The MACiE Database

MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project between the the Thornton Group at the European Bioinformatics Institute and the Mitchell Group at the University of St Andrews (initially within the Unilever Centre for Molecular Informatics part of the University of Cambridge). We have also now extended to collaboration to include the Bertini Group at the Magnetic Resonance Center (CERM) in Florence (Italy). This aspect of the collaboration incorporates the expertise of CERM with metalloproteins and we have developed Metal MACiE, a database of catalytic metal ions, with a view to understanding the functions of the roles and activity of catalytic metals in enzymes.

Enzyme-catalysed reactions are ubiquitous and essential to the chemistry of life. A great deal of knowledge, including structures, gene sequences, mechanisms, metabolic pathways and kinetic data exists, but is spread between many different databases and throughout the literature. The initial version of MACiE is completed, the world's first electronic database of the chemical mechanisms of enzymatic reactions.

Data are currently being held in ISIS/Base, CMLReact, an XML application, and MySQL. The web interface uses the MySQL implementation of MACiE, and we aim to maintain MACiE in all three environments for the foreseeable fulture. However, we expect that CMLReact and MySQL will eventually become the primary formats in which MACiE is stored and accessed.

Publications relating to MACiE

MACiE: Exploring the diversity of biochemical reactions. G. L. Holliday, C. Andreini, J. D. Fischer, S. A. Rahman, D. E. Almonacid, S. T. Williams and W. R. Pearson, Nucleic Acids Res., 40, D783-D789, 2012. Medline ID: 21605342

The structures and physicochemical properties of organic cofactors in biocatalysis. J. D. Fischer, G. L. Holliday, S. A. Rahman and J. M. Thornton, J. Mol. Biol., 403, 803-824, 2010. Medline ID: 20850456

The CoFactor database: Organic cofactors in enzyme catalysis. J. D. Fischer, G. L. Holliday and J. M. Thornton, Bioinformatics, 26, 2496-2497, 2010. Medline ID: 20679331

Metal-MACiE: a database of metals involved in biological catalysis. C. Andreini, I. Bertini, G. Cavallaro, G. L. Holliday and J. M. Thornton, Bioinformatics, 25, 2088-2089, 2009. Medline ID: 19369503

Understanding the functional roles of amino acid residues in enzyme catalysis. G. L. Holliday, J. B. O. Mitchell and J. M. Thornton, J. Mol. Biol., 390, 560-577, 2009. Medline ID: 19447117. Dataset used for this analysis.

Metal ions in biological catalysis: from enzyme databases to general principles. C. Andreini, I. Bertini, G. Cavallaro, G. L. Holliday and J. M. Thornton, J. Biol. Inorg. Chem., 13, 1205-1218, 2008. Medline ID: 18604568

The Chemistry of Protein Catalysis. G. L. Holliday, D. E. Almonacid, J. B. O. Mitchell and J. M. Thornton, J. Mol. Biol., 372, 1261-1277, 2007. Medline ID: 17727879

The Geometry of Interactions between Catalytic Residues and their Substrates.. J. W. Torrance, G. L. Holliday, J. B. O. Mitchell and J. M. Thornton. J. Mol. Biol., 369, 1140-1152, 2007. Medline ID: 17466330

Using reaction mechanism to measure enzyme similarity.. N. M. O'Boyle, G. L. Holliday, D. E. Almonacid and J. B. O. Mitchell. J. Mol. Biol., 368, 1484-1499, 2007. Medline ID: 17400244

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 and J. M. Thornton. Nucleic Acids Research, 35, D515-D520, 2007. Medline ID: 17082206

Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions. G. L. Holliday, P. Murray-Rust, and H. S. Rzepa. J. Chem. Inf. Model., 46, 145-157, 2006. Medline ID: 16426051

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 and J.B.O. Mitchell. Bioinformatics, 21, 4315, 2005. Medline ID: 16188925

CMLSnap: Animated Reaction Mechanisms. G. L. Holliday, J. B. O. Mitchell and P. Murray-Rust, Internet Journal of Chemistry, 7, Article 4, 2004

Enzyme Mechanism Annotation and Classification
(A talk from the 13th ISMB Annual International Conference describing the information contained in our database of enzyme reaction mechanisms, given by Daniel Almonacid)

Classification and Computer Representation of Enzyme Reactions. Progress Towards the Development of MACiE
(A talk from the 226th ACS National Meeting describing our database of enzyme reaction mechanisms, given by Gemma Holliday)

View who is citing the MACiE family of databases.

Institues

Funding

MACiE has benefited from funding from the following sources:

• EMBL
• Wellcome Trust
• Cambridge Overseas Trust
• Gobierno de Chile, Ministero de Planificación y Cooperación
• EPSRC
• BBSRC
• Unilever