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

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

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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Crossref · 10.1007/s00775-008-0404-5

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72 of 72 references verified0 citation errors · 0 not checkable

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  • Interaction with metals alters the physicochemical properties of proteins, promoting catalysis of enzymatic reactions, stabilizing protein structure and/or facilitating electron transport.

    “The interaction with metals alters the physico- chemical properties of proteins, thereby promoting catalysis of enzymatic reactions, stabilizing protein structure and/or facilitating electron transport 2,3 .”
  • Zinc, iron, and manganese are the transition metals most commonly used as critical cofactors or structural components in mammalian and bacterial proteins.

    “Zinc, iron, and manganese are the most common transition metals serving critical cofactor or structural roles in mammalian and bacterial proteins (Andreini et al., 2008).”

    From The Impact of Dietary Transition Metals on Host-Bacterial Interactions (2018) · cites this paper as Andreini et al., 2008

  • Metal ions, particularly iron, play a critical role in the activity of many enzymes involved in the detoxification of reactive oxygen species.

    “One striking example is the critical role of metal ions, particularly iron, in the activity of many enzymes involved in the detoxification of reactive oxygen species (ROS) [54–56].”

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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.
Venue
JBIC Journal of Biological Inorganic Chemistry
Published
2008-07-05
Volume
13
Issue
8
Pages
1205-1218
ISSN
  • 0949-8257 (ISSN-L)
  • 1432-1327
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
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
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › 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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