Cited by 1,150Metal-Catalyzed Oxygenation MechanismsEnzyme Structure and FunctionMetalloenzymes and iron-sulfur proteins

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Metal ions in biological catalysis: from enzyme databases to general principles

Andreini, Claudia, Bertini, Ivano, Cavallaro, Gabriele, Holliday, Gemma L., Thornton, Janet M.·2008·JBIC Journal of Biological Inorganic Chemistry

DOI 10.1007/s00775-008-0404-5

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Abstract

We analysed the roles and distribution of metal ions in enzymatic catalysis using available public databases and our new resource Metal-MACiE (http://www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html). In Metal-MACiE, a database of metal-based reaction mechanisms, 116 entries covering 21% of the metal-dependent enzymes and 70% of the types of enzyme-catalysed chemical transformations are annotated according to metal function. We used Metal-MACiE to assess the functions performed by metals in biological catalysis and the relative frequencies of different metals in different roles, which can be related to their individual chemical properties and availability in the environment. The overall picture emerging from the overview of Metal-MACiE is that redox-inert metal ions are used in enzymes to stabilize negative charges and to activate substrates by virtue of their Lewis acid properties, whereas redox-active metal ions can be used both as Lewis acids and as redox centres. Magnesium and zinc are by far the most common ions of the first type, while calcium is relatively less used. Magnesium, however, is most often bound to phosphate groups of substrates and interacts with the enzyme only transiently, whereas the other metals are stably bound to the enzyme. The most common metal of the second type is iron, which is prevalent in the catalysis of redox reactions, followed by manganese, cobalt, molybdenum, copper and nickel. The control of the reactivity of redox-active metal ions may involve their association with organic cofactors to form stable units. This occurs sometimes for iron and nickel, and quite often for cobalt and molybdenum.

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Authors: Andreini, C., Bertini, I., Cavallaro, G., Holliday, G. L., & Thornton, J. M.
Affiliations: University of Florence (IT)
European Bioinformatics Institute (GB)
Corresponding author: Thornton, Janet M.
ORCID: Andreini, Claudia
Bertini, Ivano
Holliday, Gemma L.
Thornton, Janet M.
Venue: JBIC Journal of Biological Inorganic Chemistry
Publisher: Springer Science and Business Media LLC
Published: 2008-07-05
Volume: 13
Issue: 8
Pages: 1205-1218
ISSN: 0949-8257 (ISSN-L)
1432-1327
DOI: 10.1007/s00775-008-0404-5
OpenAlex: W2052498582
Cited by: 1,150
References: 72
Citations by year: 2026: 68 · 2025: 92 · 2024: 108 · 2023: 89 · 2022: 92 · 2021: 105 · 2020: 87 · 2019: 80 · 2018: 53 · 2017: 59 · 2016: 62 · 2015: 38 · 2014: 47 · 2013: 44 · 2012: 41
FWCI: 16.99
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: JBIC Journal of Biological Inorganic Chemistry (publishedVersion)
PubMed (publishedVersion)
BIROn (Birkbeck, University of London) (submittedVersion)
Florence Research (University of Florence) (submittedVersion)
Funders: Wellcome Trust (062347)
Topics: Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Metalloenzymes and iron-sulfur proteins
Keywords: metal ions, metalloenzymes, enzyme catalysis, redox-active metal ions, Lewis acid catalysis, magnesium, zinc, calcium, iron, manganese, cobalt, molybdenum, copper, nickel, cofactors
MeSH terms: Enzymes, Ions, Magnesium, Manganese, Metalloproteins, Metals, Models, Chemical, Oxidation-Reduction, Oxidoreductases, Transferases, Databases, Protein, Biocatalysis

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Metal ions in biological catalysis: from enzyme databases to general principles

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