzymes may also  ...  Appendix The appendix describes the methods used in the database analysis for determining the enzyme-to-reaction mapping for both the sequence and structure space.  ... 
doi:10.1111/j.1742-4658.2011.08190.x pmid:21605342 pmcid:PMC3258480 fatcat:gwyfpzuedzfj7ls7rdxu75eyqq

A New Chemolithoautotrophic Arsenite-Oxidizing Bacterium Isolated from a Gold Mine: Phylogenetic, Physiological, and Preliminary Biochemical Studies

J. M. Santini, L. I. Sly, R. D. Schnagl, J. M. Macy
2000 Applied and Environmental Microbiology  
A previously unknown chemolithoautotrophic arsenite-oxidizing bacterium has been isolated from a gold mine in the Northern Territory of Australia.  ...  Based upon 16S rDNA phylogenetic sequence analysis, NT-26 belongs to the Agrobacterium/Rhizobium branch of the ␣-Proteobacteria and may represent a new species.  ...  For these heterotrophic bacteria, the oxidation (equation 1) is considered a detoxification mechanism rather than one that can support growth, despite the fact that the reaction is exergonic. 2H 3 AsO  ... 
doi:10.1128/aem.66.1.92-97.2000 pmid:10618208 pmcid:PMC91790 fatcat:nx6qx7rryfdvvmei5kwyoudf3q

The Natural History of Biocatalytic Mechanisms

Neetika Nath, John B. O. Mitchell, Gustavo Caetano-Anollés, Marco Punta
2014 PLoS Computational Biology  
A total of 335 enzyme reactions were retrieved from MACiE and were mapped over fold age.  ...  We define a mechanistic step type as one of the 51 mechanistic annotations given in MACiE, and each step of each of the 335 mechanisms was described using one or more of these annotations.  ...  In this study, we used 51 mechanism annotation definitions from the MACiE database, which can be associated with the steps defined for the enzyme-catalyzed reactions.  ... 
doi:10.1371/journal.pcbi.1003642 pmid:24874434 pmcid:PMC4038463 fatcat:how57kfrmrhitjsskwn4l7v6bi

Using Reaction Mechanism to Measure Enzyme Similarity

Noel M. O'Boyle, Gemma L. Holliday, Daniel E. Almonacid, John B.O. Mitchell
2007 Journal of Molecular Biology  
An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanism.  ...  The concept of reaction similarity has been well-studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism.  ...  Dataset To test our proposed measures of reaction mechanism similarity, we used version 1.1 of the MACiE database 18 of enzyme reaction mechanisms.  ... 
doi:10.1016/j.jmb.2007.02.065 pmid:17400244 pmcid:PMC3461574 fatcat:yzx56y2e2raqvlwx4sownabeny

Toward mechanistic classification of enzyme functions

Daniel E Almonacid, Patricia C Babbitt
2011 Current Opinion in Chemical Biology  
Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic  ...  Together, these provide a foundation for new classifications of enzyme function.  ...  Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California San Francisco (supported by NIH  ... 
doi:10.1016/j.cbpa.2011.03.008 pmid:21489855 pmcid:PMC3551611 fatcat:yy6jwgqljrc7bpotr5bwfhxiei

Enzyme function and its evolution

John BO Mitchell
2017 Current Opinion in Structural Biology  
With rapid increases over recent years in the determination of protein sequence and structure, alongside knowledge of thousands of enzyme functions and hundreds of chemical mechanisms, it is now possible  ...  Protein function prediction has spawned a variety of promising methods that offer the prospect of identifying enzymes across the whole range of chemical functions and over numerous species.  ...  To address this, the database MACiE [24] provides a catalogue of around 350 mechanisms in both human-readable and computer-readable forms.  ... 
doi:10.1016/ pmid:29107208 fatcat:4262jiog6zacxp4mhwwyiyfsna

Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry

Kirsten E. Beattie, Luna De Ferrari, John B. O. Mitchell
2015 Evolutionary Bioinformatics  
A MACiE mechanism identifier corresponds to a detailed enzyme mecha nism entry in the MACiE database modeled on one PDB struc ture and its associated literature.  ...  Annota tion, and Classification in Enzymes) 23, 24 database from which our enzyme mechanism assignments were taken; this database contains 335 entries of fully annotated enzyme mechanisms, each with  ...  Author contributions Assisted with the curation of the dataset and analysis of the results and wrote the report that formed the basis of the first draft of this manuscript: KEB.  ... 
doi:10.4137/ebo.s31482 pmid:26740739 pmcid:PMC4696837 fatcat:h3hwbamgcfgjhjtjln35xrnk4q
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